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Isospora brasilsatoae Oliveira and Berto n. sp. Type host: Yellow-legged thrush Turdus flavipes (Vieillot, 1818) (Aves: Passeriformes: Turdidae). Other hosts: Pale-breasted thrush Turdus leucomelas Vieillot, 1818 (Aves: Passeriformes: Turdidae); creamybellied thrush Turdus amaurochalinus Cabanis, 1850 (Aves: Passeriformes: Turdidae). Type locality: Parque Nacional do Itatiaia (22°26'57"S, 44°36'25"W), Southeastern Brazil. Other localities: Cacaria (22°42'51"S, 43°50'38"W) and Guapimirim (22°31'10"S, 43°00'36"W), also from Southeastern Brazil. Type-material: Photosyntypes, line drawing and oocysts recovered from T. flavipes in 2.5% K 2 Cr 2 O 7 solution (Williams et al. 2010) are deposited at the Museu de Zoologia at the Universidade Federal Rural do Rio de Janeiro, Brazil, under accession number MZURPTZ2018007. Photomicrographs are also deposited and available (http:// r1.ufrrj.br/labicoc/colecao.html) in the Parasitology Collection of the Laboratório de Biologia de Coccídios, at UFRRJ, under repository number P-90/2018. Photographs of the type-host specimen (symbiotype) are deposited in the same collection. ZooBank registration: To comply with the regulations set out in article 8.5 of the amended 2012 version of the International Code of Zoological Nomenclature (ICZN, 2012), details of the new species have been submitted to ZooBank. The Life Science Identifier (LSID) for Isospora brasilsatoae is urn:lsid:zoobank.org:act: 6C3FEE82- FC9C-4A58-8C17-1713532F03F3. Site of infection: Unknown. Prevalence: Four of 10 (40%). Sporulation: Exogenous. All oocysts were passed in the feces unsporulated and were fully sporulated by day 7 in K 2 Cr 2 O 7 solution at room temperature (20–25°C). Etymology: The specific name is derived from the family name of a Brazilian parasitologist Dr Marília de Carvalho Brasil Sato, given in her honor for her contribution to the study of taxonomy and ecology of parasites. Description (Figs 1; 2 A–C). Oocyst (n = 15) ovoidal to pyriform, 25-30 × 19-23 (26.8 × 21.1); length/width (L/W) ratio 1.2-1.4 (1.27). Wall bi-layered, delicate, 1.4-1.8 (1.6) thick, outer layer smooth, c. 2/3 of total thickness. Micropyle present, without micropyle cap, wrinkles or invagination of the in inner layer perceptible. Oocyst residuum absent, but 1 to 3 rounded polar granules are present. Sporocyst elongate ovoidal with tapered anterior end (where it is Stieda/sub- Stieda complex), 17-19 × 10-11 (18.1 × 10.5); L/W ratio 1.6-1.9 (1.72). Stieda body present, knob-like, 2.0 high × 2.0 wide. Sub-Stieda body present, trapezoidal, 1.5 high × 3.5 wide. Para-Stieda body absent. Sporocyst residuum present, as a distinctly sub-spherical body consisting of numerous small granules that appear to be membranebounded, 6–9 (7.5). Sporozoites vermiform, with anterior and posterior refractile bodies and striations. Remarks: Isospora brasilsatoae is different from other coccidian species of Turdidae of the New World on several aspects (Table 1). It is the only one to have a pyriform shape of the oocysts. It has a micropyle, which is a characteristic present only in the oocysts of Isospora albicollis Lainson and Shaw, 1989, Isospora sabiai Pinho, Rodrigues, Silva, Lopes, Oliveira, Ferreira, Cardozo, Luz, Ferreira, Lopes and Berto, 2017 and Isospora machadoae Pinho, Silva, Rodrigues, Lopes, Oliveira, Luz, Ferreira, Lopes and Berto, 2018 (Lainson & Shaw 1989; Pinho et al. 2017a; 2017b; 2018). From these three, but also from the others, I. brasilsatoae can be easily differentiated by having up to three rounded polar granules, sporocysts elongate ovoidal (L/W ratio> 1.6), sub- Stieda body trapezoidal, and compact residuum.

A new species of coccidia (Protozoa: Apicomplexa: Eimeriidae) found parasitizing the yellow-legged thrush Turdus flavipes (Vieillot, 1818), the pale-breasted thrush Turdus leucomelas Vieillot, 1818 and the creamy-bellied thrush Turdus amaurochalinus Cabanis, 1850 in Southeastern Brazil is described. Isospora brasilsatoae n. sp. has oocysts that are ovoidal to pyriform, 26.8 × 21.1 μm, with smooth, bilayered wall, ~1.6 μm thick. Micropyle present. Oocyst residuum absent, but one to three polar granules are present. Sporocysts are elongate ovoidal, 18.1 × 10.5 μm. Stieda body knob-like and sub-Stieda body trapezoidal. Sporocyst residuum is composed of granules that appear to be membrane-bounded. Sporozoites are vermiform with refractile bodies and striations. This is the ninth description of an Isospora sp. parasitizing a New World thrush.

Soils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus–host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.

Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata.

Eimeria psittacarae Tucunduva and Berto n. sp. Type host: White-eyed parakeet Psittacara leucophthalmus (M��ller, 1776) (Aves: Psittaciformes: Psittacidae). Type locality: Sector of Fauna of the Parque Nacional da Serra dos ��rg��os (22��29'43"S, 43��04'25"W), Southeastern Brazil. Type-material: Photosyntypes, line drawing, and oocysts in 70% ethanol are deposited at the Museu de Zoologia at the Universidade Federal Rural do Rio de Janeiro, Brazil, under accession number MZURPTZ2017004. Phototypes and line drawings are also deposited and available (http://r1.ufrrj.br/labicoc/ colecao.html) in the Parasitology Collection of the Laborat��rio de Biologia de Cocc��dios, at UFRRJ, under repository number P-84/2017. Photographs of the type-host specimen (symbiotype) are deposited in the same collection. Site of infection: Unknown. Prevalence: One of 8 (12.5%). Sporulation: Exogenous. All oocysts were passed in the feces unsporulated and were fully sporulated by day 7 in K2Cr2O7 solution at room temperature. Etymology: The specific epithet is derived from the generic name of the type host. Description (Figs 1; 2A���D). Oocyst (n = 19) ellipsoidal, 29���39 �� 22���28 (34.8 �� 24.3); length/width (L/W) ratio 1.3���1.5 (1.4). Wall bilayered, delicate, 1.61.9 (1.7) thick, outer layer smooth, c.2/3 of total thickness. Micropyle inconspicuous, but easily perceptible when there is an invagination of the inner layer, 5���8 (6.0) wide. Oocyst residuum absent, but 1 or 2 rounded polar granules are present, 2���3 (2.3). Sporocyst elongate ellipsoidal, 18���20 �� 9���10 (19.2 �� 9.7); L/W ratio 1.9���2.1 (2.1). Stieda body present, knob-like, 1.0 high �� 2.0 wide. Sub-Stieda body present, rounded, sometimes homogeneous with the Stieda body, 1.0 high �� 2.0 wide. Para-Stieda body absent. Sporocyst residuum present, as a distinctly sub-spherical body consisting of numerous small granules that appear to be membranebounded, 6���7 (6.6). Sporozoites vermiform, with single posterior refractile body and a nucleus. Remarks: Eimeria psittacarae is different from other coccidian species of Psittaciformes of the New World on several aspects (Table 1). It is the only one to have a micropyle (Fig. 2A, B). In addition, although the oocyst measurements are similar to Eimeria aratinga Upton and Wright, 1994 and Eimeria aestivae Hofstatter and Guaraldo, 2011, E. psittacarae differs from these two species in shape, number and shape of polar granules and in the details of the sporocyst residuum (Upton & Wright 1994, Hofstatter & Guaraldo, 2011)., Published as part of Tucunduva, Priscila, Rodrigues, Mariana Borges, Carvalho, Raquel Batista Junger De & Berto, Bruno Pereira, 2018, Eimeria psittacarae n. sp. (Apicomplexa: Eimeiriidae) from white-eyed parakeets Psittacara leucophthalmus (M��ller, 1776) (Psittaciformes: Psittacidae) kept for rehabilitation and reintroduction in the Parque Nacional da Serra dos ��rg��os, Southeastern Brazil, pp. 164-170 in Zootaxa 4459 (1) on page 165, DOI: 10.11646/zootaxa.4459.1.7, http://zenodo.org/record/1458458, {"references":["Upton, S. J. & Wright, T. F. (1994) A new species of Eimeria (Apicomplexa) from the orange-fronted conure, Aratinga canicularis (Psittaciformes), in Costa Rica. Acta Protozoologica, 33 (2), 117 - 119.","Hofstatter, P. G. & Guaraldo, A. A. (2011) A new eimerian species (Apicomplexa: Eimeriidae) from the blue-fronted Amazon parrot Amazona aestiva L. (Aves: Psittacidae) in Brazil. Journal of Parasitology, 97 (6), 1140 - 1141. https: // doi. org / 110.1645 / GE- 2797.1"]}

Tucunduva, Priscila, Rodrigues, Mariana Borges, Carvalho, Raquel Batista Junger De, Berto, Bruno Pereira (2018): Eimeria psittacarae n. sp. (Apicomplexa: Eimeiriidae) from white-eyed parakeets Psittacara leucophthalmus (Müller, 1776) (Psittaciformes: Psittacidae) kept for rehabilitation and reintroduction in the Parque Nacional da Serra dos Órgãos, Southeastern Brazil. Zootaxa 4459 (1): 164-170, DOI: https://doi.org/10.11646/zootaxa.4459.1.7

Background Red algae are economically valuable for food and in industry. However, their genomic information is limited, and the genomic data of only a few species of red algae have been sequenced and deposited recently. In this study, we annotated a draft genome of the macroalga Gracilariopsis lemaneiformis (Gracilariales, Rhodophyta). Results The entire 88.98 Mb genome of Gp. lemaneiformis 981 was generated from 13,825 scaffolds (≥500 bp) with an N50 length of 30,590 bp, accounting for approximately 91% of this algal genome. A total of 38.73 Mb of scaffold sequences were repetitive, and 9281 protein-coding genes were predicted. A phylogenomic analysis of 20 genomes revealed the relationship among the Chromalveolata, Rhodophyta, Chlorophyta and higher plants. Homology analysis indicated phylogenetic proximity between Gp. lemaneiformis and Chondrus crispus. The number of enzymes related to the metabolism of carbohydrates, including agar, glycoside hydrolases, glycosyltransferases, was abundant. In addition, signaling pathways associated with phytohormones such as auxin, salicylic acid and jasmonates are reported for the first time for this alga. Conclusion We sequenced and analyzed a draft genome of the red alga Gp. lemaneiformis, and revealed its carbohydrate metabolism and phytohormone signaling characteristics. This work will be helpful in research on the functional and comparative genomics of the order Gracilariales and will enrich the genomic information on marine algae. Electronic supplementary material The online version of this article (10.1186/s12870-018-1309-2) contains supplementary material, which is available to authorized users.

Aquatic photosynthetic eukaryotes represent highly diverse groups (green, red, and chromalveolate algae) derived from multiple endosymbiosis events, covering a wide spectrum of the tree of life. They are responsible for about 50% of the global photosynthesis and serve as the foundation for oceanic and fresh water food webs. Although the ecophysiology and molecular ecology of some algal species are extensively studied, some basic aspects of algal cell biology are still underexplored. The recent wealth of genomic resources from algae has opened new frontiers to decipher the role of cell signaling pathways and their function in an ecological and biotechnological context. Here, we took a bioinformatic approach to explore the distribution and conservation of TOR and autophagy-related (ATG) proteins (Atg in yeast) in diverse algal groups. Our genomic analysis demonstrates conservation of TOR and ATG proteins in green algae. In contrast, in all 5 available red algal genomes, we could not detect the sequences that encode for any of the 17 core ATG proteins examined, albeit TOR and its interacting proteins are conserved. This intriguing data suggests that the autophagy pathway is not conserved in red algae as it is in the entire eukaryote domain. In contrast, chromalveolates, despite being derived from the red-plastid lineage, retain and express ATG genes, which raises a fundamental question regarding the acquisition of ATG genes during algal evolution. Among chromalveolates, Emiliania huxleyi (Haptophyta), a bloom-forming coccolithophore, possesses the most complete set of ATG genes, and may serve as a model organism to study autophagy in marine protists with great ecological significance.

Marine biofilms are precursors for colonization by larger fouling organisms, including non-indigenous species (NIS). In this study, high-throughput sequencing (HTS) of 18S rRNA metabarcodes was used to investigate four sampling methods (modified syringe, sterilized sponge, underwater tape and sterilized swab) for characterizing eukaryotic communities in marine biofilms. PerspexTM plates were sampled in and out of water. DNA collected with tape did not amplify. Otherwise, there were no statistical differences in communities among the remaining three sampling devices or between the two environments. Sterilized sponges are recommended for ease of use underwater. In-depth HTS analysis identified diverse eukaryotic communities, dominated by Metazoa and Chromoalveolata. Among the latter, diatoms (Bacillariophyceae) were particularly abundant (33% of reads assigned to Chromalveolata). The NIS Ciona savignyi was detected in all samples. The application of HTS in marine biofilm surveillance could facilitate early detection of NIS, improving the probability of successful eradication.

The molecular diversity of freshwater microeukaryotes, particularly phytoplankton, in the Arctic Svalbard, has been relatively unexplored. Freshwater algae are considered biological indicators of environmental change and can be useful in assessing the impact of global climate change and increased environmental pollution. In this study, freshwater microeukaryotes in an Arctic reservoir at Ny-Ǻlesund (Svalbard, Norway) were studied using the hypervariable V1–V3 small subunit rRNA and 454 pyrosequencing. On the basis of 8,956 reads, we revealed high genetic diversity in eukaryotes, representing all known eukaryotic supergroups, except Excavata. “Chromalveolata” (previously supergroup Chromalveolata) and Archaeplastida were the most and least abundant supergroups, respectively. After data mining, 57 phylotypes were detected from 7,398 pyrosequences. They were dominated by stramenopiles (84 %) and Dinoflagellata (13 %), with minor contributions from Cryptophyta, Chlorophyta, and Telonemida. The detection of algae belonging to the orders Mamiellales and Monomastigales provides a window into a fraction of the ‘rare biosphere’ that had previously been undetected in such environments. Interestingly, no haptophytes were recorded. Stramenopiles and Dinoflagellata mainly comprised taxa belonging to the families Chrysophyceae, Synurophyceae, and Dinophyceae. On the basis of the proportion of operational taxonomic units, the dominant phylotypes were found to include Ochromonas spp., Mallomonas spp., and Uroglena americana. These results demonstrate the significance of a chrysophyte-dominated microeukaryotic community, which is of great potential for future studies in terms of reconstruction of past climate trends and monitoring of environmental change in the Arctic.

As a part of the AMAZE-08 campaign during the wet season in the rainforest of central Amazonia, an ultraviolet aerodynamic particle sizer (UV-APS) was operated for continuous measurements of fluorescent biological aerosol particles (FBAP). In the coarse particle size range (&gt, 1 ?m) the campaign median and quartiles of FBAP number and mass concentration were 7.3 � 104 m -3 (4.0-13.2 � 104 m-3) and 0.72 ?g m -3 (0.42-1.19 ?g m-3), respectively, accounting for 24% (11-41%) of total particle number and 47% (25-65%) of total particle mass. During the five-week campaign in February-March 2008 the concentration of coarse-mode Saharan dust particles was highly variable. In contrast, FBAP concentrations remained fairly constant over the course of weeks and had a consistent daily pattern, peaking several hours before sunrise, suggesting observed FBAP was dominated by nocturnal spore emission. This conclusion was supported by the consistent FBAP number size distribution peaking at 2.3 ?m, also attributed to fungal spores and mixed biological particles by scanning electron microscopy (SEM), light microscopy and biochemical staining. A second primary biological aerosol particle (PBAP) mode between 0.5 and 1.0 ?m was also observed by SEM, but exhibited little fluorescence and no true fungal staining. This mode may have consisted of single bacterial cells, brochosomes, various fragments of biological material, and small Chromalveolata (Chromista) spores. Particles liquid-coated with mixed organic-inorganic material constituted a large fraction of observations, and these coatings contained salts likely from primary biological origin. We provide key support for the suggestion that real-time laser-induce fluorescence (LIF) techniques using 355 nm excitation provide size-resolved concentrations of FBAP as a lower limit for the atmospheric abundance of biological particles in a pristine environment. We also show some limitations of using the instrument for ambient monitoring of weakly fluorescent particles &lt, 2 ?m. Our measurements confirm that primary biological particles, fungal spores in particular, are an important fraction of supermicron aerosol in the Amazon and that may contribute significantly to hydrological cycling, especially when coated by mixed inorganic material. � 2012 Author(s).

The Tubby-like protein (TULP) is ubiquitous among multicellular organisms but has extremely diversified functions. Although functional analyses of certain mammalian and model plant TULPs are available and phylogenies separately based on animal or plant TULPs have been reconstructed, the origin, evolutionary history, and functional divergence of TULPs remain obscure. The existence of TULP in unicellular organisms is also not found yet. In this study, 145 TULP homologs were identified from four eukaryotic supergroups—Excavata, Chromalveolata, Archaeplastida (plants), and Opistokonta (fungi and animals). In addition to the tubby domain, many TULPs also contain different motifs (F-box, WD40 repeat, or SOCS box) in their N-terminus regions, leading to their groupings into three classes, in which TULPs with no N-terminal modifications (class II) locate at the basal positions on the phylogeny. Our comparison data reveals that phosphatidylinositol 4,5-bisphosphate (PIP2) binding sites are conserved in class II TULPs, especially those that are animal derived, but not in TULPs from classes I and III. Differentiation at the three PIP2 binding sites implies that the function of class II TULPs differs from those of other two classes. We further demonstrate that only class II TULPs can be targeted to the plasma membrane, suggesting functional divergence and differentiation of TULPs. Functional divergence and differentiation of TULPs should have occurred after duplications and structural modifications around 1100 MYA as eukaryotic organisms started diversifying.

Perkinsus marinus (Phylum Perkinsozoa) is a protozoan parasite that has devastated natural and farmed oyster populations in the USA, significantly affecting the shellfish industry and the estuarine environment. The other two genera in the phylum, Parvilucifera and Rastrimonas, are parasites of microeukaryotes. The Perkinsozoa occupies a key position at the base of the dinoflagellate branch, close to its divergence from the Apicomplexa, a clade that includes parasitic protista, many harbouring a relic plastid. Thus, as a taxon that has also evolved toward parasitism, the Perkinsozoa has attracted the attention of biologists interested in the evolution of this organelle, both in its ultrastructure and the conservation, loss or transfer of its genes. A review of the recent literature reveals mounting evidence in support of the presence of a relic plastid in P. marinus, including the presence of multimembrane structures, characteristic metabolic pathways and proteins with a bipartite N-terminal extension. Further, these findings raise intriguing questions regarding the potential functions and unique adaptation of the putative plastid and/or plastid genes in the Perkinsozoa. In this review we analyse the above-mentioned evidence and evaluate the potential future directions and expected benefits of addressing such questions. Given the rapidly expanding molecular/genetic resources and methodological toolbox for Perkinsus spp., these organisms should complement the currently established models for investigating plastid evolution within the Chromalveolata.

Chloroplast genomes have retained a core set of genes from their cyanobacterial ancestor, most of them required for the light reactions of photosynthesis or functions connected with transcription and translation. Other genes have been transferred to the nucleus or were lost in a lineage-specific manner. The genomes are distinguished by the selection of genes retained, whether or not transcripts are edited, presence/absence of introns and small repeats and their physical organization. Plants and green algae have kept fewer plastid genes than either the red algae or the chromistan algae, which obtained their plastids from red algae by secondary endosymbiosis. Photosynthetic dinoflagellates have the fewest (fewer than 20), but still grow photoautotrophically. All chloroplast genomes map as a circle, but there have been extensive rearrangements of gene order even between related species. Genome sizes vary much more than gene content, depending on the extent of gene duplication and small repeats and the size of intergenic spacers.

Arctic marine unicellular eukaryotes are composed of microalgae and non-autotrophic protists. These eukaryotes comprise a well-diversified group of organisms that are either adapted to live in the upper water column of coastal and oceanic regions, here defined as phytoplankton/pelagic communities, or in bottom horizons of sea ice and known as sympagic/sea-ice-associated communities. There are approximately 5,000 recognized legitimate marine phytoplankton species and an unknown number of sympagic eukaryotes. Although pelagic and sea-ice eukaryotes have been described since the exploration phase of the Arctic regions up to the early twentieth century, no synthesis regarding information from all Arctic seas have been undertaken, and no exhaustive current information provides the exact number and composition of species on a pan-Arctic scale. In a first attempt to assess the pan-Arctic diversity of pelagic and sea-ice eukaryotes, a wealth of data from various sources (e.g., scientific publications, unpublished reports, databases) were reviewed, while taxonomic data were confirmed with current nomenclature and classification. We report a total of 2,106 marine single-celled eukaryote taxa with 1,874 phytoplankton and 1,027 sympagic taxa from four grouped pan-Arctic regions, namely Alaska, Canada, Scandinavia including Greenland and the Russian Federation. Both phytoplankton and sympagic taxa were present in four of the six super-groups of eukaryotes described by Adl et al. (J Eukaryot Microbiol 52:399-451, 2005), which are Archaeplastida (chlorophytes and prasinophytes), Chromalveolata (e.g., chrysophytes, cryptophytes, diatoms, dictyochophytes, dinoflagellates and prymnesiophytes), Excavata (euglenids) and Opisthokonta (choanoflagellates). The bulk of this marine biodiversity of Arctic microorganisms consists of large cells (>20 μm) mainly due to examination at low magnification under light microscopy. Future efforts should focus enhancing our knowledge of the biological diversity of small cells (

The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (≤2 μm diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer-probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of "mixed lineage gene affiliations" among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton. © 2010 The Author.

A patchily distributed gene family is often taken as evidence for horizontal gene transfer (HGT) events, but it may also result solely from multiple gene losses. The RJL family of uncharacterised Ras-like GTPases was previously suggested to have undergone HGT events between protists and deuterostome metazoans, owing to the apparent absence of RJL in intermediate groups (Nepomuceno-Silva, J.L., de Melo, L.D., Mendonca, S.M., Paixao, J.C., Lopes, U.G., 2004. RJLs: a new family of Ras-related GTP-binding proteins. Gene 327, 221–232). We have reanalysed the phylogenetic distribution and phylogeny of the RJL family, taking advantage of the recent expansion of sequence data available from diverse eukaryotes. We found that RJL orthologs are much more widely distributed than previously assumed. At least one representative encoding an RJL protein could be identified for each of the six major eukaryotic “supergroups” (Opisthokonta, Amoebozoa, Excavata, Archaeplastida, Chromalveolata, and Rhizaria) as well as for a species of Apusomonadida, a deep lineage that may not be specifically related to any of the recognized supergroups. Phylogenetic analyses do not support HGT of RJL genes between the major eukaryotic lineages, indicating that the RJL family was present in the last eukaryotic common ancestor and was lost several times over the course of eukaryotic evolution. Interestingly, RJL was lost from all taxa lacking flagellated cells and from a few lineages that build structurally unusual or reduced flagella, raising the intriguing possibility that RJL proteins are functionally associated with the flagellar apparatus. The RJL GTPase domain has been fused with the DnaJ domain on two separate occasions: in the Holozoa (before the split of Metazoa and choanoflagellates), giving rise to the previously known Rbj type of RJL with the DnaJ domain at the C-terminus, and independently in Alveolata resulting in novel proteins with the DnaJ domain at the N-terminus. These independent fusions suggest that RJL proteins may generally function via regulating the DnaJ–Hsp70 module.

Programmed cell death (PCD) represents a significant component of normal growth and development in multicellular organisms. Recently, PCD-like processes have been reported in single-celled eukaryotes, implying that some components of the PCD machinery existed early in eukaryotic evolution. This study provides a comparative analysis of PCD-related sequences across more than 50 unicellular genera from four eukaryotic supergroups: Unikonts, Excavata, Chromalveolata, and Plantae. A complex set of PCD-related sequences that correspond to domains or proteins associated with all main functional classes--from ligands and receptors to executors of PCD--was found in many unicellular lineages. Several PCD domains and proteins previously thought to be restricted to animals or land plants are also present in unicellular species. Noteworthy, the yeast, Saccharomyces cerevisiae--used as an experimental model system for PCD research, has a rather reduced set of PCD-related sequences relative to other unicellular species. The phylogenetic distribution of the PCD-related sequences identified in unicellular lineages suggests that the genetic basis for the evolution of the complex PCD machinery present in extant multicellular lineages has been established early in the evolution of eukaryotes. The shaping of the PCD machinery in multicellular lineages involved the duplication, co-option, recruitment, and shuffling of domains already present in their unicellular ancestors.

The establishment of a new plastid organelle by secondary endosymbiosis represents a series of events of massive complexity, and yet we know it has taken place multiple times because both green and red algae have been taken up by other eukaryotic lineages. Exactly how many times these events have succeeded, however, has been a matter of debate that significantly impacts how we view plastid evolution, protein targeting, and eukaryotic relationships. On the green side it is now largely accepted that two independent events led to plastids of euglenids and chlorarachniophytes. How many times red algae have been taken up is less clear, because there are many more lineages with red alga-derived plastids (cryptomonads, haptophytes, heterokonts, dinoflagellates and apicomplexa) and the relationships between these lineages are less clear. Ten years ago, Cavalier-Smith proposed that these plastids were all derived from a single endosymbiosis, an idea that was dubbed the chromalveolate hypothesis. No one observation has yet supported the chromalveolate hypothesis as a whole, but molecular data from plastid-encoded and plastid-targeted proteins have provided strong support for several components of the overall hypothesis, and evidence for cryptic plastids and new photosynthetic lineages (e.g. Chromera) have transformed our view of plastid distribution within the group. Collectively, these data are most easily reconciled with a single origin of the chromalveolate plastids, although the phylogeny of chromalveolate host lineages (and potentially Rhizaria) remain to be reconciled with this plastid data.

Dyneins are responsible for essential movements in eukaryotic cells. The motor activity of each dynein complex resides in its complement of heavy chains. In the present study, we examined 136 heavy chain sequences from the completed genomes of 11 diverse model organisms, including examples from Viridiplantae, Excavata, Chromalveolata, and Metazoa. In many cases, we discovered dynein heavy chains previously not identified. For example, Tetrahymena expresses a total of 25 DYH genes rather than the previously identified 14. The Tetrahymena DYH genes are nonaxonemal DYH1 and DYH2; axonemal outer arm alpha, beta, and gamma; axonemal two-headed inner arm 1alpha and 1beta; and 18 single-headed inner arm heavy chains. The heavy chains divide into nine classes; six of these are highly conserved in sequence and number of isoforms in a given organism. The other three are single-headed inner arm dyneins, whose numbers vary significantly in different organisms. These findings lead to two conclusions. One, the last common ancestor of all eukaryotes expressed nine different dynein heavy chains. Two, subsequent to the divergences leading to different organisms, additional dynein heavy chains emerged. These newer dyneins are not well conserved across species and the variation may reflect different motility requirements in different organisms. Together, these results suggest that each of the nine classes of dyneins is functionally distinct, but members within some of the classes are not specialized. An understanding of the relationships among the various dynein heavy chains is important when deducing functions across species.

Despite their importance to evolution, ecology, and cell biology, eukaryotes that acquired plastids through secondary endosymbiosis remain poorly studied from a genomic standpoint. Chromalveolata, a eukaryotic supergroup proposed to have descended from a heterotrophic eukaryote that acquired a red algal plastid by secondary endosymbiosis, includes four major lineages (alveolates, cryptophytes, haptophytes, and heterokonts). The chromalveolates exhibit remarkable diversity of cellular organization, and the available data suggest that they exhibit equal diversity in their genome organization. One of the most obvious differences in cellular organization is the retention of a highly reduced red algal nucleus in cryptophytes (also known as cryptomonads), but there are other major differences among chromalveolate lineages, including the loss of photosynthesis in multiple lineages. Although the hypothesis of chromalveolate monophyly is appealing, there is limited support for the hypothesis from nuclear genes, and questions have even been raised about the monophyly of chromalveolate plastids. Evidence for the chromalveolate hypothesis from large-scale nuclear data sets is reviewed, and alternative hypotheses are described. The potential for integrating information from chromalveolate genomics into functional genomics is described, emphasizing both the methodological challenges and the opportunities for future phylogenomic analyses of these groups.

Genome biology and evolution 8(3), 878-895 (2016). doi:10.1093/gbe/evw036, Published by Oxford Univ. Press, Oxford

Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the putative eukaryotic supergroup Chromalveolata (chromists [cryptophytes, haptophytes, stramenopiles] and alveolates [apicomplexans, ciliates, and dinoflagellates]). The chromalveolates are postulated to be monophyletic on the basis of plastid pigmentation in photosynthetic members, plastid gene and genome relationships, nuclear "host" phylogenies of some chromalveolate lineages, unique gene duplication and replacements shared by these taxa, and the evolutionary history of components of the plastid import and translocation systems. However the phylogenetic position of cryptophytes and haptophytes and the monophyly of chromalveolates as a whole remain to be substantiated. Here we assess chromalveolate monophyly using a multigene dataset of nuclear genes that includes members of all 6 eukaryotic supergroups. An automated phylogenomics pipeline followed by targeted database searches was used to assemble a 16-protein dataset (6,735 aa) from 46 taxa for tree inference. Maximum likelihood and Bayesian analyses of these data support the monophyly of haptophytes and cryptophytes. This relationship is consistent with a gene replacement via horizontal gene transfer of plastid-encoded rpl36 that is uniquely shared by these taxa. The haptophytes + cryptophytes are sister to a clade that includes all other chromalveolates and, surprisingly, two members of the Rhizaria, Reticulomyxa filosa and Bigelowiella natans. The association of the two Rhizaria with chromalveolates is supported by the approximately unbiased (AU)-test and when the fastest evolving amino acid sites are removed from the 16-protein alignment.

Rodrigues, Mariana Borges, Silva, Lidiane Maria Da, Lopes, Bruno Do Bomfim, Berto, Bruno Pereira, Luz, Hermes Ribeiro, Ferreira, Ildemar, Lopes, Carlos Wilson Gomes (2015): A new species of Isospora Schneider, 1881 (Apicomplexa: Eimeiriidae) from the grey-hooded attila Attila rufus Vieillot, 1819 (Passeriformes: Tyrannidae) on the Marambaia island, Brazil. Zootaxa 4034 (1): 193-196, DOI: http://dx.doi.org/10.11646/zootaxa.4034.1.10

Isospora attilae n. sp. Type host. Grey-hooded attila Attila rufus (Vieillot, 1819) (Aves: Passeriformes: Tyrannidae). Type locality. Marambaia Island (23 °04'S, 43 ° 53 'W), Rio de Janeiro, Brazil. Site of infection. Not investigated Type-material. Oocysts in 70–100 % ethanol, phototypes and line drawings are deposited and available (http:// r 1.ufrrj.br/lcc) in the Parasitology Collection of the Laboratório de Coccídios e Coccidioses, at UFRRJ, located in Seropédica, Rio de Janeiro, Brazil. Photographs of the type-host specimens (symbiotypes) are deposited in the same collection. The repository number is P- 57 / 2015. Etymology. The specific epithet is derived from the generic name of the type host. Description (Figs 1 a–c; 2 a–c). Oocyst shape (n = 17) sub-spherical to ellipsoidal; oocyst wall bilayered; wall thickness 1.3 (1.1–1.5); outer wall smooth, c. 2 / 3 of total thickness; L × W = 20.3 × 19.0 (18–22 × 18–21), L/W ratio = 1.07 (1.0– 1.2); M, and OR absent, PG present, one or two. Sporocyst shape (n = 13) ellipsoidal; L × W = 13.5 × 7.9 (12– 15 × 7–9); L/W ratio = 1.73 (1.6–1.9); SB present, knob-like, 1.0 high × 2.0 wide; SSB present, rounded to trapezoidal, 2.5 high × 4.0 wide; PSB absent; SR present, composed of granules of different sizes; SZ vermiform with 1 posterior SRB and centrally located N. Remarks. Isospora attilae differs from other Isospora species from the passerines of same family (Table 1). Isospora mionectesi has oocysts and sporocysts larger than I. attilae. Isospora feroxis is very similar to I. attilae, however, it can be distinguished by SB flattened and ovoidal shape of sporocyst (Berto et al., 2009 a; Berto et. al. 2009 b). Coccidia Host Reference Oöcysts Shape Measurements (µm) Shape index Wall (µm) Polar granule sub- spheroidal 18.7 × 18.0 1.1 c. 1.2 present (18–20 × 17–20) (1.0– 1.1) usually 2 Isospora Mionectes Berto et al. ellipsoidal 28.3 × 21.2 1.3 bi-layered, present, 1 or mionectesi rufiventris Cabanis, (2009 b) (23-31 × 19-23) (1.2–1.4) c. 1.3 2 1846 Isospora ovoidal 11.7 × 8.5 present present diffuse feroxis (11–13 × 8-10) flattened prominent, Isospora Mionectes Berto et al. elongate 19.7 × 11.7 present present subspheric mionectesi rufiventris Cabanis, (2009 b) ellipsoidal (17-22 × 10-13) rounded prominent al, 1846 compact Isospora Attila rufus current work ellipsoidal 13,5 × 7,9 present present rounded diffuse attilae (Vieillot, 1819) (12-15 × 7-9) knob like to trapezoidal

SummaryFilamentous fungi and oomycetes are eukaryotic microorganisms that grow by producing networks of thread-like hyphae, which secrete enzymes to break down complex nutrients, such as wood and plant material, and recover the resulting simple sugars and amino acids by osmotrophy. These organisms are extremely similar in both appearance and lifestyle [1] and include some of the most economically important plant pathogens [2, 3]. However, the morphological similarity of fungi and oomycetes is misleading because they represent some of the most distantly related eukaryote evolutionary groupings, and their shared osmotrophic growth habit is interpreted as being the result of convergent evolution [3–5]. The fungi branch with the animals, whereas the oomycetes branch with photosynthetic algae as part of the Chromalveolata [6–10]. In this report, we provide strong phylogenetic evidence that multiple horizontal gene transfers (HGT) have occurred from filamentous ascomycete fungi to the distantly related oomycetes. We also present evidence that a subset of the associated gene families was initially the product of prokaryote-to-fungi HGT. The predicted functions of the gene products associated with fungi-to-oomycete HGT suggest that this process has played a significant role in the evolution of the osmotrophic, filamentous lifestyle on two separate branches of the eukaryote tree.

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ''kingdoms.'' The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

Summary Between 1 and 1.5 billion years ago [1, 2], eukaryotic organisms acquired the ability to convert light into chemical energy through endosymbiosis with a Cyanobacterium (e.g., [3–5]). This event gave rise to "primary" plastids, which are present in green plants, red algae, and glaucophytes ("Plantae" sensu Cavalier-Smith [6]). The widely accepted view that primary plastids arose only once [5] implies two predictions: (1) all plastids form a monophyletic group, as do (2) primary photosynthetic eukaryotes. Nonetheless, unequivocal support for both predictions is lacking (e.g., [7–12]). In this report, we present two phylogenomic analyses, with 50 genes from 16 plastid and 15 cyanobacterial genomes and with 143 nuclear genes from 34 eukaryotic species, respectively. The nuclear dataset includes new sequences from glaucophytes, the less-studied group of primary photosynthetic eukaryotes. We find significant support for both predictions. Taken together, our analyses provide the first strong support for a single endosymbiotic event that gave rise to primary photosynthetic eukaryotes, the Plantae. Because our dataset does not cover the entire eukaryotic diversity (but only four of six major groups in [13]), further testing of the monophyly of Plantae should include representatives from eukaryotic lineages for which currently insufficient sequence information is available.

A global phylogeny of major eukaryotic lineages is a significant and ongoing challenge to molecular phylogenetics. Currently, there are five hypothesized major lineages or ‘supergroups' of eukaryotes. One of these, the chromalveolates, represents a large fraction of protist and algal diversity. The chromalveolate hypothesis was originally based on similarities between the photosynthetic organelles (plastids) found in many of its members and has been supported by analyses of plastid-related genes. However, since plastids can move between eukaryotic lineages, it is important to provide additional support from data generated from the nuclear-cytosolic host lineage. Genes coding for six different cytosolic proteins from a variety of chromalveolates (yielding 68 new gene sequences) have been characterized so that multiple gene analyses, including all six major lineages of chromalveolates, could be compared and concatenated with data representing all five hypothesized supergroups. Overall support for much of the phylogenies is decreased over previous analyses that concatenated fewer genes for fewer taxa. Nevertheless, four of the six chromalveolate lineages (apicomplexans, ciliates, dinoflagellates and heterokonts) consistently form a monophyletic assemblage, whereas the remaining two (cryptomonads and haptophytes) form a weakly supported group. Whereas these results are consistent with the monophyly of chromalveolates inferred from plastid data, testing this hypothesis is going to require a substantial increase in data from a wide variety of organisms.

Plastids (photosynthetic organelles of plants and algae) are known to have spread between eukaryotic lineages by secondary endosymbiosis, that is, by the uptake of a eukaryotic alga by another eukaryote. But the number of times this has taken place is controversial. This is particularly so in the case of eukaryotes with plastids derived from red algae, which are numerous and diverse. Despite their diversity, it has been suggested that all these eukaryotes share a recent common ancestor and that their plastids originated in a single endosymbiosis, the so-called “chromalveolate hypothesis.” Here we describe a novel molecular character that supports the chromalveolate hypothesis. Fructose-1,6-bisphosphate aldolase (FBA) is a glycolytic and Calvin cycle enzyme that exists as two nonhomologous types, class I and class II. Red algal plastid-targeted FBA is a class I enzyme related to homologues from plants and green algae, and it would be predicted that the plastid-targeted FBA from algae with red algal secondary endosymbionts should be related to this class I enzyme. However, we show that plastid-targeted FBA of heterokonts, cryptomonads, haptophytes, and dinoflagellates (all photosynthetic chromalveolates) are class II plastid-targeted enzymes, completely unlike those of red algal plastids. The chromalveolate enzymes form a strongly supported group in FBA phylogeny, and their common possession of this unexpected plastid characteristic provides new evidence for their close relationship and a common origin for their plastids.

Plastids (the photosynthetic organelles of plants and algae) originated through endosymbiosis between a cyanobacterium and a eukaryote and subsequently spread to other eukaryotes by secondary endosymbioses between two eukaryotes. Mounting evidence favors a single origin for plastids of apicomplexans, cryptophytes, dinoflagellates, haptophytes, and heterokonts (together with their nonphotosynthetic relatives, termed chromalveolates), but so far, no single molecular marker has been described that supports this common origin. One piece of evidence comes from plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which originated by a gene duplication of the cytosolic form. However, no plastid GAPDH has been characterized from haptophytes, leaving an important piece of the puzzle missing. We have sequenced genes encoding cytosolic, mitochondrion-targeted, and plastid-targeted GAPDH proteins from a number of haptophytes and heterokonts and found haptophyte homologs that branch within a strongly supported clade of chromalveolate plastid-targeted genes, being more closely related to an apicomplexan homolog than was expected. The evolution of plastid-targeted GAPDH supports red algal ancestry of apicomplexan plastids and raises a number of questions about the importance of plastid loss and the possibility of cryptic plastids in nonphotosynthetic lineages such as ciliates.

Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated rapidly into glaucophytes, green plants and red algae. Secondary symbiogeneses subsequently transferred plastids laterally into different hosts, making yet more complex cell chimaeras--probably only thrice: from a red alga to the corticoflagellate ancestor of chromalveolates (Chromista plus Alveolata), from green algae to a secondarily uniciliate cercozoan to form chlorarachneans and independently to a biciliate excavate to yield photosynthetic euglenoids. Tertiary symbiogenesis involving eukaryotic algal symbionts replaced peridinin-containing plastids in two or three dinoflagellate lineages, but yielded no major novel groups. The origin and well-resolved primary bifurcation of eukaryotes probably occurred in the Cryogenian Period, about 850 million years ago, much more recently than suggested by unwarranted backward extrapolations of molecular 'clocks' or dubious interpretations as 'eukaryotic' of earlier large microbial fossils or still more ancient steranes. The origin of chloroplasts and the symbiogenetic incorporation of a red alga into a corticoflagellate to create chromalveolates may both have occurred in a big bang after the Varangerian snowball Earth melted about 580 million years ago, thereby stimulating the ensuing Cambrian explosion of animals and protists in the form of simultaneous, poorly resolved opisthokont and anterokont radiations.

Isospora pitiguari n. sp. Type host: Rufous-browed peppershrike Cyclarhis gujanensis Gmelin, 1789 (Aves: Passeriformes: Vireonidae). Type locality. Marambaia Island (23 °04’S, 43 ° 53 ’W), Rio de Janeiro, Brazil. Site of infection. Not investigated. Type-material. One-half of the oocysts were kept in 10 % aqueous buffered formalin (v/v) and the other half were stored in 70 % ethanol according Duszynski & Gardner (1991). Both samples were deposited in the Parasitology Collection, in the Department of Animal Parasitology, at UFRRJ, located in Seropédica, Rio de Janeiro, Brazil. Phototypes and line drawings were deposited as well. The repository number is P- 46 / 2013. Etymology. The specific epitaph is derived from the common local name for the host, which is ‘pitiguari’. Description (Figs 1 a–c; 2 a–c). Oocyst shape (n = 11) spherical to sub-spherical; oocyst wall bilayered; wall thickness 1.5 (1.3–1.6); outer wall smooth, c. 2 / 3 of total thickness; L × W = 26.8 × 25.7 (23–28 × 23–28), L/W ratio = 1.0 (1.0– 1.1); M, PG and OR: absent. Sporocyst shape (n = 11) rounded to slightly ovoidal; L × W = 14.4 × 11.6 (13–15 × 10–13); L/W ratio = 1.2 (1.2–1.3); SB present, flattened, 0.5 high × 2.5 wide; SSB present, prominent, rounded, 2.0 high × 3.0 wide; PSB absent; SR present, composed of granules of different sizes; SZ vermiform with 1 posterior SRB and centrally located N. Remarks. Isospora pitiguari differs from other Isospora species from the passerines of same Parvorder (Table 1). In I. pitiguari lack PG, which is present in Isospora brachyrhynchi Wobester & Cawthorn, 1985, Isospora cyanocoracis Upton, Current & Clubb, 1985, Isospora calocitta Upton, Wright & Langen, 1995 and Isospora samoaensis Adamczyk, McQuistion & LaPointe, 2004. Besides, these four species have elongated/ ovoidal sporocysts, whereas in I. pitiguari the sporocysts are sub-spherical (Berto et al. 2011).

Lopes, Bruno Do Bomfim, Berto, Bruno Pereira, Luz, Hermes Ribeiro, Galvão, Gideão Da Silva, Ferreira, Ildemar, Lopes, Carlos Wilson Gomes (2014): Isospora pitiguari n. sp. (Apicomplexa: Eimeriidae) from the rufous-browed peppershrike (Aves: Passeriformes: Vireonidae) Cyclarhis gujanensis Gmelin, 1789. Zootaxa 3760 (1): 95-100, DOI: http://dx.doi.org/10.11646/zootaxa.3760.1.7

Water moulds, particularly the aquatic oomycetes, form part of the rich aquatic fungal flora of ponds and rivers and the soils of nearby areas. Class Oomycota has orders like Lagenidiales, Leptomitales, Rhipidiales, Peronosporales and Saprolegniales with their related families. Cellulose containing cell walls, biflagellate (dissimilar) zoospores, diploid life cycle pattern and its algal affinities have led to its taxonomic shifting from true fungi to pseudo-fungi and were kept under Heterokontophyta (Kingdom: Chromalveolata) with algae – the Stramenopiles. The Oomycota were once classified as fungi because of their filamentous growth and because they feed on decaying matter like fungi. The cell wall of oomycetes, however, is not composed of chitin, as in the fungi, but is made up of a mix of cellulosic compounds and glycan. The nuclei within the filaments are diploid, with two sets of genetic information, not haploid as in the fungi. The free-swimming spores, which are produced, bear two dissimilar flagella, one with mastigonemes; this feature is common in the chromists, as is the presence of the chemical mycolaminarin, an energy storage molecule similar to those found in kelps and diatoms. Thus, although oomycetes are in the minority as heterotrophic chromists, they quite definitely belong with these other chromist groups. With its separate entity as a group of pseudo-fungi, oomycetes need to be identified as an individual branch of study called – ‘Oomycetology’. The investigations on higher fungi have moved forward at a constant pace and are touching new heights; however, the scientific explorations and advanced studies in the field of water moulds (Oomycetology) are continuously going down in general and in the Indian scenario in particular and have arrived at the verge of extinction. Therefore, a special attention is required to revitalize it so that the studies in this branch of mycology may go on to regain its proper place. Taxonomy, ecology, physiology, biochemistry and fish mycopathology have been done in this field but have been restricted to a few working groups and limited centres of study. Majority of the researches in this field have been focused on taxonomic studies and molecular characterization only followed by the studies on fish mycopathology. The studies on ecology, physiology and biochemistry of this group of pseudo-fungi are very meagre; however, early initial studies done on all these aspects may pave way for more advanced studies in the future. Further, the ecological data obtained and hypothesis given from one geographical region need to be confirmed from other different geographical areas. The detailed studies in physiology and biochemistry of these members should be done to understand clearly the metabolic phenomenon therein. Therefore, this particular branch has enormous possibilities of investigations in the future.

The phylum Apicomplexa encompasses a large number of intracellular protozoan parasites, including the causative agents of malaria (Plasmodium), toxoplasmosis (Toxoplasma), and many other human and animal diseases. Apicomplexa have recently been found to contain a relic, nonphotosynthetic plastid that has attracted considerable interest as a possible target for therapeutics. This plastid is known to have been acquired by secondary endosymbiosis, but when this occurred and from which type of alga it was acquired remain uncertain. Based on the molecular phylogeny of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes, we provide evidence that the apicomplexan plastid is homologous to plastids found in dinoflagellates-close relatives of apicomplexa that contain secondary plastids of red algal origin. Surprisingly, apicomplexan and dinoflagellate plastid-targeted GAPDH sequences were also found to be closely related to the plastid-targeted GAPDH genes of heterokonts and cryptomonads, two other groups that contain secondary plastids of red algal origin. These results address several outstanding issues: (1) apicomplexan and dinoflagellate plastids appear to be the result of a single endosymbiotic event which occurred relatively early in eukaryotic evolution, also giving rise to the plastids of heterokonts and perhaps cryptomonads; (2) apicomplexan plastids are derived from a red algal ancestor; and (3) the ancestral state of apicomplexan parasites was photosynthetic.

The biggest unsolved problems in chloroplast evolution are the origins of dinoflagellate and euglenoid chloroplasts,which have envelopes of three membranes not two like plants and chromists, and of the sporozoan plastid, bounded by four smooth membranes. I review evidence that all three of these protozoan plastid types originated by secondary symbiogenesis from eukaryotic symbionts. Instead of separate symbiogenetic events, I argue that dinoflagellate and sporozoan plastids are directly related and that the common ancestor of dinoflagellates and Sporozoa was photosynthetic. I suggest that the last common ancestor of all Alveolata was photosynthetic and acquired its chlorophyll c-containing plastids in the same endosymbiogenetic event as those of Chromista. Chromistaand Alveolata are postulated to be a clade designated chrornalveolates. I propose that euglenoids obtained their plastids from the same(possibly ulvophycean) green alga as chlorarachneans and that Discicristata (Euglenozoa plus Percolozoa) and Cercozoa (the group including chlorarachneans) form a clade designated cabozoa (protozoa with chlorophyll a + b). If both theories are correct, there were only two secondary symbiogenetic events (witnessed by the chlorarachnean and cryptomonad nucleormorphs) in the history of life, not seven as commonly assumed. This greatly reduces the postulated number of independent origins of chloroplast protein-targeting machinery and of gene transfers from endosymbiont to host nuclei. I discuss the membrane and plastid losses and innovations in protein targeting implied by these theories, the comparative evidence for them, and their implications for eukaryote megaphylogeny. The principle of evolutionary conservatism leads to a novel theory for the function of periplastid vesicles in membrane biogenesis ofchlorarachneans and chromists and of the key steps in secondary symbiogenesis. Protozoan classification is also slightly revised by abandoning the probably polyphyletic infrakingdom Actinopoda, grouping Foraminifera and Radiolaria as a new infrakingdom Retaria,placing Heliozoa within a revised infrakingdom Sarcomastigota, establishing a new flagellate phylum Loukozoa for Jakobea plus Anaeromonadea within an emended subkingdom Eozoa, and ranking Archezoa as an infrakingdom within Eozoa.

Amino acid compositions were predicted from data sets of 47 non-animal and 58 invertebrate animal complete mitochondrial genomes, which were chosen alphabetically based on scientific names without considering biological characteristics. Using Ward’s clustering method with amino acid composition or nucleotide content as traits, non-animals were classified into Plantae, Chromalveolata, and Fungi, and invertebrates were classified into Animalia and primitive groups, Amoebozoa, Excavata, Protista, and Choanozoa. A combined sample set of primitive eukaryotes was also examined by cluster analysis using amino acid composition and nucleotide content. Some Amoebozoa comprised a single cluster, whereas other Amoebozoa were grouped with other organisms (Excavata, Prosista, Chromaleolata, Fungi and Plantae), indicating their close relationships. Choanozoa (choanoflagellates; Monosiga brevicollis ), considered the closest living relatives of animals, were found to be instead closely related to Fungi ( Smittium culisetae , Pleurotus ostreatus , and Epidermophyton floccosum ) and Excavata ( Malawimonas jakobiformis ). Our results demonstrate that amino acid composition and nucleotide content are useful indices for characterizing non-animal and invertebrate complete mitochondrial genomes.

Background Cardiolipin (CL) is an important component in mitochondrial inner and bacterial membranes. Its appearance in these two biomembranes has been considered as evidence of the endosymbiotic origin of mitochondria. But CL was reported to be synthesized through two distinct enzymes--CLS_cap and CLS_pld in eukaryotes and bacteria. Therefore, how the CL biosynthesis pathway evolved is an interesting question. Results Phylogenetic distribution investigation of CL synthase (CLS) showed: most bacteria have CLS_pld pathway, but in partial bacteria including proteobacteria and actinobacteria CLS_cap pathway has already appeared; in eukaryotes, Supergroup Opisthokonta and Archaeplastida, and Subgroup Stramenopiles, which all contain multicellular organisms, possess CLS_cap pathway, while Supergroup Amoebozoa and Excavata and Subgroup Alveolata, which all consist exclusively of unicellular eukaryotes, bear CLS_pld pathway; amitochondriate protists in any supergroups have neither. Phylogenetic analysis indicated the CLS_cap in eukaryotes have the closest relationship with those of alpha proteobacteria, while the CLS_pld in eukaryotes share a common ancestor but have no close correlation with those of any particular bacteria. Conclusions The first eukaryote common ancestor (FECA) inherited the CLS_pld from its bacterial ancestor (e. g. the bacterial partner according to any of the hypotheses about eukaryote evolution); later, when the FECA evolved into the last eukaryote common ancestor (LECA), the endosymbiotic mitochondria (alpha proteobacteria) brought in CLS_cap, and then in some LECA individuals the CLS_cap substituted the CLS_pld, and these LECAs would evolve into the protist lineages from which multicellular eukaryotes could arise, while in the other LECAs the CLS_pld was retained and the CLS_cap was lost, and these LECAs would evolve into the protist lineages possessing CLS_pld. Besides, our work indicated CL maturation pathway arose after the emergence of eukaryotes probably through mechanisms such as duplication of other genes, and gene duplication and loss occurred frequently at different lineage levels, increasing the pathway diversity probably to fit the complicated cellular process in various cells. Our work also implies the classification putting Stramenopiles and Alveolata together to form Chromalveolata may be unreasonable; the absence of CL synthesis and maturation pathways in amitochondriate protists is most probably due to secondary loss.

Biotrophic eukaryotic plant pathogens require a living host for their growth and form an intimate haustorial interface with parasitized cells. Evolution to biotrophy occurred independently in fungal rusts and powdery mildews, and in oomycete white rusts and downy mildews. Biotroph evolution and molecular mechanisms of biotrophy are poorly understood. It has been proposed, but not shown, that obligate biotrophy results from (i) reduced selection for maintenance of biosynthetic pathways and (ii) gain of mechanisms to evade host recognition or suppress host defence. Here we use Illumina sequencing to define the genome, transcriptome, and gene models for the obligate biotroph oomycete and Arabidopsis parasite, Albugo laibachii. A. laibachii is a member of the Chromalveolata, which incorporates Heterokonts (containing the oomycetes), Apicomplexa (which includes human parasites like Plasmodium falciparum and Toxoplasma gondii), and four other taxa. From comparisons with other oomycete plant pathogens and other chromalveolates, we reveal independent loss of molybdenum-cofactor-requiring enzymes in downy mildews, white rusts, and the malaria parasite P. falciparum. Biotrophy also requires “effectors” to suppress host defence; we reveal RXLR and Crinkler effectors shared with other oomycetes, and also discover and verify a novel class of effectors, the “CHXCs”, by showing effector delivery and effector functionality. Our findings suggest that evolution to progressively more intimate association between host and parasite results in reduced selection for retention of certain biosynthetic pathways, and particularly reduced selection for retention of molybdopterin-requiring biosynthetic pathways. These mechanisms are not only relevant to plant pathogenic oomycetes but also to human pathogens within the Chromalveolata., Author Summary Plant pathogens that cannot grow except on their hosts are called obligate biotrophs. How such biotrophy evolves is poorly understood. In this study, we sequenced the genome of the obligate biotroph white rust pathogen (Albugo laibachii, Oomycota) of Arabidopsis. From comparisons with other oomycete plant pathogens, diatoms, and the human pathogen Plasmodium falciparum, we reveal a loss of important metabolic enzymes. We also reveal the appearance of defence-suppressing “effectors”, some carrying motifs known from other oomycete effectors, and discover and experimentally verify a novel class of effectors that share a CHXC motif within 50 amino acids of the signal peptide cleavage site. Obligate biotrophy involves an intimate association within host cells at the haustorial interface (where the parasite penetrates the host cell's cell wall), where nutrients are acquired from the host and effectors are delivered to the host. We found that A. laibachii, like Hyaloperonospora arabidopsidis and Plasmodium falciparum, lacks molybdopterin-requiring biosynthetic pathways, suggesting relaxed selection for retention of, or even selection against, this pathway. We propose that when defence suppression becomes sufficiently effective, hosts become such a reliable source of nutrients that a free-living phase can be lost. These mechanisms leading to obligate biotrophy and host specificity are relevant not only to plant pathogenic oomycetes but also to human pathogens.

​AtAt first glance, diatoms, malaria parasites, and fungus-like plant pathogens called oomycetes look wildly different. But these organisms all have something in common: they belong to a group called the Chromalveolata that contains genes from algae. This diversity of lifestyles within a single group presents an opportunity to learn how the various strategies evolved. For example, oomycetes include both necrotrophs, which feed on dead plant tissue, and obligate biotrophs, which require living hosts. In addition, biotrophy evolved independently in two groups of oomycetes in the same lineage, the white rusts such as Albugo laibachii and the downy mildews such as the Irish potato famine pathogen Phytophthora infestans and Hyaloperonospora arabidopsidis, which infects the plant Arabidopsis thaliana. White blister rust of Arabidopsis thaliana, caused by the obligate biotroph oomycete Albugo laibachii, found in a field plot in Norwich, and later single-spore purified and sequenced. Recent research on H. arabidopsidis has linked biotrophy to massive gene loss in biosynthetic metabolic pathways. This makes sense because there is less selection to synthesize products when the host provides them. Biotrophy is also thought to result from gaining ways to circumvent host defenses. However, the evolution and molecular mechanisms of this lifestyle are poorly understood. In this issue of PLoS Biology, Kemen, Jones, and colleagues confirm that obligate biotrophy entails pathway loss in oomycetes, and report a new class of molecules that suppress host plant defenses. First, the researchers sequenced the genome of the white rust A. laibachii that, like the downy mildew H. arabidopsidis, is an obligate biotroph and parasitizes A. thaliana. Then they identified A. laibachii genes that code for proteins. This entailed extracting complementary DNA (which is made from the messenger RNAs that are translated into proteins) from A. thaliana leaves infected with A. laibachii, and then matching it to this white rust's genome sequences. The researchers also assigned A. laibachii genes to metabolic pathways using computational and manual prediction strategies. To investigate the origins of biotrophy, the researchers compared genes from the two biotrophs (A. laibachii and H. arabidopsidis) with those of a hemibiotroph (Phytophthora infestans) and a necrotroph (Pythium ultimum) in the same oomycete lineage. The two biotrophs were the least related, confirming that this lifestyle arose twice in this lineage. To identify gene losses linked to biotrophy, the researchers looked for genes that were present in the hemibiotroph and the necrotroph but missing in the biotrophs. Both biotrophs were missing genes in nitrogen and sulfur acquisition pathways. This is in keeping with the hypothesis that the evolution of biotrophy involves losing biosynthetic pathways. Likewise, the findings validate the other hypothesized component of biotroph evolution, suppression of host defenses. Biotrophic oomycetes form structures called haustoria that take up nutrients from and counteract defenses by their hosts. Outgrowths from intercellular hyphae enter plant cells and differentiate into haustoria, creating an intimate interface between host and parasite plasma membranes. Plants defend against invasion partly with disease resistance proteins that can recognize pathogen molecules. However, pathogens counteract plant defenses with secreted proteins called effectors, and in oomycetes some effectors have sequence motifs such as “RxLR”. Comparison of secreted proteins from two A. laibachii strains revealed a new class of effectors with a CHxC motif. The researchers validated the CHxC effectors with a translocation assay that confers avirulence, which involves fusing the N-terminus of potential effectors to a known avirulence protein. The findings showed that one of the new CHxC effectors conferred avirulence as effectively as a previously known class of A. laibachii effectors. To develop a model of how biotrophy evolves, the researchers determined the molecular divergence of A. laibachii from other Chromalveolata species with a variety of lifestyles: the other biotroph (H. arabidopsidis), the hemibiotroph (P. infestans), and the necrotroph (P. ultimum) in the same oomycete lineage, as well as a diatom (Thalassiosira pseudonana) and the malaria parasite Plasmodium falciparum. The researchers then assessed gene and metabolic pathway gains and losses amongst these species. For example, all of the oomycetes that form haustoria have also lost the pathway to make thiamine. In addition, like the oomycete biotrophs, the malaria parasite has lost molybdopterin-requiring pathways. This parasite also forms a structure that functions like a haustorium, taking up nutrients from the host and delivering secreted proteins to suppress host defenses. Based on the gene and metabolic pathway patterns amongst these Chromalveolata species of known relatedness, the researchers propose that the first step towards obligate biotrophy in oomycetes is suppressing host defenses. This facilitates haustoria formation, letting oomycetes get nutrients from their hosts and so ultimately leading to the loss of biosynthetic pathways. This pathway loss then results in absolute dependence on the host. This works sheds light on the origins and mechanisms of biotrophy, revealing a new class of avirulence proteins that can nullify plant defenses, and supporting the hypothesis that this lifestyle results from a combination of gaining ways to overcome host defenses and losing the ability to make nutrients. Understanding how organisms become obligate biotrophs that depend on specific hosts could also help lead to protections against human parasites in the Chromalveolata, including the malaria parasite and Toxoplasma gondii, which causes toxoplasmosis and can be fatal to fetuses and people with compromised immune systems. Kemen E, Gardiner A, Schultz-Larsen T, Kemen AC, Balmuth AL, et al. (2011) Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis. doi:10.1371/journal.pbio.1001094