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BackgroundThe Easter Island spiny lobster Panulirus pascuensis (Reed, 1954) or ‘Ura’ in the Rapa Nui language, is a little known species native to the south eastern Pacific Ocean, distributed along the coasts of Easter Island, Pitcairn Island, and the Salas y Gómez Ridge. In Easter Island, P. pascuensis is the target of a small and profitable and probably overexploited fishery. In this study, we profited from a series of bioinformatic analyses to mine biological insight from low-pass short-read next generation sequencing datasets; we have estimated genome size and ploidy in P. pascuensis using a k-mer strategy, discovered, annotated, and quantified mobile elements in the nuclear genome, assembled the 45S rRNA nuclear DNA cassette and mitochondrial chromosome, and explored the phylogenetic position of P. pascuensis within the genus Panulirus using the signal retrieved from translated mitochondrial protein coding genes.ResultsK-mer analyses predicted P. pascuensis to be diploid with a haploid genome size ranging between 2.75 Gbp (with k-mer = 51) and 3.39 Gbp (with k-mer = 18). In P. pascuensis, repetitive elements comprise at least a half and a maximum of three fourths of the nuclear genome. Almost a third (64.94%) of the repetitive elements present in the studied nuclear genome were not assigned to any known family of transposable elements. Taking into consideration only annotated repetitive elements, the most abundant were classified as Long Interspersed Nuclear Elements (22.81%). Less common repetitive elements included Long Terminal Repeats (2.88%), Satellite DNA (2.66%), and DNA transposons (2.45%), among a few others. The 45S rRNA DNA cassette of P. pascuensis was partially assembled into two contigs. One contig, 2,226 bp long, encoded a partially assembled 5′ ETS the entire ssrDNA (1,861 bp), and a partial ITS1. A second contig, 6,714 bp long, encoded a partially assembled ITS1, the entire 5.8S rDNA (158 bp), the entire ITS2, the entire lsrDNA (4,938 bp), and a partial 3′ ETS (549 bp). The mitochondrial genome of P. pascuensis was 15,613 bp long and contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes (12S ribosomal RNA [rrnS] and 16S ribosomal RNA [rrnL]). A phylomitogenomic analysis based on PCGs retrieved Panulirus pascuensis as sister to a fully supported clade comprising P. cygnus and P. longipes.ConclusionWe expect that the information generated in this study will guide the assembly of a chromosome-level nuclear genome for P. pascuensis in the near future. The newly assembled 45S rRNA nuclear DNA cassette and mitochondrial chromosome can support bioprospecting and biomonitoring of P. pascuensis using environmental DNA. The same elements can help to survey the public market place and detect mislabelling of this and other spiny lobsters. Overall, the genomic resources generated in this study will aid in supporting fisheries management and conservation strategies in this iconic spiny lobster that is likely experiencing overexploitation.

Members of the bacterial genus Rickettsia were originally identified as causative agents of vector-borne diseases in mammals. However, many Rickettsia species are arthropod symbionts and close relatives of ‘ Candidatus Megaira’, which are symbiotic associates of microeukaryotes. Here, we clarify the evolutionary relationships between these organisms by assembling 26 genomes of Rickettsia species from understudied groups, including the Torix group, and two genomes of ‘ Ca . Megaira’ from various insects and microeukaryotes. Our analyses of the new genomes, in comparison with previously described ones, indicate that the accessory genome diversity and broad host range of Torix Rickettsia are comparable to those of all other Rickettsia combined. Therefore, the Torix clade may play unrecognized roles in invertebrate biology and physiology. We argue this clade should be given its own genus status, for which we propose the name ‘ Candidatus Tisiphia’. The bacterial genus Rickettsia includes vector-borne pathogens and arthropod symbionts that are close relatives of symbionts of microeukaryotes classified under the genus ‘ Candidatus Megaira’. Here, Davison et al. clarify the evolutionary relationships between these organisms by assembling 28 genomes of understudied species, and propose that a distinct clade known as Torix Rickettsia should be considered a separate genus.

Background The Peruvian ‘chanque’ or Chilean ‘loco’ Concholepas concholepas is an economically, ecologically, and culturally important muricid gastropod heavily exploited by artisanal fisheries in the temperate southeastern Pacific Ocean. In this study, we have profited from a set of bioinformatics tools to recover important biological information of C. concholepas from low-coverage short-read NGS datasets. Specifically, we calculated the size of the nuclear genome, ploidy, and estimated transposable elements content using an in silico k-mer approach, we discovered, annotated, and quantified those transposable elements, we assembled and annotated the 45S rDNA RNA operon and mitochondrial genome, and we confirmed the phylogenetic position of C. concholepas within the muricid subfamily Rapaninae based on translated protein coding genes. Results Using a k-mer approach, the haploid genome size estimated for the predicted diploid genome of C. concholepas varied between 1.83 Gbp (with kmer = 24) and 2.32 Gbp (with kmer = 36). Between half and two thirds of the nuclear genome of C. concholepas was composed of transposable elements. The most common transposable elements were classified as Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements, which were more abundant than DNA transposons, simple repeats, and Long Terminal Repeats. Less abundant repeat elements included Helitron mobile elements, 45S rRNA DNA, and Satellite DNA, among a few others.The 45S rRNA DNA operon of C. concholepas that encodes for the ssrRNA, 5.8S rRNA, and lsrRNA genes was assembled into a single contig 8,090 bp long. The assembled mitochondrial genome of C. concholepas is 15,449 bp long and encodes 13 protein coding genes, two ribosomal genes, and 22 transfer RNAs. Conclusion The information gained by this study will inform the assembly of a high quality nuclear genome for C. concholepas and will support bioprospecting and biomonitoring using environmental DNA to advance development of conservation and management plans in this overexploited marine snail.

Eastern Poison Ivy ( Toxicodendron radicans, Anacardiaceae) is well known in Eastern North America for causing contact dermatitis, an itchy and painful rash in most people who come in contact with it.  We present the whole genome sequence and annotation of this species. A total of 96,255,779 paired-ends reads consisting of 28.9 G bases were obtained by sequencing one leaf from a wild-collected plant.  The reads were assembled by a de novo method followed by alignment to related species. Annotation was performed via GenMark-ES. The raw and assembled data is publicly available via GenBank: Sequence Read Archive ( SRR10325927) and Assembly ( GCA_009867345).

Asian mock vipers of the genus Psammodynastes and African forest snakes of the genus Buhoma are two genera belonging to the snake superfamily Elapoidea. The phylogenetic placements of Psammodynastes and Buhoma within Elapoidea has been extremely unstable which has resulted in their uncertain and debated taxonomy. We used ultraconserved elements and traditional nuclear and mitochondrial markers to infer the phylogenetic relationships of these two genera with other elapoids. Psammodynastes , for which a reference genome has been sequenced, were found, with strong branch support, to be a relatively early diverging split within Elapoidea that is sister to a clade consisting of Elapidae, Micrelapidae and Lamprophiidae. Hence, we allocate Psammodynastes to its own family, Psammodynastidae new family . However, the phylogenetic position of Buhoma could not be resolved with a high degree of confidence. Attempts to identify the possible sources of conflict in the rapid radiation of elapoid snakes suggest that both hybridisation/introgression during the rapid diversification, including possible ghost introgression, as well as incomplete lineage sorting likely have had a confounding role. The usual practice of combining mitochondrial loci with nuclear genomic data appears to mislead phylogeny reconstructions in rapid radiation scenarios, especially in the absence of genome scale data.

Habitat transitions have shaped the evolutionary trajectory of many clades. Sea catfishes (Ariidae) have repeatedly undergone ecological transitions, including colonizing freshwaters from marine environments, leading to an adaptive radiation in Australia and New Guinea alongside non-radiating freshwater lineages elsewhere. Here, we generate and analyze one long-read reference genome and 66 short-read whole genome assemblies, in conjunction with genomic data for 54 additional species. We investigate how three major ecological transitions have shaped genomic variation among ariids over their ~ 50 million-year evolutionary history. Our results show that relatively younger freshwater lineages exhibit a higher incidence of positive selection than their more ancient marine counterparts. They also display a larger disparity in body shapes, a trend that correlates with a heightened occurrence of positive selection on genes associated with body size and elongation. Although positive selection in the Australia and New Guinea radiation does not stand out compared to non-radiating lineages overall, selection across the prolactin gene family during the marine-to-freshwater transition suggests that strong osmoregulatory adaptations may have facilitated their colonization and radiation. Our findings underscore the significant role of selection in shaping the genome and organismal traits in response to habitat shifts across macroevolutionary scales. Ecological transitions, like shifts between habitats, can shape genomic variation. By analyzing genomes from 66 sea catfish species, this study finds that younger freshwater lineages show more positive selection and body shape disparity, with prolactin gene adaptations likely aiding their colonization and radiation.

African lovebirds are popular pet parrots commonly hybridized by breeders leading to genetic admixture. Trade escapees and land use change have now led lovebirds to genetically admix in the wild. Sampling origin is therefore of utmost importance when deriving genetic data from lovebird species to reconstruct phylogeny or historical demographic events as the inclusion of taxa of hybrid origin is a source of spurious results. Here we present complete genomes of all nine currently recognized lovebird species. Each species is represented by an archival geo-referenced individual collected within their natural range.

Cephalopods are harvested in increasingly large quantities but understanding how to control and manage their stocks, and tracking the routes of the consumption that exploits them, lag behind what has been developed for exploiting finfish. This review attempts to redress the imbalance by considering the status of the major cephalopod stock species and the traceability of cephalopod seafood along the trade value chain. It begins with a general overview of the most important exploited cephalopods, their stock status and their market. Four major cephalopod resources are identified: the three squid species Todarodes pacificus , Dosidicus gigas and Illex argentinus ; and one species of octopus, Octopus vulgaris . The techniques and problems of stock assessment (to assess sustainability) are reviewed briefly and the problems and possible solutions for assessing benthic stock such as those of octopuses are considered. An example of a stock well managed in the long term is presented to illustrate the value of careful monitoring and management: the squid Doryteuthis gahi available in Falkland Islands waters. Issues surrounding identification, mislabelling and illegal, unreported and unregulated (IUU) fishing are then reviewed, followed by a discussion of approaches and techniques of traceability as applied to cephalopods. Finally, some of the mobile apps currently available and in development for tracking seafood are compared. This review concludes with observations on the necessity for the strengthening and international coordination of legislation, and more rigorous standards for seafood labelling and for taxonomic curation of DNA sequences available in public databases for use in seafood identification.

The Sweetleaf ( Stevia rebaudiana: Asteraceae) is widely grown for use as a sweetener.  We present the whole genome sequence and annotation of this species.  A total of 146,838,888 paired-end reads consisting of 22.2G bases were obtained by sequencing one leaf from a commercially grown seedling.  The reads were assembled by a de-novo method followed by alignment to related species.   Annotation was performed via GenMark-ES. The raw and assembled data is publicly available via GenBank: Sequence Read Archive ( SRR6792730) and Assembly ( GCA_009936405).

Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element dynamics are not well understood. Together with phenotypic traits, they are commonly referred to as the “C-value enigma”. The order Zoantharia are benthic cnidarians found from intertidal zones to the deep sea, and some species are particularly abundant in coral reefs. Despite their high ecological relevance, zoantharians have yet to be largely studied from the genomic point of view. This study aims at investigating the role of the repeatome (total content of repeated elements) in genome size variations across the order Zoantharia. To this end, whole-genomes of 32 zoantharian species representing five families were sequenced. Genome sizes were estimated and the abundances of different repeat classes were assessed. In addition, the repeat overlap between species was assessed by a sequence clustering method. The genome sizes in the dataset varied up to 2.4 fold magnitude. Significant correlations between genome size, repeated DNA content and transposable elements, respectively (Pearson’s correlation test R 2  = 0.47, p  = 0.0016; R 2  = 0.22, p  = 0.05) were found, suggesting their involvement in the dynamics of genome expansion and reduction. In all species, long interspersed nuclear elements and DNA transposons were the most abundant identified elements. These transposable elements also appeared to have had a recent expansion event. This was in contrast to the comparative clustering analysis which revealed species-specific patterns of satellite elements’ amplification. In summary, the genome sizes of zoantharians likely result from the complex dynamics of repeated elements. Finally, the majority of repeated elements (up to 70%) could not be annotated to a known repeat class, highlighting the need to further investigate non-model cnidarian genomes. More research is needed to understand how repeated DNA dynamics relate to zoantharian evolution and their biology.