Search

The West-Palaearctic Colobopsis ant populations have long been considered a single species (Colobopsis truncata). We studied the diversity of this species by employing a multidisciplinary approach and combining data from our surveys, museum and private collections, and citizen science platforms. As a result, we have revealed the existence of a second species, which we describe as Colobopsis imitans sp. nov., distributed allopatrically from Co. truncata and living in the Maghreb, Sicily and southern Iberia. While the pigmentation of Co. truncata is reminiscent of Dolichoderus quadripunctatus, that of Co. imitans is similar to Crematogaster scutellaris, with which Co. imitans lives in close spatial association, and whose foraging trails it habitually follows, similar to Camponotus lateralis and other ant-mimicking ants. The isolation between Co. imitans and Co. truncata seems to have occurred relatively recently because of significant, yet not extreme, morphometric differentiation, and to mtDNA polyphyly. Both Co. imitans and Co. truncata appear to employ mimicry of an unpalatable or aggressive ant species as an important defensive strategy; this ‘choice’ of a different model species is motivated by biogeographic reasons and appears to act as a critical evolutionary driver of their diversification.

Stingless bees often associate with termites, while association with ants is uncommon due to the high costs related to the aggressiveness of ants. Few combative genera of stingless bees can associate with a larger number of hosts, including ants. Here, we describe for the first time the association between a stingless bee (Partamona testacea) and the aggressive predator bullet ant (Paraponera clavata). In the study area, the colonies of P. testacea we spotted were all associated with P. clavata or Atta sp. ants. COI mitochondrial gene sequences of bees associated with bullet ants and leafcutter ants did not show any divergence, thus revealing no evidence that the two nesting strategies represent a case of cryptic speciation and specialisation on specific hosts. Bees are not unarmed respect to the bullet ants; when ants attempted to penetrate in the colony entrance, they were dragged inside the nest and covered by a resin-like substance. Behavioural experiments focused on ants in arenas and focused on bees at their nest entrance proved that the ants are significantly less aggressive toward associated bees and that guard bees are less alarmed when associated ants are presented. We verified by Gas Chromatography and Mass Spectrometry that P. testacea maintains its species-specific cuticular signature in the association with different ant species and that ants and bees possess typical colony signatures. The differential behavioural responses expressed toward associated colony members by both species are likely based on learning these heterospecific cuticular signatures as it occurs in ant parabiotic associations.

Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans), the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans), the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively), even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases, moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.

The term drywood termites was introduced for those species nesting and feeding in wood with low or no moisture. The term is used as a synonym for the family Kalotermitidae, although not all kalotermitids exhibit the same substrate prefer- ence. There are, in fact, many species living in rotten or damp wood logs (such as Neotermes). Kalotermitidae are placed among the lower ter- mites, a paraphyletic group that includes early- branching termite lineages and is characterized by the presence of symbiotic flagellates in their gut.

Although DNA transposons often generated internal deleted derivatives such as miniature inverted-repeat transposable elements, short internally deleted elements (SIDEs) derived from nonlong terminal-repeat retrotransposons are rare. Here, we found a novel SIDE, named Persaeus, that originated from the chicken repeat 1 (CR1) retrotransposon Zenon and it has been found widespread in Lepidoptera insects. Our findings suggested that Persaeus and the partner Zenon have experienced a transposition burst in their host genomes and the copy number of Persaeus and Zenon in assayed genomes are significantly correlated. Accordingly, the activity though age analysis indicated that the replication wave of Persaeus coincided with that of Zenon. Phylogenetic analyses suggested that Persaeus may have evolved at least four times independently, and that it has been vertically transferred into its host genomes. Together, our results provide new insights into the evolution dynamics of SIDEs and its partner non-LTRs.

Crustaceans of the order Notostraca (Branchiopoda) are distributed worldwide and are known for the remarkable morphological stasis between their extant and Permian fossil species. Moreover, these crustaceans show relevant ecological traits and a wide range of reproductive strategies. However, genomic studies on notostracans are fairly limited. Here, we present the genome sequences of two notostracan taxa, Lepidurus arcticus and Lepidurus apus lubbocki. Taking advantage of the small genome sizes (~0.11pg) of these taxa, genomes were sequenced for one individual per species with one run on the Illumina HiSeq X platform. We finally assembled 73.2Mbp (L.arcticus) and 90.3Mbp (L.apus lubbocki) long genomes. Assemblies cover up to 84% of the estimated genome size, with a gene completeness >97% for both genomes. In total, 13%–16% of the assembled genomes consist of repeats, and based on read mapping, L.apus lubbocki shows a significantly lower transposable element content than L.arcticus. The analysis of 2,376 orthologous genes indicates an ~7% divergence between the two Lepidurus taxa, with a nucleotide substitution rate significantly lower than that of Daphnia taxa. Ka/Ks analysis suggests purifying selection in both branchiopod lineages, raising the question of whether the low substitution rate of Lepidurus is correlated with morphological conservation or is linked to specific biological traits. Our analysis demonstrates that, in these organisms, it is possible to obtain high-quality draft genomes from single individuals with a relatively low sequencing effort. This result makes Lepidurus and Notostraca interesting models for genomic studies at taxonomic, ecological and evolutionary levels.

Phasmatodea species diversity lies almost entirely within its suborder Euphasmatodea, which exhibits a pantropical distribution and is considered to derive from a recent and rapid evolutionary radiation. To shed light on Euphasmatodea origins and diversification, we assembled the mitogenomes of 17 species from transcriptomic sequencing data and analysed them along with 22 already available Phasmatodea mitogenomes and 33 mitogenomes representing most of the Polyneoptera lineages. Maximum Likelihood and Bayesian Inference approaches retrieved consistent topologies, both showing the widespread conflict between phylogenetic approaches and traditional systematics. We performed a divergence time analysis leveraging ten fossil specimens representative of most polyneopteran lineages: the time tree obtained supports an older radiation of the clade with respect to previous hypotheses. Euphasmatodea diversification is inferred to have started ~ 187 million years ago, suggesting that the Triassic-Jurassic mass extinction and the breakup of Pangea could have contributed to the process. We also investigated Euphasmatodea mitogenomes patterns of dN, dS and dN/dS ratio throughout our time-tree, trying to characterize the selective regime which may have shaped the clade evolution.

The concept that complex ancestral traits can never be re-acquired after their loss has grown popular since its initial formulation and its often referred to as Dollos law. Nonetheless, several macroevolutionary evidences - along with molecular ones - suggest instances where complex phenotypes could have been lost throughout a clade evolutionary history and subsequently reverted to their former state in derived lineages. One of the first and most notable rejection of Dollos law is represented by wing evolution in phasmids: this polyneopteran order of insects - which comprises stick and leaf insects - has played a central role in initiating a long-standing debate on the topic. In this study, a new and comprehensive molecular phylogeny of over 300 Phasmatodea species is used as a framework for investigating wings evolutionary patterns in the clade, taking into consideration several sources of uncertainty and all the methodological recommendations which have been proposed to test Dollos law rejection. Macroevolutionary analyses support a dynamic and reversible evolution of wings, with multiple transitions to ancestral states taking place after their loss. Our findings suggest that neither wings or flight have acted as drivers of Phasmatodea species diversification and that brachyptery is an unstable state, when not co-opted for non-aerodynamic adaptations. We also explored the impact on our results of different assumptions relative to the probability of reversals and losses: we found that until reversals are assumed over 30 times more unlikely than losses, they are consistently inferred despite uncertainty in tree and model parameters. Our findings demonstrate that wings evolution can be a reversible and dynamic process in phasmids and contribute to shape our understanding of complex phenotypes evolution.

The stick-insect genus Pijnackeria includes four diploid bisexual and two polyploid (3n, 4n) parthenogenetic species. Earlier analyses of the tetraploid parthenogen P. hispanica using mitochondrial markers allowed tracing its maternal ancestry to Pijnackeria originis, while no maternal nuclear contribution was found, thus suggesting an androgenetic and hybrid origin. The recently described Pijnackeria recondita—showing, among other features, a specific antennal structure linking it to the tetraploid parthenogen—prompted us to check whether the new species could be theunknown paternal ancestorof P. hispanica. In this work, we use karyology and molecular analysis of the mitochondrial gene cytochrome c oxidase subunit 2 (cox2) and the nuclear gene elongation factor 1 subunit α (ef1-α) to investigate the origin of such a complex tetraploid hybrid parthenogen. The molecular analysis supported P. recondita as being a paternal ancestor of P. hispanica, but also suggested that two more fathering species have to be taken into account: P. barbarae and the unknown paternal ancestor of the triploid hybrid P. masettii. Therefore, P. hispanica is apparently a polyphyletic chimeric androgen, which we propose to indicate as an androgenetic complex. Our data also revealed that P. hispanica is between 1.96 Myr and 3.31 Myr old, making it the oldest parthenogenetic taxon discovered among insects.

Transposable elements are widely distributed within genomes where they may significantly impact their evolution and cell functions. Short interspersed elements (SINEs) are non-autonomous, fast-evolving elements, but some of them carry a highly conserved domain (HCD), whose sequence remained substantially unchanged throughout the metazoan evolution. SINEs carrying the HCD called V are absent in amniote genomes, but V-like sequences were found within the miniature inverted-repeat transposable element (MITE) MER6 in Homo sapiens. In the present work, the genomic distribution and evolution of MER6 are investigated, in order to reconstruct the origin of human V domain and to envisage its possible functional role. The analysis of 85 tetrapod genomes revealed that MER6 and its variant MER6A are found in primates, while only the MER6A variant was found in bats and eulipotyphlans. These MITEs appeared no longer active, in line with literature data on mammalian DNA transposons. Moreover, they appeared to have originated from a Mariner element found in turtles and from a V-SINE from bony fishes. MER6 insertions were found within genes and conserved in mRNAs: in line with previous hypothesis on functional role of HCDs, the MER6 V domain may be important for cell function also in mammals.

Background Transposable elements (TEs) are common and often present with high copy numbers in cellular genomes. Unlike in cellular organisms, TEs were previously thought to be either rare or absent in viruses. Almost all reported TEs display only one or two copies per viral genome. In addition, the discovery of pandoraviruses with genomes up to 2.5-Mb emphasizes the need for biologists to rethink the fundamental nature of the relationship between viruses and cellular life. Results Herein, we performed the first comprehensive analysis of miniature inverted-repeat transposable elements (MITEs) in the 5170 viral genomes for which sequences are currently available. Four hundred and fifty one copies of ten miniature inverted-repeat transposable elements (MITEs) were found and each MITE had reached relatively large copy numbers (some up to 90) in viruses. Eight MITEs belonging to two DNA superfamilies (hobo/Activator/Tam3 and Chapaev–Mirage–CACTA) were for the first time identified in viruses, further expanding the organismal range of these two superfamilies. TEs may play important roles in shaping the evolution of pandoravirus genomes, which were here found to be very rich in MITEs. We also show that putative autonomous partners of seven MITEs are present in the genomes of viral hosts, suggesting that viruses may borrow the transpositional machinery of their cellular hosts’ autonomous elements to spread MITEs and colonize their own genomes. The presence of seven similar MITEs in viral hosts, suggesting horizontal transfers (HTs) as the major mechanism for MITEs propagation. Conclusions Our discovery highlights that TEs contribute to shape genome evolution of pandoraviruses. We concluded that as for cellular organisms, TEs are part of the pandoraviruses’ diverse mobilome. Electronic supplementary material The online version of this article (10.1186/s13100-018-0125-4) contains supplementary material, which is available to authorized users.

Background The crustacean class Branchiopoda includes fairy shrimps, clam shrimps, tadpole shrimps, and water fleas. Branchiopods, which are well known for their great variety of reproductive strategies, date back to the Cambrian and extant taxa can be mainly found in freshwater habitats, also including ephemeral ponds. Mitochondrial genomes of the notostracan taxa Lepidurus apus lubbocki (Italy), L. arcticus (Iceland) and Triops cancriformis (an Italian and a Spanish population) are here characterized for the first time and analyzed together with available branchiopod mitogenomes. Results Overall, branchiopod mitogenomes share the basic structure congruent with the ancestral Pancrustacea model. On the other hand, rearrangements involving tRNAs and the control region are observed among analyzed taxa. Remarkably, an unassigned region in the L. apus lubbocki mitogenome showed a chimeric structure, likely resulting from a non-homologous recombination event between the two flanking trnC and trnY genes. Notably, Anostraca and Onychocaudata mitogenomes showed increased GC content compared to both Notostraca and the common ancestor, and a significantly higher substitution rate, which does not correlate with selective pressures, as suggested by dN/dS values. Conclusions Branchiopod mitogenomes appear rather well-conserved, although gene rearrangements have occurred. For the first time, it is reported a putative non-homologous recombination event involving a mitogenome, which produced a pseudogenic tRNA sequence. In addition, in line with data in the literature, we explain the higher substitution rate of Anostraca and Onychocaudata with the inferred GC substitution bias that occurred during their evolution. Electronic supplementary material The online version of this article (10.1186/s40851-019-0131-5) contains supplementary material, which is available to authorized users.

Thousands of eukaryotes transcriptomes have been generated, mainly to investigate nuclear genes expression, and the amount of available data is constantly increasing. A neglected but promising use of this large amount of data is to assemble organelle genomes. To assess the reliability of this approach, we attempted to reconstruct complete mitochondrial genomes from RNA-Seq experiments of Reticulitermes termite species, for which transcriptomes and conspecific mitogenomes are available. We successfully assembled complete molecules, although a few gaps corresponding to tRNAs had to be filled manually. We also reconstructed, for the first time, the mitogenome of Reticulitermes banyulensis. The accuracy and completeness of mitogenomes reconstruction appeared independent from transcriptome size, read length and sequencing design (single/paired end), and using reference genomes from congeneric or intra-familial taxa did not significantly affect the assembly. Transcriptome-derived mitogenomes were found highly similar to the conspecific ones obtained from genome sequencing (nucleotide divergence ranging from 0% to 3.5%) and yielded a congruent phylogenetic tree. Reads from contaminants and nuclear transcripts, although slowing down the process, did not result in chimeric sequence reconstruction. We suggest that the described approach has the potential to increase the number of available mitogenomes by exploiting the rapidly increasing number of transcriptomes.

Terminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous LTR retrotransposons consisting of two terminal direct repeats surrounding a short internal domain. The detection and characterization of these elements has been mainly limited to plants. Here we present the frst fnding of a TRIM element in bivalves, and among the frst known in the kingdom Animalia. Class Bivalvia has high ecological and commercial importance in marine ecosystems and aquaculture, and, in recent years, an increasing number of genomic studies has addressed to these organisms. We have identifed biv-TRIM in several bivalve species: Donax trunculus, Ruditapes decussatus, R. philippinarum, Venerupis corrugata, Polititapes rhomboides, Venus verrucosa, Dosinia exoleta, Glycymeris glycymeris, Cerastoderma edule, Magallana gigas, Mytilus galloprovincialis. biv-TRIM has several characteristics typical for this group of elements, exhibiting diferent variations. In addition to canonically structured elements, solo-TDRs and tandem repeats were detected. The presence of this element in the genome of each species is

Transposable elements (TEs) are self-replicating, mobile DNA sequences which constitute a significant fraction of eukaryotic genomes. They are generally considered selfish DNA, as their replication and random insertion may have deleterious effects on genome functionalities, although some beneficial effects and evolutionary potential have been recognized. Short interspersed elements (SINEs) are non-autonomous TEs with a modular structure: a small RNA-related head, a body, and a long interspersed element-related tail. Despite their high turnover rate and de novo emergence, the body may retain highly conserved domains (HCDs) shared among divergent SINE families: in metazoans, at least nine HCD-SINEs have been recognized. Data mining on public molecular databases allowed the retrieval of 16 new HCD-SINE families from cnidarian, molluscs, arthropods, and vertebrates. Tracking the ancestry of HCDs on the metazoan phylogeny revealed that some of them date back to the Radiata-Bilateria split. Moreover, phylogenetic and age versus divergence analyses of the most ancient HCDs suggested that long-term vertical inheritance is the rule, with few horizontal transfer events. We suggest that the evolutionary conservation of HCDs may be linked to their potential to serve as recombination hotspots. This indirectly affects host genomes by maintaining active and diverse SINE lineages, whose insertions may impact (either positively or negatively) on the evolution of the genome.

Transposable elements (TEs) are selfish genetic elements whose self-replication is contrasted by the host genome. In this context, host reproductive strategies are predicted to impact on both TEs load and activity. The presence and insertion distribution of the non-LTR retrotransposon R2 was here studied in populations of the strictly bisexual Bacillus grandii maretimi and of the obligatory parthenogenetic Bacillus atticus atticus. Furthermore, data were also obtained from the offspring of selected B. a. atticus females. At the population level, the gonochoric B. g. maretimi showed a significantly higher R2 load than the obligatory parthenogenetic B. a. atticus. The comparison with bisexual and unisexual Bacillus rossius populations showed that their values were higher than those recorded for B. a. atticus and similar, or even higher, than those of B. g. maretimi. Consistently, an R2 load reduction is scored in B. a. atticus offspring even if with a great variance. On the whole, data here produced indicate that in the obligatory unisexual B. a. atticus R2 is active and that mechanisms of molecular turnover are effective. Furthermore, progeny analyses show that, at variance of the facultative parthenogenetic B. rossius, the R2 activity is held at a lower rate. Modeling parental-offspring inheritance, suggests that in B. a. atticus recombination plays a major role in eliminating insertions rather than selection, as previously suggested for unisexual B. rossius progeny, even if in both cases a high variance is observed. In addition to this, mechanisms of R2 silencing or chances of clonal selection cannot be ruled out.

Biological invasions are among key factors of ecological changes, and social insects appear as highly successful invasive animals. Subterranean termites of the holarctic genus Reticulitermes are present in Europe with six native and one invasive (the nearctic R. flavipes) species. The species R. urbis shows a disjunct distribution in the Western Balkans, Eastern Italy and Southern France. Previous molecular and population genetics data suggested that the taxon originated from the Balkans, and that Italian and French populations are invasive, but it is still unknown how many introduction events occurred and from which Balkan source populations. To address these questions, a population genetics analysis was performed on a larger sampling than previous studies, using mitochondrial cytochrome oxidase II and 6 microsatellite markers on 47 colonies collected across the whole distribution area. Mitochondrial analysis confirmed the presence of two major lineages where colonies from Balkans, Italy, and France intermingle. Similarly, microsatellite loci analysis indicated the presence of two genetic clusters, though not corresponding to the two mitochondrial clades, each including colonies from the three sampled areas and with individuals showing mixed cluster membership. Overall, French and Italian populations showed indications of bottleneck (reduced genetic diversity and change of allele frequencies) and do not appear genetically differentiated from the Balkan population. Results presented here support a history of multiple introductions in Italy and France, in a scenario consistent with continuous exchanges between native and invasive areas, as expected along human trades routes.

At least 12 genes (FH, HIF2A, MAX, NF1, RET, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127,andVHL) have been implicated in inherited predisposition to phaeochromocytoma (PCC), paraganglioma (PGL), or head and neck paraganglioma (HNPGL) and a germline mutation may be detected in more than 30% of cases. Knowledge of somatic mutations contributing to PCC/PGL/HNPGL pathogenesis has received less attention though mutations inHRAS, HIF2A, NF1, RET,andVHLhave been reported. To further elucidate the role of somatic mutation in PCC/PGL/HNPGL tumourigenesis, we employed a next generation sequencing strategy to analyse “mutation hotspots” in 50 human cancer genes. Mutations were identified forHRAS(c.37G>C; p.G13R and c.182A>G; p.Q61R) in 7.1% (6/85); forBRAF(c.1799T>A; p.V600E) in 1.2% (1/85) of tumours; and forTP53(c.1010G>A; p.R337H) in 2.35% (2/85) of cases. Twenty-one tumours harboured mutations in inherited PCC/PGL/HNPGL genes and noHRAS, BRAF, orTP53mutations occurred in this group. Combining our data with previous reports ofHRASmutations in PCC/PGL we find that the mean frequency ofHRAS/BRAFmutations in sporadic PCC/PGL is 8.9% (24/269) and in PCC/PGL with an inherited gene mutation 0% (0/148) suggesting thatHRAS/BRAFmutations and inherited PCC/PGL genes mutations might be mutually exclusive. We report the first evidence forBRAFmutations in the pathogenesis of PCC/PGL/HNPGL.

Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s). The analyses of their relationships indicated that these elements share the same 3′-tail, which would have allowed both elements to rise to high copy number by exploiting the C. milii L2-2_CM long interspersed element (LINE) enzymes. Molecular clock analysis on SINE activity in C. milii genome evidenced two replication bursts occurring right after two major events in the holocephalan evolution: the end-Permian mass extinction and the radiation of modern Holocephali. Accordingly, the same analysis on the coelacanth homologous elements, LmeSINE1, identified a replication wave close to the split age of the two extant Latimeria species. The genomic distribution of the studied SINEs pointed out contrasting results: some elements were preferentially sorted out from gene regions, but accumulated in flanking regions, while others appear more conserved within genes. Moreover, data from the C. milii transcriptome suggest that these SINEs could be involved in miRNA biogenesis and may be targets for miRNA-based regulation.

Horizontal transfer (HT) is an event in which the genetic material is transferred from one species to another, even if distantly related, and it has been demonstrated as a possible essential part of the lifecycle of transposable elements (TEs). However, previous studies on the non-LTR R2 retrotransposon, a metazoan-wide distributed element, indicated its vertical transmission since the Radiata-Bilateria split. Here we present the first possible instances of R2 HT in stick insects of the genus Bacillus (Phasmida). Six R2 elements were characterized in the strictly bisexual subspecies B. grandii grandii, B. grandii benazzii and B. grandii maretimi and in the obligatory parthenogenetic taxon B. atticus. These elements were compared with those previously retrieved in the facultative parthenogenetic species B. rossius. Phylogenetic inconsistencies between element and host taxa, and age versus divergence analyses agree and support at least two HT events. These HT events can be explained by taking into consideration the complex Bacillus reproductive biology, which includes also hybridogenesis, gynogenesis and androgenesis. Through these non-canonical reproductive modes, R2 elements may have been transferred between Bacillus genomes. Our data suggest, therefore, a possible role of hybridization for TEs survival and the consequent reshaping of involved genomes.

Theoretical and empirical studies have shown differential management of transposable elements in organisms with different reproductive strategies. To investigate this issue, we analysed the R2 retroelement structure and variability in parthenogenetic and bisexual populations of Bacillus rossius stick insects, as well as insertions inheritance in the offspring of parthenogenetic isolates and of crosses. The B. rossius genome hosts a functional (R2Br(fun) ) and a degenerate (R2Br(deg) ) element, their presence correlating with neither reproductive strategies nor population distribution. The median-joining network method indicated that R2Br(fun) duplicates through a multiple source model, while R2Br(deg) is apparently still duplicating via a master gene model. Offspring analyses showed that unisexual and bisexual offspring have a similar number of R2Br-occupied sites. Multiple or recent shifts from gonochoric to parthenogenetic reproduction may explain the observed data. Moreover, insertion frequency spectra show that higher-frequency insertions in unisexual offspring significantly outnumber those in bisexual offspring. This suggests that unisexual offspring eliminate insertions with lower efficiency. A comparison with simulated insertion frequencies shows that inherited insertions in unisexual and bisexual offspring are significantly different from the expectation. On the whole, different mechanisms of R2 elimination in unisexual vs bisexual offspring and a complex interplay between recombination effectiveness, natural selection and time can explain the observed data.

The repetitive DNA content of the stick insect species Bacillus rossius (facultative parthenogenetic), Bacillus grandii (gonochoric), and Bacillus atticus (obligate parthenogenetic) was analyzed through the survey of random genomic libraries roughly corresponding to 0.006% of the genome. By repeat masking, 19 families of transposable elements were identified (two LTR and six non-LTR retrotransposons; 11 DNA transposons). Moreover, a de novo analysis revealed, among the three libraries, the first MITE family observed in polyneopteran genomes. On the whole, transposable element abundance represented 23.3% of the genome in B. rossius, 22.9% in B. atticus, and 18% in B. grandii. Tandem repeat content in the three libraries is much lower: 1.32%, 0.64%, and 1.86% in B. rossius, B. grandii, and B. atticus, respectively. Microsatellites are the most abundant in all species. Minisatellites were only found in B. rossius and B. atticus, and five monomers belonging to the Bag320 satellite family were detected in B. atticus. Assuming the survey provides adequate representation of the relative genome, the obligate parthenogenetic species (B. atticus), compared with the other two species analyzed, does not show a lower transposable element content, as expected from some theoretical and empirical studies.

Invasive species cause severe environmental and economic problems. The invasive success of social insects often appears to be related to their ability to adjust their social organization to new environments. To gain a better understanding of the biology of invasive termites, this study investigated the social organization of the subterranean termite, Reticulitermes urbis, analyzing the breeding structure and the number of reproductives within colonies from three introduced populations. By using eight microsatellite loci to determine the genetic structure, it was found that all the colonies from the three populations were headed by both primary reproductives (kings and queens) and secondary reproductives (neotenics) to form extended-family colonies. R. urbis appears to be the only Reticulitermes species with a social organization based solely on extended-families in both native and introduced populations, suggesting that there is no change in their social organization on introduction. F-statistics indicated that there were few neotenics within the colonies from urban areas, which did not agree with results from previous studies and field observations. This suggests that although several neotenics may be produced, only few become active reproductives. The results also imply that the invasive success of R. urbis may be based on different reproductive strategies in urban and semiurbanized areas. The factors influencing an individual to differentiate into a neotenic in Reticulitermes species are discussed.

Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata–Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs.

The Holarctic genusReticulitermesshows seven species within the Mediterranean Basin. While phylogeny and systematics at continental level has been deeply investigated, a few studies concentrated on local ranges. To gain a clearer picture of the diversity and evolution of the Italian speciesReticulitermes lucifugus, we analyzed the mitochondrial cytochrome oxidase II (COII) gene marker in newly collected colonies across the Peninsula. Data were gathered with allR. lucifugussequences available from previous studies; COII sequences of the closely related Iberian taxa were also added to the data set. Maximum-likelihood, median-joining and statistical parsimony network elaborations on the resulting 119 colonies all agreed in indicating that: (i) the Sardo-Corsican subspeciesR. lucifugus corsicus, strictly related to Southern Italian populations (including the Sicilian ones), is phylogenetically closer to the IberianReticulitermes grassei; and (ii)R. lucifugus lucifuguspeninsular populations are structured into three clusters. The phylogenetic relationships and the biogeography of extant taxa suggest a scenario in whichR. lucifugusancestors colonized the Italian region through the Sardo-Corsican microplate during its Oligocene-Miocene anticlockwise rotation. Moreover, well after the colonization took place, northward range expansion might have produced the presently observed genetic diversity, as inferred from haplotype and nucleotide diversity estimates. On the whole, this study highlights the evolution of ItalianReticulitermestaxa and supports the importance of a wide taxon sampling especially when dealing with organisms easily dispersed by human activities.

The existence of altruism in social insects is commonly attributed to altruistic individuals gaining indirect fitness through kin selection. However, recent studies suggest that such individuals might also gain direct fitness through reproduction. Experimental studies on primitive wood-dwelling termites revealed that colony fusion often causes the death of primary reproductives (queen and king), allowing opportunities for workers to inherit the nest by developing into replacement reproductives (neotenics). Therefore, colony fusion has been proposed as an important factor that may have favoured sociality in termites. However, whether colony fusion occurs frequently in natural populations of wood-dwelling termites remains an open question. We analyzed eleven colonies of the wood-dwelling termite Kalotermes flavicollis (Kalotermitidae), using two mitochondrial and five nuclear microsatellite markers. Nine out of eleven colonies (82%) were mixed-families, with offspring of three or more primary reproductives. To our knowledge, this result represents the highest frequency of mixed-family colonies ever reported in termites. Moreover, genetic mixing of colonies appeared extreme in two ways. First, the number of haplotypes per colony was exceptionally high (up to nine), indicating that colonies were composed of multiple queens’ offspring. Second, some mixed-family colonies included individuals belonging to two highly divergent genetic lineages. F-statistics and relatedness values suggest that mixed-family colonies most likely result from colony fusion, giving support to accelerated nest inheritance theory. These findings, being quite rare in termites, raise important questions about the mode of foundation of mixed-family colonies and the evolutionary forces that maintain them within populations.

Short interspersed elements (SINEs) are non-autonomous retrotransposons that are widespread in eukaryotic genomes. They exhibit a chimeric sequence structure consisting of a small RNA-related head, an anonymous body and an AT-rich tail. Although their turnover and de novo emergence is rapid, some SINE elements found in distantly related species retain similarity in certain core segments (or highly conserved domains, HCD). We have characterized a new SINE element named RUDI in the bivalve molluscs Ruditapes decussatus and R. philippinarum and found this element to be widely distributed in the genomes of a number of mollusc species. An unexpected structural feature of RUDI is the HCD domain type V, which was first found in non-amniote vertebrate SINEs and in the SINE from one cnidarian species. In addition to the V domain, the overall sequence conservation pattern of RUDI elements resembles that found in ancient AmnSINE (~310 Myr old) and Au SINE (~320 Myr old) families, suggesting that RUDI might be among the most ancient SINE families. Sequence conservation suggests a monophyletic origin of RUDI. Nucleotide variability and phylogenetic analyses suggest long-term vertical inheritance combined with at least one horizontal transfer event as the most parsimonious explanation for the observed taxonomic distribution.

Background Satellite DNA (satDNA) sequences are typically arranged as arrays of tandemly repeated monomers. Due to the similarity among monomers, their organizational pattern and abundance, satDNAs are hardly accessible to structural and functional studies and still represent the most obscure genome component. Although many satDNA arrays of diverse length and even single monomers exist in the genome, surprisingly little is known about transition from satDNAs to other sequences. Studying satDNA monomers at junctions and identifying DNA sequences adjacent to them can help to understand the processes that (re)distribute satDNAs and significance that evolution of these sequence elements might have in creating the genomic landscape. Results We explored sets of randomly selected satDNA-harboring genomic fragments in four mollusc species to examine satDNA transition sites, and the nature of adjacent sequences. All examined junctions are characterized by abrupt transitions from satDNAs to other sequences. Among them, junctions of only one examined satDNA mapped non-randomly (within the palindrome), indicating that well-defined sequence feature is not a necessary prerequisite in the junction formation. In the studied sample, satDNA flanking sequences can be roughly classified into two groups. The first group is composed of anonymous DNA sequences which occasionally include short segments of transposable elements (TEs) as well as segments of other satDNA sequences. In the second group, satDNA repeats and the array flanking sequences are identified as parts of TEs of the Helitron superfamily. There, some array flanking regions hold fragmented satDNA monomers alternating with anonymous sequences of comparable length as missing monomer parts, suggesting a process of sequence reorganization by a mechanism able to excise short monomer parts and replace them with unrelated sequences. Conclusions The observed architecture of satDNA transition sites can be explained as a result of insertion and/or recombination events involving short arrays of satDNA monomers and TEs, in combination with hypothetical transposition-related ability of satDNA monomers to be shuffled independently in the genome. We conclude that satDNAs and TEs can form a complex network of sequences which essentially share the propagation mechanisms and in synergy shape the genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3347-1) contains supplementary material, which is available to authorized users.

The full-length element of the non-LTR retrotransposon R2 is here characterized in three European isopteran species: the more primitive Kalotermes flavicollis (Kalotermitidae), including two highly divergent mitochondrial lineages, and the more derived Reticulitermes lucifugus and R. urbis (Rhinotermitidae). Partial 3' sequences for R. grassei and R. balkanensis were also analyzed. The essential structural features of R2 elements are conserved in termites. Phylogenetic analysis revealed that termite elements belong to the same clade and that their phylogeny is fully compatible with the phylogeny of their host species. The study of the number and the frequency of R2 insertion variants in four R. urbis colonies suggests a greatly reduced, or completely absent, recent element activity.

The R2 retrotransposon is here characterized in bisexual populations of the European crustacean Triops cancriformis. The isolated element matches well with the general aspects of the R2 family and it is highly differentiated from that of the congeneric North American Triops longicaudatus. The analysis of 5' truncations indicates that R2 dynamics in T. cancriformis populations show a high turnover rate as observed in Drosophila simulans. For the first time in the literature, though, individuals harboring truncation variants, but lacking the complete element, are found. Present results suggest that transposition-mediated deletion mechanisms, possibly involving genomic turnover processes acting on rDNAs, can dramatically decrease the copy number or even delete R2 from the ribosomal locus. The presence of R2 does not seem to impact on the nucleotide variation of inserted 28S rDNA with respect to the uninserted genes. On the other hand, a low level of polymorphism characterizes rDNA units because new 28S variants continuously spread across the ribosomal array. Again, the interplay between transposition-mediated deletion and molecular drive may explain this pattern.

The genetic variability of the tadpole shrimp Triops cancriformis was studied through the analysis of 12 nuclear microsatellite loci. Seven of these loci were newly obtained from an enriched genomic library using a trinucleotide biotinylated probe (CAG)11. The study was conducted on six populations that previous genetic studies demonstrated to be poorly differentiated, notwithstanding their different reproductive strategies (gonochorism, parthenogenesis, androdioecy). The newly isolated microsatellite loci showed a higher genetic variability than those previously isolated, probably in relation with their different motif structure. Different patterns of variability were scored at both locus and population levels, the latter probably being caused by the different reproductive modalities. Wright's F‐statistics, AMOVA, and ISOLDE analyses showed that populations are well structured and isolated, again as a result of different reproductive modalities, but also of geographic distances and low migration flow.

Leptestheria dahalacensis genome harbours repeats of the LEP150 satellite DNA family linked to 5S gene, within the ribosomal intergenic spacer. In genetically isolated samples, the sequence analysis of the region (5S, flanking region, first satellite monomer: unit A, second satellite monomer: unit B) evidenced three 5S variants. The alpha and gamma variants share a greater homology. They co-occur in the Central European samples, while in the Italian one, the highly divergent alpha and beta variants are present. In phylogenetic analyses, A and B LEP150 monomers show a peculiar clustering; this was further confirmed through the sequencing for the alpha variant of four monomers at the 5' and 3' tails (units A, B, C, D and D', C', B', A', respectively). Horizontal homogenisation was observed only across C, D, C' and D' units. Furthermore, repeat sequence diversity decrease toward terminal repeats, at variance of literature data. The pattern of variation observed is explained taking into account the presence at the LEP150 array borders of two loci under natural selection: the 5S rRNA gene, upstream, and the rDNA transcription promoter, downstream. These elements may drive the dynamics of flanking regions and linked repeats in a process similar to selective sweep. At variance of classical genetic hitchhiking, the selective sweep here scored should be realized and maintained through an interplay of selection and molecular drive.

The genetic variability of the gonochoric Leptestheria dahalacensis (Ruppel, 1837) was studied through the analysis of mitochondrial and nuclear (microsatellite loci) markers in eight Italian and two Central European populations. Mitochondrial data exhibited a low variability, as only six mitotypes were scored: five in Italy and one for both Central European samples, with a very low number of substitutions. All analysed microsatellite loci were variable, with 3–5 alleles per locus and 1–4 alleles per population. All populations were at the Hardy–Weinberg equilibrium, with the exceptions of two samples for locus ldAC-16, due to heterozygote excess, and of four populations for locus ldAC-11, probably linked to the presence of null alleles. A substantial population structuring was found between Central European and Italian samples for both utilized markers. This observation may be explained by isolation by distance and/or recent isolation events. On the other hand, the absence of a clear inter-pond variability in Italian sample comparisons may be ascribed to high dispersal ability in the short range.

Meiosis is the biological process that, after a cycle of DNA replication, halves the cellular chromosome complement, leading to the formation of haploid gametes. Haploidization is achieved via two successive rounds of chromosome segregation, meiosis I and II. In mammals, during prophase of meiosis I, homologous chromosomes align and synapse through a recombination-mediated mechanism initiated by the introduction of DNA double-strand breaks (DSBs) by the SPO11 protein. In male mice, if SPO11 expression and DSB number are reduced below heterozygosity levels, chromosome synapsis is delayed, chromosome tangles form at pachynema, and defective cells are eliminated by apoptosis at epithelial stage IV at a spermatogenesis-specific endpoint. Whether DSB levels produced in Spo11+/− spermatocytes represent, or approximate, the threshold level required to guarantee successful homologous chromosome pairing is unknown. Using a mouse model that expresses Spo11 from a bacterial artificial chromosome, within a Spo11−/− background, we demonstrate that when SPO11 expression is reduced and DSBs at zygonema are decreased (approximately 40 % below wild-type level), meiotic chromosome pairing is normal. Conversely, DMC1 foci number is increased at pachynema, suggesting that under these experimental conditions, DSBs are likely made with delayed kinetics at zygonema. In addition, we provide evidences that when zygotene-like cells receive enough DSBs before chromosome tangles develop, chromosome synapsis can be completed in most cells, preventing their apoptotic elimination. Electronic supplementary material The online version of this article (doi:10.1007/s00412-015-0544-7) contains supplementary material, which is available to authorized users.

International audience; Termites of the genus Reticulitermes are ecologically and economically important wood-feeding socialinsects that are widespread in the Holarctic region. Despite their importance, no study has yet attemptedto reconstruct a global time-scaled phylogeny of Reticulitermes termites. In this study, we sequencedmitochondrial (2096 bp) and nuclear (829 bp) loci from 61 Reticulitermes specimens, collected acrossthe genus’ entire range, and one specimen of Coptotermes formosanus, which served as an outgroup.Bayesian and Maximum likelihood analyses conducted on the mitochondrial and nuclear sequencessupport the existence of four main lineages that span four global geographical regions: North America(NA lineage), western Europe (WE lineage), a region including eastern Europe and western Asia(EA +WA lineage), and eastern Asia (EA lineage). The mitochondrial data allowed us to clarify the phylogeneticrelationships among these lineages. They were also used to infer a chronogram that was timescaled based on age estimates for termite fossils (including the oldest Reticulitermes fossils, which dateback to the late Eocene–early Oligocene). Our results support the hypothesis that the extantReticulitermes lineage first differentiated in North America. The first divergence event in the ancestral lineageof Reticulitermes occurred in the early Miocene and separated the Nearctic lineages (i.e., the NA lineages)from the Palearctic lineages (i.e., WE, EE + WA, and EA lineages). Our analyses revealed that themain lineages of Reticulitermes diversified because of vicariance and migration events, which were probablyinduced by major paleogeographic and paleoclimatic changes that occurred during the Cenozoic era.This is the first global and comprehensive phylogenetic study of Reticulitermes termites, and it provides acrucial foundation for studying the evolution of phenotypic and life-history traits in Reticulitermes. Forinstance, the phylogeny we obtained suggested that ‘asexual queen succession’, a unique reproductivesystem, independently evolved at least three times during the diversification of the genus.

Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder and the leading genetic cause of death in infants. Despite the disease-causing gene, survival motor neuron (SMN1), encodes a ubiquitous protein, SMN1 deficiency preferentially affects spinal motor neurons (MNs), leaving the basis of this selective cell damage still unexplained. As neural stem cells (NSCs) are multipotent self-renewing cells that can differentiate into neurons, they represent an in vitro model for elucidating the pathogenetic mechanism of neurodegenerative diseases such as SMA. Here we characterize for the first time neural stem cells (NSCs) derived from embryonic spinal cords of a severe SMNΔ7 SMA mouse model. SMNΔ7 NSCs behave as their wild type (WT) counterparts, when we consider neurosphere formation ability and the expression levels of specific regional and self-renewal markers. However, they show a perturbed cell cycle phase distribution and an increased proliferation rate compared to wild type cells. Moreover, SMNΔ7 NSCs are characterized by the differential expression of a limited number of miRNAs, among which miR-335-5p and miR-100-5p, reduced in SMNΔ7 NSCs compared to WT cells. We suggest that such miRNAs may be related to the proliferation differences characterizing SMNΔ7 NSCs, and may be potentially involved in the molecular mechanisms of SMA.

Tunga penetrans is a widely distributed sand flea, infecting men and domestic animals. It originated in South America, but it is now also endemic of Sub-Saharan Africa due to a recent accidental introduction. Previous genetic analyses indicated a very limited variability in the Ecuadorian populations; on the other hand, samples from Madagascar resulted to be genetically isolated. To better examine the genetic variability of T. penetrans, a wider sampling was analysed for mitochondrial (cytochrome oxidase II) and nuclear (ribosomal internal transcribed spacer [ITS] 2) DNA sequences. The mitochondrial marker confirms the low genetic variability, with few haplotypes characterizing the majority of individuals from different populations. Haplotype distribution is in agreement with a recent colonization of Africa and with a rapid spreading across this continent. Moreover, a consistent gene flow between the Pacific and Atlantic South American populations emerges, possibly due to human and/or animal cross-Andean dispersal. On the other hand, the ITS2 marker depicts a sharply diverging pattern with samples collected in Ecuador unequivocally distinguished from the Brazilian and African ones. On the whole, taking into account also the molecular features of the marker used, data here presented are better interpreted in the light of a high dispersal ability of T. penetrans, probably reducing the phylogeographic signal.

Nuclear ribosomal DNA constitutes a multigene family, with tandemly arranged units linked by an intergenic spacer (IGS), which contains initiation/termination transcription signals and usually tandemly arranged subrepeats. The structure and variability of the IGS region are analyzed here in hermaphroditic and parthenogenetic populations of the "living fossil" Triops cancriformis (Branchiopoda, Notostraca). The results indicate the presence of concerted evolution at the population level for this G+C-rich IGS region as a whole, with the major amount of genetic variability found outside the subrepeat region. The subrepeats region is composed of 3 complete repeats (a, c, d) intermingled with 3 repeat fragments (b, e, f) and unrelated sequences. The most striking datum is the absolute identity of subrepeats (except type d) occupying the same position in different individuals/populations. A putative promoter sequence is present upstream of the 18S rRNA gene, but not in subrepeats, which is at variance with other arthropod IGSs. The absence of a promoter sequence in the subrepeats and subrepeat sequence conservation suggests that this region acts as an enhancer simply by its repetitive nature, as observed in some vertebrates. The putative external transcribed spacer (840 bp) shows hairpin structures, as in yeasts, protozoans, Drosophila, and vertebrates.Key words: concerted evolution, Crustacea, external transcribed spacer, intergenic spacer, ribosomal DNA, subrepeats, Triops cancriformis.

Relationships of nine Italian Chrysotoxum species were analysed using morphological and molecular data. The morphology-derived cladogram revealed three well-defined groups: (i) C. cautum, (ii) the arcuatum group (C. arcuatum, C. fasciola- tum) and (iii) the festivum group (C. festivum - C. vernale, C. bicinctum, C. elegans, C. octomaculatum and C. parmense). Trees inferred from COI-tRNALeu-COII sequences were largely in agreement, but they identified (i) C. parmense as an isolated branch, (ii) C. festivum and C. vernale as separate entities, (iii) C. elegans within a paraphyletic C. festivum clade. ITS2 trees were partially unresolved but C. parmense sequence emerged as a sister to the festivum group. The monophyly of the festivum group derived from morphological data was rejected by a phylogenetic test performed on combined molecular data set. The diagnostic value of some morphological characters commonly used to identify Chrysotoxum species is therefore questioned.

R2 is an extensively investigated non-LTR retrotransposon that specifically inserts into the 28S rRNA gene sequences of a wide range of metazoans, disrupting its functionality. During R2 integration, first strand synthesis can be incomplete so that 5’ end deleted copies are occasionally inserted. While active R2 copies repopulate the locus by retrotransposing, the non-functional truncated elements should frequently be eliminated by molecular drive processes leading to the concerted evolution of the rDNA array(s). Although, multiple R2 lineages have been discovered in the genome of many animals, the rDNA of the stick insect Bacillus rossius exhibits a peculiar situation: it harbors both a canonical, functional R2 element (R2Brfun) as well as a full-length but degenerate element (R2Brdeg). An intensive sequencing survey in the present study reveals that all truncated variants in stick insects are present in multiple copies suggesting they were duplicated by unequal recombination. Sequencing results also demonstrate that all R2Brdeg copies are full-length, i. e. they have no associated 5' end deletions, and functional assays indicate they have lost the active ribozyme necessary for R2 RNA maturation. Although it cannot be completely ruled out, it seems unlikely that the degenerate elements replicate via reverse transcription, exploiting the R2Brfun element enzymatic machinery, but rather via genomic amplification of inserted 28S by unequal recombination. That inactive copies (both R2Brdeg or 5'-truncated elements) are not eliminated in a short term in stick insects contrasts with findings for the Drosophila R2, suggesting a widely different management of rDNA loci and a lower efficiency of the molecular drive while achieving the concerted evolution.

Transposable elements (TEs) are discrete DNA sequences which are able to replicate and jump into different genomic locations. Miniature inverted-repeats TEs (MITEs) are non-autonomous DNA elements whose origin is still poorly understood. Recently, some MITEs were found to contain core repeats that can be arranged in tandem arrays; in some instances, these arrays have even given rise to satellite DNAs in the (peri)centromeric region of the host chromosomes. I report the discovery and analysis of three new MITEs found in the genome of several termite species (hence the name terMITEs) in two different families. For two of the MITEs (terMITE1-Tc1/mariner superfamily; terMITE2-piggyBac superfamily), evidence of past mobility was retrieved. Moreover, these two MITEs contained core repeats, 16 bp and 114 bp long respectively, exhibiting copy number variation. In terMITE2, the tandem duplication appeared associated with element degeneration, in line with a recently proposed evolutionary model on MITEs and the origin of tandem arrays. Concerning their genomic distribution, terMITE1 and terMITE3 appeared more frequently inserted close to coding regions while terMITE2 was mostly associated with TEs. Although MITEs are commonly distributed in coding regions, terMITE2 distribution is in line with that of other insects' piggyBac-related elements and of other small TEs found in termite genomes. This has been explained through insertional preference rather than through selective processes. Data presented here add to the knowledge on the poorly exploited polyneopteran genomes and will provide an interesting framework in which to study TEs' evolution and host's life history traits.

The rate of mitochondrial DNA evolution and the speciation pattern in relation to glacial periods are tested in the European taxa of the eusocial genus Reticulitermes. The linearized tree obtained from cytochrome oxidase II sequences and a geological event calibration shows a substitution rate 100-fold higher than that usually applied for insect mitochondrial DNA. An accelerated rate of evolution has also been observed in social Vespidae (Hymenoptera); we therefore suggest the involvement of eusociality in mediating gene pool drift. The role of the last ice age in speciation pattern of Reticulitermes taxa is supported by molecular data, but a four refugia model better explains genetic diversity, phyletic relationships and present-day distribution of these termites.

A new species of the genus Tungo, T. trimamillata has recently been described on the basis of several morphological traits. To explore the taxonomic status of this flea with respect to T. penetrans, we undertook a molecular analysis of cytochrome oxydase II and 16S rDNA mitochondrial genes and of the internal transcribed spacer 2 nuclear marker on samples of both species. Maximum Parsimony evaluations of the three data set indicate a differentiation compatible with a specific rank between the two fleas with very high levels of divergence. Both mitochondrial and nuclear data are in line with a recent bottleneck in the Malagasy population of T. penetrans, possibly due to the recent colonisation of Africa via human transportation. Further, significantly lower mitochondrial variability in the Ecuadorian populations of T. penetrans with respect to the T. trimamillata ones is also evidenced.

A SINE element (called Talua) has been isolated from Reticulitermes lucifugus genome, by means of sequence comparison between clones obtained through genomic restriction and aspecific PCR amplification. It posses all the structural features commonly found in short interspersed elements: (i) a RNA polymerase III internal promoter, (ii) flanking short direct repeats and (iii) a poly (A) tail. BLAST search reveals significant homology with other previously described SINEs and tRNAs. The repeats are G+C-rich, but they are located in A+T-rich regions. This biased genomic distribution results from the analysis of adjacent regions. A Talua element was also found in a microsatellite-containing clone from Cryptotermes secundus. The presence of the SINE also in the Kalotermitidae family, suggests the usefulness of Talua as a taxonomic marker at the family level. The importance of this element on termite genome evolution is discussed.

The molecular characterisation of 18 new populations of Reticulitermes is here presented for COII and 16S genes; results are elaborated and compared to all available ones, at distances and gene trees (Maximum Parsimony, Maximum likelihood, Bayesian analysis) levels. Within the R. lucifugus complex, a subspecific rank of differentiation appears tenable for Italian (R. lucifugus lucifugus, R. lucifugus corsicus) and European (R. lucifugus banyulensis, R. lucifugus grassei) taxa; a subspecific differentiation emerges also for the Sicilian samples. The existence of two different entities in the area formerly defined as inhabited by R. balkanensis is demonstrated; The north-eastern Italian Reticulitermes sp. is found to be more widely distributed in northern and south-eastern Italy and shows a close relationship to the sample from Peloponnese; the GenBank sample from continental Greece, on the contrary, appears more related to other eastern taxa such as R. lucifugus from Turkey and R. clypeatus from Israel; the distribution and differentiation of eastern Reticulitermes taxa are explained through the role that southern Balkans should have played as glacial refuge. Present data also evidences instances of anthropic involvement in taxa distribution; for one of these, the importation of at least a family group is taken into account.

The sequence-specific correction of a mutated gene (e.g., point mutation) by the Small Fragment Homologous Replacement (SFHR) method is a highly attractive approach for gene therapy. Small DNA fragments (SDFs) were used in SFHR to modify endogenous genomic DNA in both human and murine cells. The advantage of this gene targeting approach is to maintain the physiologic expression pattern of targeted genes without altering the regulatory sequences (e.g., promoter, enhancer), but the application of this technique requires the knowledge of the sequence to be targeted. In our recent study, an optimized SFHR protocol was used to replace the eGFP mutant sequence in SV-40-transformed mouse embryonic fibroblast (MEF-SV40), with the wild-type eGFP sequence. Nevertheless in the past, SFHR has been used to correct several mutant genes, each related to a specific genetic disease (e.g., spinal muscular atrophy, cystic fibrosis, severe combined immune deficiency). Several parameters can be modified to optimize the gene modification efficiency, as described in our recent study. In this chapter we describe the main guidelines that should be followed in SFHR application, in order to increase technique efficiency.

Biological traits and colony structure are difficult to analyze in subterranean termites owing to their cryptic lifestyle and their often elusive breeding system. However, the use of molecular markers in a population genetics framework allows the investigation of such aspects. We present here the colony genetic structures of 12 samples collected along the Italian peninsula of two Reticulitermes species (the native R. lucifugus and the introduced R. urbis) analyzed through nuclear microsatellite markers. Reproductive strategies and colony breeding systems differ between the two species. Secondary reproductives of R. lucifugus, collected in three colonies, are all females; genotyping comparisons between these females and their nest mate workers clearly indicate the presence of asexual queen succession (AQS) events in this species, as observed in the Japanese R. speratus and in the North-American R. virginicus. Two other R. lucifugus colonies have a mixed family genetic pattern, possibly as the result of colony fusion events: accordingly, relatedness estimates indicate the presence of genetically unrelated workers. On the contrary, all R. urbis colonies have a genetic structure compatible with the presence of multiple secondary reproductives, as expected on the basis of previous analyses. Moreover, neotenics’ sex ratio is balanced and their heterozygosity is comparable to that of nest mate workers, suggesting that AQS is lacking in this taxon. The differences observed in such biological traits between the two species are discussed in the light of their invasive potential.

Cellular responses and molecular mechanisms activated by exogenous DNA that invades cells are only partially understood. This limits the practical use of gene targeting strategies. Small fragment homologous replacement (SFHR) uses a small exogenous wild-type DNA fragment to restore the endogenous wild-type sequence; unfortunately, this mechanism has a low frequency of correction. In this study, we used a mouse embryonic fibroblast cell line with a stably integrated mutated gene for enhanced green fluorescence protein. The restoration of a wild-type sequence can be detected by flow cytometry analysis. We quantitatively analyzed the expression of 84 DNA repair genes and 84 cell cycle control genes. Peculiar temporal gene expression patterns were observed for both pathways. Different DNA repair pathways, not only homologous recombination, as well as the three main cell cycle checkpoints appeared to mediate the cellular response. Eighteen genes were selected as highly significant target/effectors of SFHR. We identified a wide interconnection between SFHR, DNA repair, and cell cycle control. Our results increase the knowledge of the molecular mechanisms involved in cell invasion by exogenous DNA and SFHR. Specific molecular targets of both the cell cycle and DNA repair machineries were selected for manipulation to enhance the practical application of SFHR.

The 28S rRNA genes of several metazoans are interrupted by site-specific targeting non-LTR retrotransposons, such as R2. R2 elements have been deeply analyzed but aspects of their retrotransposition mechanism and the origin of the wide diversity observed are still debated. We characterized six new R2 lineages in four tadpole shrimp species (Notostraca), samples deriving from a parthenogenetic population of Triops cancriformis (R2Tc_it) and from bisexual Lepidurus populations of L. lubbocki (R2Ll), L. couesii (R2LcA, R2LcB, R2LcC) and L. arcticus (R2La). All elements fit the canonical R2 structure but R2Ll which turned out to be a chimera with an additional ORF originating from another R2. Consistently with data on LINEs, R2Ll could be the result of recombination due to reverse transcriptase template jump. The analysis of 28S/R2 5′ end junctions further suggests aberrant homologous recombination, as observed in RNA viruses.

Spinal muscular atrophy (SMA) is an inherited neurodegenerative disorder and the first genetic cause of death in childhood. SMA is caused by low levels of survival motor neuron (SMN) protein that induce selective loss of α-motor neurons (MNs) in the spinal cord, resulting in progressive muscle atrophy and consequent respiratory failure. To date, no effective treatment is available to counteract the course of the disease. Among the different therapeutic strategies with potential clinical applications, the evaluation of trophic and/or protective agents able to antagonize MNs degeneration represents an attractive opportunity to develop valid therapies. Here we investigated the effects of IPLEX (recombinant human insulinlike growth factor 1 (rhIGF-1) complexed with recombinant human IGF-1 binding protein 3 (rhIGFBP-3)) on a severe mouse model of SMA. Interestingly, molecular and biochemical analyses of IGF-1 carried out in SMA mice before drug administration revealed marked reductions of IGF-1 circulating levels and hepatic mRNA expression. In this study, we found that perinatal administration of IPLEX, even if does not influence survival and body weight of mice, results in reduced degeneration of MNs, increased muscle fiber size and in amelioration of motor functions in SMA mice. Additionally, we show that phenotypic changes observed are not SMN-dependent, since no significant SMN modification was addressed in treated mice. Collectively, our data indicate IPLEX as a good therapeutic candidate to hinder the progression of the neurodegenerative process in SMA.