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Phyllosticta citricarpa is an important citrus-pathogen and a quarantine organism in the European Union. Its recently described relative, P. paracitricarpa, is very closely related and not listed as a quarantine organism. P. paracitricarpa is very difficult to distinguish from P. citricarpa, since its morphological features overlap and the barcoding gene sequences that were originally used to delimit them as distinct species have a low number of species-specific polymorphisms that have subsequently been shown to overlap between the two clades. Therefore, we performed extensive genomic analyses to determine whether the genetic variation between P. citricarpa and P. paracitricarpa strains should be considered to represent infraspecific variation within P. citricarpa, or whether it is indicative of distinct species. Using a phylogenomic analysis with 3,000 single copy ortholog genes and whole-genome comparisons, we determined that the variation between P. citricarpa and P. paracitricarpa can be considered as infraspecies variation within P. citricarpa. We also determined the level of variation in mitochondrial assemblies of several Phyllosticta species and concluded there are only minimal differences between the assemblies of P. citricarpa and P. paracitricarpa. Thus, using several orthogonal approaches, we here demonstrate that variation within the nuclear and mitochondrial genomes of other Phyllosticta species is larger than variation between genomes obtained from P. citricarpa and P. paracitricarpa strains. Thus, P. citricarpa and P. paracitricarpa should be considered as conspecific.

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (>20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the 'Williams' haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of 'Fiskeby III,' a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to leap to the next level.

Some Basidiomycete fungi are important plant pathogens, and certain species have been associated with the grapevine trunk disease esca. We present the genomes of 4 species associated with esca: Fomitiporia mediterranea, Fomitiporia polymorpha, Tropicoporus texanus, and Inonotus vitis. We generated high-quality phased genome assemblies using long-read sequencing. The genomic and functional comparisons identified potential virulence factors, suggesting their roles in disease development. Similar to other white-rot fungi known for their ability to degrade lignocellulosic substrates, these 4 genomes encoded a variety of lignin peroxidases and carbohydrate-active enzymes (CAZymes) such as CBM1, AA9, and AA2. The analysis of gene family expansion and contraction revealed dynamic evolutionary patterns, particularly in genes related to secondary metabolite production, plant cell wall decomposition, and xenobiotic degradation. The availability of these genomes will serve as a reference for further studies of diversity and evolution of virulence factors and their roles in esca symptoms and host resistance.

UNLABELLED: To gain insights into the diversity of Pseudomonas syringae sensu lato affecting sweet cherry in California, we sequenced and analyzed the phylogenomic and genomic architecture of 86 fluorescent pseudomonads isolated from symptomatic and asymptomatic cherry tissues. Fifty-eight isolates were phylogenetically placed within the P. syringae species complex and taxonomically classified into five genomospecies: P. syringae pv. syringae, P. syringae, Pseudomonas cerasi, Pseudomonas viridiflava, and A. We annotated components of the type III secretion system and phytotoxin-encoding genes and correlated the data with pathogenicity phenotypes. Intact probable regulatory protein HrpR was annotated in the genomic sequences of all isolates of P. syringae pv. syringae, P. syringae, P. cerasi, and A. Isolates of P. viridiflava had atypical probable regulatory protein HrpR. Syringomycin and syringopeptin-encoding genes were annotated in isolates of all genomospecies except for A and P. viridiflava. All isolates of P. syringae pv. syringae caused cankers, leaf spots, and fruit lesions in the field. In contrast, all isolates of P. syringae and P. cerasi and some isolates of P. viridiflava caused only cankers. Isolates of genomospecies A could not cause any symptoms suggesting phytotoxins are essential for pathogenicity. On detached immature cherry fruit pathogenicity assays, isolates of all five genomospecies produced symptoms (black-dark brown lesions). However, symptoms of isolates of genomospecies A were significantly (P < 0.01) less severe than those of other genomospecies. We also mined for genes conferring resistance to copper and kasugamycin and correlated these data with in vitro antibiotic sensitivity tests. IMPORTANCE: Comprehensive identification of phytopathogens and an in-depth understanding of their genomic architecture, particularly virulence determinants and antibiotic-resistant genes, are critical for several practical reasons. These include disease diagnosis, improved knowledge of disease epidemiology, pathogen diversity, and determination of the best possible management strategies. In this study, we provide the first report of the presence and pathogenicity of genomospecies Pseudomonas cerasi and Pseudomonas viridiflava in California sweet cherry. More importantly, we report a relatively high level of resistance to copper among the population of Pseudomonas syringae pv. syringae (47.5%). This implies copper cannot be effectively used to control bacterial blast and bacterial canker of sweet cherries. On the other hand, no isolates were resistant to kasugamycin, an indication that kasugamycin could be effectively used for the control of bacterial blast and bacterial canker. Our findings are important to improve the management of bacterial blast and bacterial canker of sweet cherries in California.

Schizophyllum commune is a mushroom-forming fungus notable for its distinctive fruiting bodies with split gills. It is used as a model organism to study mushroom development, lignocellulose degradation and mating type loci. It is a hypervariable species with considerable genetic and phenotypic diversity between the strains. In this study, we systematically phenotyped 16 dikaryotic strains for aspects of mushroom development and 18 monokaryotic strains for lignocellulose degradation. There was considerable heterogeneity among the strains regarding these phenotypes. The majority of the strains developed mushrooms with varying morphologies, although some strains only grew vegetatively under the tested conditions. Growth on various carbon sources showed strain-specific profiles. The genomes of seven monokaryotic strains were sequenced and analyzed together with six previously published genome sequences. Moreover, the related species Schizophyllum fasciatum was sequenced. Although there was considerable genetic variation between the genome assemblies, the genes related to mushroom formation and lignocellulose degradation were well conserved. These sequenced genomes, in combination with the high phenotypic diversity, will provide a solid basis for functional genomics analyses of the strains of S. commune.

Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.

Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis is that genes which are more likely to be transferred, such as those on plasmids, should be more likely to code for cooperative traits. Testing this prediction requires identifying all genes for cooperation in bacterial genomes. However, previous studies used a method which likely misses some of these genes for cooperation. To solve this, we used a new genomics tool, SOCfinder, which uses three distinct modules to identify all kinds of genes for cooperation. We compared where these genes were located across 4648 genomes from 146 bacterial species. In contrast to the prediction of the hypothesis, we found no evidence that plasmid genes are more likely to code for cooperative traits. Instead, we found the opposite-that genes for cooperation were more likely to be carried on chromosomes. Overall, the vast majority of genes for cooperation are not located on plasmids, suggesting that the more general mechanism of kin selection is sufficient to explain the prevalence of cooperation across bacteria.

The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.

Smoky rubyspot damselflies (Hetaerina titia Drury, 1773) are one of the most commonly encountered odonates along streams and rivers on both slopes of Central America and the Atlantic drainages in the United States and southern Canada. Owing to their highly variable wing pigmentation, they have become a model system for studying sexual selection and interspecific behavioral interference. Here, we sequence and assemble the genome of a female smoky rubyspot. Of the primary assembly (i.e. the principle pseudohaplotype), 98.8% is made up of 12 chromosomal pseudomolecules (2N = 22A + X). There are 75 scaffolds in total, an N50 of 120 Mb, a contig-N50 of 0.64 Mb, and a high arthropod BUSCO score [C: 97.6% (S: 97.3%, D: 0.3%), F: 0.8%, M: 1.6%]. We then compare our assembly to that of the blue-tailed damselfly genome (Ischnura elegans), the most complete damselfly assembly to date, and a recently published assembly for an American rubyspot damselfly (Hetaerina americana). Collectively, these resources make Hetaerina a genome-enabled genus for further studies of the ecological and evolutionary forces shaping biological diversity.

Long non-coding RNAs (lncRNAs) have begun to receive overdue attention for their regulatory roles in gene expression and other cellular processes. Although most lncRNAs are lowly expressed and tissue-specific, notable exceptions include MALAT1 and its genomic neighbor NEAT1, two highly and ubiquitously expressed oncogenes with roles in transcriptional regulation and RNA splicing. Previous studies have suggested that NEAT1 is found only in mammals, while MALAT1 is present in all gnathostomes (jawed vertebrates) except birds. Here we show that these assertions are incomplete, likely due to the challenges associated with properly identifying these two lncRNAs. Using phylogenetic analysis and structure-aware annotation of publicly available genomic and RNA-seq coverage data, we show that NEAT1 is a common feature of tetrapod genomes except birds and squamates. Conversely, we identify MALAT1 in representative species of all major gnathostome clades, including birds. Our in-depth examination of MALAT1, NEAT1, and their genomic context in a wide range of vertebrate species allows us to reconstruct the series of events that led to the formation of the locus containing these genes in taxa from cartilaginous fish to mammals. This evolutionary history includes the independent loss of NEAT1 in birds and squamates, since NEAT1 is found in the closest living relatives of both clades (crocodilians and tuataras, respectively). These data clarify the origins and relationships of MALAT1 and NEAT1 and highlight an opportunity to study the change and continuity in lncRNA structure and function over deep evolutionary time.

Background: The confused taxonomic classification of Crucigenia is mainly inferred through morphological evidence and few nuclear genes and chloroplast genomic fragments. The phylogenetic status of C. quadrata, as the type species of Crucigenia, remains considerably controversial. Additionally, there are currently no reports on the chloroplast genome of Crucigenia. Results: In this study, we utilize molecular phylogenetics and comparative genomics to show that C. quadrata belongs to Chlorophyceae rather than Trebouxiophyceae. The Bayesian and maximum likelihood (ML) phylogenetic trees support a monophyletic group of C. quadrata and Scenedesmaceae (Chlorophyceae) species. Our study presents the first complete chloroplast genome of C. quadrata, which is 197,184 bp in length and has a GC content of 31%. It has a typical quadripartite structure, and the chloroplast genome codons exhibit usage bias. Nucleotide diversity analysis highlights six genes (ccsA, psbF, chlN, cemA, rps3, rps18) as hotspots for genetic variation. Coding gene sequence divergence analyses indicate that four genes (cemA, clpP, psaA, rps3) are subject to positive selection. Conclusions: The determination of the phylogenetic status and the comparative chloroplast genomic analyses of C. quadrata will not only be useful in enhancing our understanding of the intricacy of Crucigenia taxonomy but also provide the important basis for studying the evolution of the incertae sedis taxa within Trebouxiophyceae. [ABSTRACT FROM AUTHOR]

Background: Stress responses are key the survival of parasites and, consequently, also the evolutionary success of these organisms. Despite this importance, our understanding of the evolution of molecular pathways dealing with environmental stressors in parasitic animals remains limited. Here, we tested the link between adaptive evolution of parasite stress response genes and their ecological diversity and species richness. We comparatively investigated antioxidant, heat shock, osmoregulatory, and behaviour-related genes (foraging) in two model parasitic flatworm lineages with contrasting ecological diversity, Cichlidogyrus and Kapentagyrus (Platyhelminthes: Monopisthocotyla), through whole-genome sequencing of 11 species followed by in silico exon bait capture as well as phylogenetic and codon analyses. Results: We assembled the sequences of 48 stress-related genes and report the first foraging (For) gene orthologs in flatworms. We found duplications of heat shock (Hsp) and oxidative stress genes in Cichlidogyrus compared to Kapentagyrus. We also observed positive selection patterns in genes related to mitochondrial protein import (Hsp) and behaviour (For) in species of Cichlidogyrus infecting East African cichlids—a host lineage under adaptive radiation. These patterns are consistent with a potential adaptation linked to a co-radiation of these parasites and their hosts. Additionally, the absence of cytochrome P450 and kappa and sigma-class glutathione S-transferases in monogenean flatworms is reported, genes considered essential for metazoan life. Conclusions: This study potentially identifies the first molecular function linked to a flatworm radiation. Furthermore, the observed gene duplications and positive selection indicate the potentially important role of stress responses for the ecological adaptation of parasite species. [ABSTRACT FROM AUTHOR]

Background: Avian mycoplasmas are small bacteria associated with several pathogenic conditions in many wild and poultry bird species. Extensive genomic data are available for many avian mycoplasmas, yet no comparative studies focusing on this group of mycoplasmas have been undertaken so far. Results: Here, based on the comparison of forty avian mycoplasma genomes belonging to ten different species, we provide insightful information on the phylogeny, pan/core genome, energetic metabolism, and virulence of these avian pathogens. Analyses disclosed considerable inter- and intra-species genomic variabilities, with genome sizes that can vary by twice as much. Phylogenetic analysis based on concatenated orthologous genes revealed that avian mycoplasmas fell into either Hominis or Pneumoniae groups within the Mollicutes and could split into various clusters. No host co-evolution of avian mycoplasmas can be inferred from the proposed phylogenetic scheme. With 3,237 different gene clusters, the avian mycoplasma group under study proved diverse enough to have an open pan genome. However, a set of 150 gene clusters was found to be shared between all avian mycoplasmas, which is likely encoding essential functions. Comparison of energy metabolism pathways showed that avian mycoplasmas rely on various sources of energy. Superposition between phylogenetic and energy metabolism groups revealed that the glycolytic mycoplasmas belong to two distinct phylogenetic groups (Hominis and Pneumoniae), while all the arginine-utilizing mycoplasmas belong only to Hominis group. This can stand for different evolutionary strategies followed by avian mycoplasmas and further emphasizes the diversity within this group. Virulence determinants survey showed that the involved gene arsenals vary significantly within and between species, and could even be found in species often reported apathogenic. Immunoglobulin-blocking proteins were detected in almost all avian mycoplasmas. Although these systems are not exclusive to this group, they seem to present some particular features making them unique among mycoplasmas. Conclusion: This comparative genomic study uncovered the significant variable nature of avian mycoplasmas, furthering our knowledge on their biological attributes and evoking new hallmarks. [ABSTRACT FROM AUTHOR]

The sunflower (Helianthus annuus L.), belonging to the Asteraceae family, is the world's fourth most important oil crop. Sunflower cultivars are categorized into oilseed and confectionery types. Here, we present chromosome-level genome assemblies of two Chinese sunflower cultivars-oilseed and confectionery-using PacBio HiFi and Hi-C sequencing. The oilseed cultivar, OXS, has a genome assembly spanning 3.03 Gb with 99.58% of sequences anchored to 17 chromosomes and a contig N50 length of 154.78 Mb. The first published confectionery cultivar genome, YDS, mirrors this closely with a 3.02 Gb assembly, contig N50 length of 153.87 Mb and 99.40% of sequences mapped similarly. Gene completeness reached 98.2% for OXS and 98.4% for YDS, with LTR Assembly Index scores of 24.73 and 25.85, respectively. Comparative genomics identified rapidly evolving gene families linked to synthesis, growth, and stress defense. Additionally, we found high collinearity between the YDS and OXS genomes, despite three significant inversions, and detected 15,056 large deletions and insertions. These findings lay a robust foundation for advanced genomic research and breeding innovations in sunflowers. [ABSTRACT FROM AUTHOR]

dna2bit is an ultra-fast software specifically engineered for microbial genome analysis, particularly adept at calculating genome distances within metagenome and single amplified genome datasets. Distinguished from existing software such as Mash and Dashing, dna2bit employs feature hashing technique and Hamming distance to achieve enhanced speed and memory utilization, without sacrifice in the accuracy of average nucleotide identity calculations. dna2bit has promising applications in various domains such as average nucleotide identity approximation, metagenomic sequence clustering, and homology querying. dna2bit significantly boosts computational efficiency in handling large datasets including single amplified genomes, thereby facilitating a better understanding of the population heterogeneity and comparative genomics of microorganisms. dna2bit is available at https://github.com/lijuzeng/dna2bit. [ABSTRACT FROM AUTHOR]

Enterobacter asburiae (E. asburiae) is a gram-negative rod-shaped bacterium which has emerging significance as an opportunistic pathogen having high virulence pattern and drug resistant properties. In this study, we present the detailed analysis of the whole genome sequence of a multidrug-resistant (MDR) E. asburiae strain BDW1M3 from Bangladesh. The isolate was collected from an infected foot wound of a diabetic foot ulcer patient. Through sophisticated genomic techniques encompassing whole genome sequencing and in-depth bioinformatic analyses, this research unveils a profound understanding of the isolate's antimicrobial resistance patterns, virulence determinants, biosynthetic gene clusters, metabolic pathways and pathogenic potential. The isolate displayed resistance to Ampicillin, Fosfomycin, Cefoxitin, Tigecycline, Meropenem, Linezolid, Vancomycin antibiotics and demonstrated the capacity for biofilm formation. Several antimicrobial resistance genes such as blaACT−2,fosA2, baeR, qnrE2, vanA and numbers of virulence genes including ybaJ, csrA, barA, uvrY, pgaD, hlyD, hlyC, terC, purD were detected. Metal resistance genes investigation revealed the presence of cusCFBA operon system, and many other genes including zntA, zitB, czrB. Prophage region of Myoviridae was detected. Comparative genomics with 47 whole genome sequence (n = 47) shed light on the genetic diversity of E. asburiae strains from diverse sources and countries, with a notable observation that strains from both human and non-human origins exhibited significant pathogenicity potential, genomic and phylogenomic relations hinting at potential cross-species transmission. Pangenome analysis indicated toward an expanding pangenome of E. asburiae. Further research and in-depth comprehensive studies are required to investigate the prevalence of E. asburiae in Bangladesh and emphasize towards unraveling the bacterium's inherent pathogenic potential and the intricate molecular mechanisms that underlie its resistance traits and virulence properties. [ABSTRACT FROM AUTHOR]

Background: Tea-oil Camellia within the genus Camellia is renowned for its premium Camellia oil, often described as "Oriental olive oil". So far, only one partial mitochondrial genomes of Tea-oil Camellia have been published (no main Tea-oil Camellia cultivars), and comparative mitochondrial genomic studies of Camellia remain limited. Results: In this study, we first reconstructed the entire mitochondrial genome of C. drupifera to gain insights into its genetic structure and evolutionary history. Through our analysis, we observed a characteristic multi-branched configuration in the mitochondrial genomes of C. drupifera. A thorough examination of the protein-coding regions (PCGs) across Camellia species identified gene losses that occurred during their evolution. Notably, repeat sequences showed a weak correlation between the abundance of simple sequence repeats (SSRs) and genome size of Camellia. Additionally, despite of the considerable variations in the sizes of Camellia mitochondrial genomes, there was little diversity in GC content and gene composition. The phylogenetic tree derived from mitochondrial data was inconsistent with that generated from chloroplast data. Conclusions: In conclusion, our study provides valuable insights into the molecular characteristics and evolutionary mechanisms of multi-branch mitochondrial structures in Camellia. The high-resolution mitogenome of C. drupifera enhances our understanding of multi-branch mitogenomes and lays a solid groundwork for future advancements in genomic improvement and germplasm innovation within Tea-oil Camellia. [ABSTRACT FROM AUTHOR]

Background: The advent of next generation sequencing technologies has enabled a surge in the number of whole genome sequences in public databases, and our understanding of the composition and evolution of bacterial genomes. Besides model organisms and pathogens, some attention has been dedicated to industrial bacteria, notably members of the Lactobacillaceae family that are commonly studied and formulated as probiotic bacteria. Of particular interest is Lactobacillus acidophilus NCFM, an extensively studied strain that has been widely commercialized for decades and is being used for the delivery of vaccines and therapeutics. Results: Here, we revisit the L. acidophilus genome, which was sequenced twenty years ago, and determined the core and pan genomes of 114 publicly available L. acidophilus strains, spanning commercial isolates, academic strains and clones from the scientific literature. Results indicate a predictable high level of homogeneity within the species, but also reveal surprising mis-assemblies. Furthermore, by investigating twenty one available L. acidophilus NCFM-derived variants, we document overall genomic stability, with no observed genomic re-arrangement or inversions. Conclusion: This study provides a comparative analysis of the currently available genomes for L. acidophilus and examines microevolution patterns for several strains derived from L. acidophilus NCFM, which revealed no to very few SNPs with strains sequenced at different points in time using different sequencing technologies and platforms. This re-affirms its suitability for industrial deployment as a probiotic and its use as an engineering chassis and delivery modality for novel biotherapeutics. [ABSTRACT FROM AUTHOR]

Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex determination and in some lineages, the ability to regenerate limbs and organs. Although genomic approaches would shed light on these unique traits and aid conservation, sequencing and assembly of amphibian genomes has lagged behind other taxa due to their comparatively large genome sizes. Fortunately, the development of long‐read sequencing technologies and initiatives has led to a recent burst of new amphibian genome assemblies. Although growing, the field of amphibian genomics suffers from the lack of annotation resources, tools for working with challenging genomes and lack of high‐quality assemblies in multiple clades of amphibians. Here, we analyse 51 publicly available amphibian genomes to evaluate their usefulness for functional genomics research. We report considerable variation in genome assembly quality and completeness and report some of the highest transposable element and repeat contents of any vertebrate. Additionally, we detected an association between transposable element content and climatic variables. Our analysis provides evidence of conserved genome synteny despite the long divergence times of this group, but we also highlight inconsistencies in chromosome naming and orientation across genome assemblies. We discuss sequencing gaps in the phylogeny and suggest key targets for future sequencing endeavours. Finally, we propose increased investment in amphibian genomics research to promote their conservation. [ABSTRACT FROM AUTHOR]

Recent application of whole genome sequencing in the investigation of foodborne illness outbreaks has facilitated the identification of Reoccurring, Emerging, or Persistent (REP) bacterial strains that have caused illnesses over extended periods of time. Here, the complete genomes of two Escherichia coli O157:H7 (EcO157) outbreak strains belonging to REPEXH01 and REPEXH02, respectively, were sequenced and annotated. Comparative genomics and phenotypic analyses were carried out to identify REP-associated traits. The REPEXH01 strain PNUSAE013245 belonged to clade 8 and shared >96% CDSs with the 2006 spinach-associated outbreak strain EC4115. A 79-Kb genomic island was identified only in PNUSAE013245, and encoded functions related to heavy metals and antibiotic resistances. The REPEXH02 strain PNUSAE043864 belonged to clade 2, like the 2006 Taco John's restaurants-associated outbreak strain TW14588 and the REPEXH02 strain 2019C-3201. These three strains differed mainly in plasmids and prophages repertoire. Unlike 2019C-3201, PNUSAE043864 carried only the virulence plasmid pO157; unlike TW14588, PNUSAE043864 carried one Stx2a-encoding prophage. Phenotypic assays revealed that all clade 2 strains produced greater amounts of biofilms than the clade 8 strains, although there were no significant differences in adhesion of EcO157 to romaine lettuce. The persistence of EcO157 was further evaluated by quantifying populations of culturable cells, persisters, and Viable But Not Culturable (VBNC) cells for strains inoculated in river water and incubated at 15°C for 14 weeks. The fractions of culturable cells were comparable among the strains tested until 10 weeks post inoculation, when the three clade 2 strains exhibited significantly greater survival than strain PNUSAE013245. The population of persisters for all strains except PNUSAE013245 increased when the incubation time increased and reached up to 24–30% of the total culturable cells. The population of VBNC increased for all strains during the incubation and reached up to 65–80% of the total population. Both persisters and VBNC cells represent the dormancy state of pathogen cells that have increased tolerance to antibiotics and sanitizers. Presence of high portions of persisters and VBNC cells in agricultural environments highlights the need to understand the physiology of bacterial pathogens in leafy greens production environments and the challenges in developing effective control strategies. [ABSTRACT FROM AUTHOR]

A new fungal species, Penicillium psychrofluorescens sp. nov. is described as a member of section Torulomyces. The new species is sister to P. catalonicum, and was isolated from soil collected from Robinson Ridge, East Antarctica, following enrichment cultivation under oligotrophic conditions supplemented with excess hydrogen gas. Penicillium psychrofluorescens is named for its intense autofluorescence derived from a combination of compounds that may include NADPH, porphyrins, and secondary metabolites, such as polyketides. Comparative genomics with both Antarctic and mesophilic Penicillium spp. shows that Penicillium psychrofluorescens has a wide repertoire of glycoside hydrolases, but almost no polysaccharide lyases, has comparably large effector proteins, lacks the machinery to use nitrate as an N-source, but has the genes for the assimilation of phosphorus from phosphonates via oxidative pathway. The strain was found to have 30 biosynthetic gene clusters (BGCs), the majority of which were unrelated to known compound BGCs. Given the remarkable diversity of natural products already characterised from Penicillium spp. and the presence of >30 BGCs with low similarity to known genes, there is biotechnological potential within this novel species that is yet to be explored. [ABSTRACT FROM AUTHOR]

Cadmium, a toxic heavy metal, poses significant global concern. A strain of the genus Pseudomonas, CD3, demonstrating significant cadmium resistance (up to 3 mM CdCl2.H2O) was identified from a pool of 26 cadmium-resistant bacteria isolated from cadmium-contaminated soil samples from Malda, India. The minimum inhibitory concentrations (MICs) for cadmium and other heavy metals/metalloids were determined with clarity using a modified chemically-defined medium inoculated with variable inoculum density. Formation of biofilm enabled CD3 cells to resist up to 0.75 mM CdCl2.H2O. Survival and growth of CD3 cells in presence of > 1 mM CdCl2.H2O was dependent on efflux mechanism. Efflux mechanism in CD3 was confirmed by atomic absorption spectroscopy. Resistance to cadmium was inducible when grown in presence of ≥ 1.0 mM CdCl2.H2O. Minimum concentration of cadmium or zinc or cobalt salts required for induction of cadmium resistance was determined. Whole-genome-based phylogenetic tools identified CD3 as the closest relative to Pseudomonas aeruginosa DSM50071T. Bioinformatic analyses revealed a complex network of regulations, with BfmR playing a crucial role in the functions of CzcR and CzcS, essential for biofilm formation and receptor signalling pathways. Comparative genomics and mutation landscape analyses of cadmium-resistance genes in P. aeruginosa strains revealed dynamism in evolution of cadmium resistance. [ABSTRACT FROM AUTHOR]

Background: Fervidobacterium is a genus of thermophilic anaerobic Gram-negative rod-shaped bacteria belonging to the phylum Thermotogota. They can grow through fermentation on a wide range of sugars and protein-rich substrates. Some can also break down feather keratin, which has significant biotechnological potential. Fervidobacteria genomes have undergone several horizontal gene transfer events, sharing DNA with unrelated microbial taxa. Despite increasing biotechnological and evolutionary interest in this genus, only seven species have been described to date. Here, we present and describe six new and complete Fervidobacterium genomes, including the type strains Fervidobacterium gondwanense CBS-1 T, F. islandicum H-21 T and F. thailandense FC2004T, one novel isolate from Georgia (strain GSH) and two strains (DSM 21710 and DSM 13770) that have not been previously described along with an evolutionary and phylogenomic analysis of the genus. Results: The complete genomes were around 2 Mb with approximately 2,000 CDS identified and annotated in each of them and a G + C content ranging from 38.9 mol% to 45.8 mol%. Phylogenomic comparisons of all currently available Fervidobacterium genomes, including OrthoANI and TYGS analyses, as well as a phylogenetic analysis based on the 16S rRNA gene, identified six species and nine subspecies clusters across the genus, with a consistent topology and a distant and separately branching species, Fervidobacterium thailandense. F. thailandense harbored the highest number of transposases, CRISPR clusters, pseudo genes and horizontally transferred regions The pan genome of the genus showed that 44% of the genes belong to the cloud pangenome, with most of the singletons found also in F. thailandense. Conclusions: The additional genome sequences described in this work and the comparison with all available Fervidobacterium genome sequences provided new insights into the evolutionary history of this genus and supported a phylogenetic reclassification. The phylogenomic results from OrthoANI and TYGS analyses revealed that F. riparium and F. gondwanense belong to the same genome species, and includes Fervidobacterium sp. 13770, while “F. pennivorans” strain DYC belongs to a separate genome species, whereas Fervidobacterium sp. 21710 and Fervidobacterium sp. GSH within the Fervidobacterium pennivorans clade represent two subspecies. F. changbaicum is reclassified as F. islandicum. [ABSTRACT FROM AUTHOR]

Background: Caryophyllaceae contains 100 genera and 3000 species, many of which are valuable both ecologically and economically. However, as past research has shown, the fundamental phylogenetic relationships of Caryophyllaceae are still debatable, and molecular dating based on chloroplast genomes has not been thoroughly examined for the entire family. Methods: In this study, the complete chloroplast genome sequences of Arenaria kansuensis Maxim., A. roborowskii Maxim., A. przewalskii Maxim., and Silene aprica Turcz were described. Additionally, the four newly generated along with eighteen published chloroplast genomes of Caryophyllaceae were included for comparative genomics analysis. Results: These 22 chloroplast genomes had typical quadripartite structure, with 128–134 distinct genes and lengths ranging from 133,621 bp to 153,957 bp. The 22 Caryophyllaceae chloroplast genomes showed significant variations in the number of long repeats and SSR types; mononucleotide repeats (A/T) and palindromic repeats were the most common types. Three substantially divergent areas containing atpB-rbcL, rbcL-accD, and accD were found by further comparative study, which could serve as effective molecular markers. The codon bias of chloroplast genomes in Caryophyllaceae were mainly affected by natural selection, but other factors such as mutation pressure could also affect the codon bias to some extent. Fourteen optimal codons were identified in the chloroplast genome of Caryophyllaceae. Phylogenetic analysis demonstrated that the monophyly of any of the three recognized subfamilies within Caryophyllaceae was not supported by our data. Meanwhile, seven well-supported clades correspond to 8 tribes were found in phylogenetic trees. The results of molecular dating demonstrated that the divergence between Caryophyllaceae and Amaranthaceae was estimated to occur in 69 Ma. The Paronychieae was the oldest tribe of the eight tribes included in this study, diverged at 59.92 Ma. Conclusion: This study provides resources for further investigations on the identification, genetic engineering, evolution, and phylogeny of Caryophyllaceae species. [ABSTRACT FROM AUTHOR]

The Malvaceae family, comprising 9 subfamilies and 4,225 species, includes economically significant taxa, such as Ceiba pentandra, Gossypium ekmanianum, Gossypium stephensii, Kokia drynarioides, Talipariti hamabo, and Durio zibethinus. Chloroplast (cp) genome research is crucial for elucidating the evolutionary divergence and species identification within this family. In this study, we assembled and annotated cp genomes of six Malvaceae species, conducting comprehensive comparative genomic and phylogenomic analyses. The assembled genomes range from 160,495 to 163,970 bp in size, with 125–129 genes annotated. Notable differences were observed in the IR (inverted repeat) regions, and SSR analysis revealed that Durio zibethinus has the highest number of specific variation sites. Among the six species, Talipariti hamabo uniquely exhibits more palindromic repeats than forward repeats. Seven highly mutated regions were identified, offering potential markers for species identification. Phylogenetic reconstruction using the maximum likelihood method revealed two primary clades within Malvaceae: Byttneriina and Malvadendrina. Within Malvadendrina, the subfamily Helicteroideae represents the earliest divergence, followed by Sterculioideae. This study provides a robust phylogenetic framework and valuable insights into the classification and evolutionary history of Malvaceae species. [ABSTRACT FROM AUTHOR]

Premise Methods Results Discussion Orthology inference is crucial for comparative genomics, and multiple algorithms have been developed to identify putative orthologs for downstream analyses. Despite the abundance of proposed solutions, including publicly available benchmarks, it is difficult to assess which tool is most suitable for plant species, which commonly have complex genomic histories.We explored the performance of four orthology inference algorithms—OrthoFinder, SonicParanoid, Broccoli, and OrthNet—on eight Brassicaceae genomes in two groups: one group comprising only diploids and another set comprising the diploids, two mesopolyploids, and one recent hexaploid genome.The composition of the orthogroups reflected the species' ploidy and genomic histories, with the diploid set having a higher proportion of identical orthogroups. While the diploid + higher ploidy set had a lower proportion of orthogroups with identical compositions, the average degree of similarity between the orthogroups was not different from the diploid set.Three algorithms—OrthoFinder, SonicParanoid, and Broccoli—are helpful for initial orthology predictions. Results produced using OrthNet were generally outliers but could still provide detailed information about gene colinearity. With our Brassicaceae dataset, slight discrepancies were found across the orthology inference algorithms, necessitating additional analyses such as tree inference to fine‐tune results. [ABSTRACT FROM AUTHOR]

Tef [ Eragrostis tef (Zucc.) Trotter] is the major staple crop for millions of people in Ethiopia and Eritrea and is believed to have been domesticated several thousand years ago. Tef has the smallest grains of all the cereals, which directly impacts its productivity and presents numerous challenges to its cultivation. In this study, we assessed the natural variation in seed size of 189 tef and 11 accessions of its wild progenitor Indian lovegrass (Eragrostis pilosa (L.) P. Beauv.) and explored the mineral distribution of representative accessions. Our findings revealed significant natural variation in seed size and mineral concentration among both the tef and E. pilosa accessions. We observed significant variation in seed length, seed width, and seed area among the accessions of both Eragrostis spp. we analyzed. Using representative accessions of both species, we also found significant variation in 1000-grain weight. The observed variation in seed size attributes prompted us to use comparative genomics to identify seed size regulating genes based on the well-studied and closely related monocot cereal rice [ Oryza sativa (L.)]. Using this approach, we identified putative orthologous genes in the tef genome that belong to a number of key pathways known to regulate seed size in rice. Phylogenetic analysis of putative tef orthologs of ubiquitin-proteasome, G-protein, MAPK, and brassinosteroid (BR)-family genes indicate significant similarity to seed size regulating genes in rice and other cereals. Because tef is known to be more nutrient-dense than other more common cereals such as rice, wheat, and maize, we also studied the mineral concentration of selected accessions using ICP-OES and explored their distribution within the seeds using synchrotron-based X-ray fluorescence (SXRF) microscopy. The findings showed significant variation in seed mineral concentration and mineral distribution among the selected accessions of both Eragrostis spp. This study highlights the natural variation in seed size attributes, mineral concentration, and distribution, while establishing the basis for understanding the genetic mechanisms regulating these traits. We hope our findings will lead to a better understanding of the evolution of tef at the genetic level and for the development of elite tef cultivars to improve seed size, yield, and quality of the grains. [ABSTRACT FROM AUTHOR]

The halotolerant yeast Scheffersomyces spartinae, commonly found in marine environments, holds significant potential for various industrial applications. Despite this, its genetic characteristics have been relatively underexplored. In this study, we isolated a strain of S. spartinae named YMxiao from seawater in Zhoushan City, China. Through scanning electron microscopy and flow cytometry, we characterized S. spartinae YMxiao cells as urn-shaped, demonstrating asymmetric division via budding, and possessing a diploid genome. Compared to the model yeast Saccharomyces cerevisiae, S. spartinae YMxiao exhibited greater tolerance to various stressful conditions. Furthermore, S. spartinae YMxiao was capable of utilizing xylose, mannitol, sorbitol, and arabinose as sole carbon sources for growth. We conducted whole-genome sequencing of S. spartinae YMxiao using a combination of Nanopore and Illumina technologies, resulting in a telomere-to-telomere complete genome assembly of 12 Mb. Genome annotation identified 5311 protein-coding genes, 214 tRNA genes, and 236 transposable elements distributed across 8 chromosomes. Comparative genomics between S. spartinae strains YMxiao and ARV011 revealed genomic variations and evolutionary patterns within this species. Notably, certain genes in S. spartinae strains were found to be under strong positive selection. Additionally, we developed a genetic manipulation protocol that successfully enabled gene knockouts in S. spartinae. Our findings not only enhance our understanding of the S. spartinae genome but also provide a foundation for future research into its potential biotechnological applications. Key points: • The unique phenotypes and genetic characteristics of S. spartinae were disclosed. • Comparative genomics showed vast genetic variations between S. spartinae strains. • Genetic manipulation protocol was established for S. spartinae strain. [ABSTRACT FROM AUTHOR]

Background: Bacterial wilt disease, caused by Ralstonia solanacearum, seriously threaten the quality and yield of peanut (Arachis hypogaea L.). Identification of proteins inducing host immune response in R. solanacearum is an important way towards exploring resistance genes in peanut. In previous study, we found that the pathogenicity was significant different between peanut R. solanacearum ZKRS126 and ZKRS146. In this study, comparative genomics analysis was performed to reveal the difference of the genomes between ZKRS126 and ZKRS146, as well as the function of the strain specific gene rsmA in triggering immunity. Results: Compared with ZKRS146, ZKRS126 caused less cell death in the peanut leaves and its proliferation and pathogenicity were significantly attenuated. Whole genome sequencing revealed that the genomes of ZKRS126 and ZKRS146 were composed of one chromosome, one megaplasmid and one small plasmid. The genome size of ZKRS126 (6,059,912 bp) was slightly larger than that of ZKRS146 (6,053,081 bp). Comparative genomics analysis showed that the genetic relationship between ZKRS126 and ZKRS146 was very close. In both ZKRS126 and ZKRS146, 73 Type III secretion system-secreted effectors (T3Es) were identified by retrieving the effector repertoire, respectively. The gene sequences of T3Es were identical between ZKRS126 and ZKRS146. Comparing all the coding genes between ZKRS126 and ZKRS146, 42 specific genes were identified in ZKRS126 and 43 in ZKRS146. Loss of the specific gene rsmA in ZKRS126 resulted in more virulence, and complementarity of rsmA in mutant strains recovered hypovirulence. The cAMP assay demonstrated RsmA was not a T3E. In Nicotiania benthamiana leaves, transient expression of rsmA significantly induced the up-regulated expression of marker genes in HR, PTI, SA, and JA pathways, indicating RsmA might trigger the plant immunity by activating the immune-related pathways. Conclusions: This study not only obtained the complete genomes of two peanut R. solanacearum strains, but also revealed their differences in the genome levels through comparing analysis. The function verification of RsmA provided the way for the identification of immunity elicitors, which will accelerate the breeding of bacterial wilt-resistant peanut varieties in the future. [ABSTRACT FROM AUTHOR]

Quinoa (Chenopodium quinoa) is an important crop for the future challenges of food and nutrient security. Deep characterization of quinoa diversity is needed to support the agronomic improvement and adaptation of quinoa as its worldwide cultivation expands. In this study, we report the construction of chromosome-scale genome assemblies of eight quinoa accessions covering the range of phenotypic and genetic diversity of both lowland and highland quinoas. The assemblies were produced from a combination of PacBio HiFi reads and Bionano Saphyr optical maps, with total assembly sizes averaging 1.28 Gb with a mean N50 of 71.1 Mb. Between 43,733 and 48,564 gene models were predicted for the eight new quinoa genomes, and on average, 66% of each quinoa genome was classified as repetitive sequences. Alignment between the eight genome assemblies allowed the identification of structural rearrangements including inversions, translocations, and duplications. These eight novel quinoa genome assemblies provide a resource for association genetics, comparative genomics, and pan-genome analyses for the discovery of genetic components and variations underlying agriculturally important traits. [ABSTRACT FROM AUTHOR]