The extant reptiles are one of the most diverse clades among terrestrial vertebrates and one of a few groups with instances of parthenogenesis. Due to the hybrid origin of parthenogenetic species, reference genomes of the parental species as well as of the parthenogenetic progeny are indispensable to explore the genetic foundations of parthenogenetic reproduction. Here, we report on the first genome assembly of rock lizard Darevskia valentini, a paternal species for several parthenogenetic lineages. The novel genome was used in the reconstruction of the comprehensive phylogeny of Squamata inferred independently from 7369 trees of single-copy orthologs and a supermatrix of 378 conserved proteins. We also investigated Hox clusters, the loci that are often regarded as playing an important role in the speciation of animal groups with drastically diverse morphology. We demonstrated that Hox clusters of D. valentini are invaded with transposons and contain the HoxC1 gene that has been considered to be lost in the amniote ancestor. This study provides confirmation for previous works and releases new genomic data that will contribute to future discoveries on the mechanisms of parthenogenesis as well as support comparative studies among reptiles.
Despite the recent advances in high-throughput sequencing, analysis of the metagenome of the whole microbial population still remains a challenge. In particular, the metagenome-assembled genomes (MAGs) are often fragmented due to interspecies repeats, uneven coverage and vastly different strain abundance. MAGs are usually constructed via a dedicated binning process that uses different features of input data in order to cluster contigs that might belong to the same species. This process has some limitations and therefore binners usually discard input contigs that are shorter than several kilobases. Therefore, binning of even simple metagenome assemblies can miss a decent fraction of contigs and resulting MAGs oftentimes do not contain important conservative sequences that might be of great interest of researcher. In this work we present BinSPreader - a novel binning refiner tool that exploits the assembly graph topology and other connectivity information to refine the existing binning, correct binning errors, propagate binning from longer contigs to shorter contigs and infer contigs belonging to multiple bins. Furthermore, BinSPreader can split input reads in accordance with the resulting binning, predicting reads potentially belonging to multiple MAGs. We show that BinSPreader could effectively complete the binning, increasing the completeness of the bins without sacrificing the purity and could predict contigs belonging to several MAGs.
Darevskia rock lizards include 29 sexual and seven parthenogenetic species of hybrid origin distributed in the Caucasus. All seven parthenogenetic species of the genus Darevskia were formed as a result of interspecific hybridization of only four sexual species. It remains unknown what are the main advantages of interspecific hybridization along with switching on parthenogenetic reproduction in evolution of reptiles. Data on whole transcriptome sequencing of parthenogens and their parental ancestors can provide value impact in solving this problem. Here we have sequenced ovary tissue transcriptomes from unisexual parthenogenetic lizard D. unisexualis and its parental bisexual ancestors to facilitate the subsequent annotation and to obtain the collinear characteristics for comparison with other lizard species. Here we report generated RNAseq data from total mRNA of ovary tissues of D. unisexualis, D. valentini and D. raddei with 58932755, 51634041 and 62788216 reads. Obtained RNA reads were assembled by Trinity assembler and 95141, 62123, 61836 contigs were identified with N50 values of 2409, 2801 and 2827 respectively. For further analysis top Gene Ontology terms were annotated for all species and transcript number was calculated. The raw data were deposited in the NCBI SRA database (BioProject PRJNA773939 ). The assemblies are available in Mendeley Data and can be accessed via doi: 10.17632/rtd8cx7zc3.1 .
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