Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction
| العنوان: | Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction |
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| المؤلفون: | Einhard Schierenberg, Hiroshi Kagoshima, Christopher Kraus, Yumiko Ueta, Michael Kroiher, Hideaki Hiraki, Philipp H. Schiffer, Yuji Kohara |
| المصدر: | BMC Genomics BMC Genomics, Vol 18, Iss 1, Pp 1-18 (2017) |
| بيانات النشر: | Springer Science and Business Media LLC, 2017. |
| سنة النشر: | 2017 |
| مصطلحات موضوعية: | 0301 basic medicine, Genome evolution, lcsh:QH426-470, Nematoda, lcsh:Biotechnology, Parthenogenesis, Genome, 03 medical and health sciences, lcsh:TP248.13-248.65, Gene density, Genetics, Animals, Genome size, Gene, Alleles, Caenorhabditis elegans, Nematode, Cohesin, Genome assembly, Allelic expression, biology, Gene Expression Profiling, Molecular Sequence Annotation, Genomics, Genome project, biology.organism_classification, Caenorhabditis, lcsh:Genetics, Meiosis, 030104 developmental biology, Research Article, Biotechnology |
| الوصف: | Background Sexual reproduction involving the fusion of egg and sperm is prevailing among eukaryotes. In contrast, the nematode Diploscapter coronatus, a close relative of the model Caenorhabditis elegans, reproduces parthenogenetically. Neither males nor sperm have been observed and some steps of meiosis are apparently skipped in this species. To uncover the genomic changes associated with the evolution of parthenogenesis in this nematode, we carried out a genome analysis. Results We obtained a 170 Mbp draft genome in only 511 scaffolds with a N50 length of 1 Mbp. Nearly 90% of these scaffolds constitute homologous pairs with a 5.7% heterozygosity on average and inversions and translocations, meaning that the 170 Mbp sequences correspond to the diploid genome. Fluorescent staining shows that the D. coronatus genome consists of two chromosomes (2n = 2). In our genome annotation, we found orthologs of 59% of the C. elegans genes. However, a number of genes were missing or very divergent. These include genes involved in sex determination (e.g. xol-1, tra-2) and meiosis (e.g. the kleisins rec-8 and coh-3/4) giving a possible explanation for the absence of males and the second meiotic division. The high degree of heterozygosity allowed us to analyze the expression level of individual alleles. Most of the homologous pairs show very similar expression levels but others exhibit a 2–5-fold difference. Conclusions Our high-quality draft genome of D. coronatus reveals the peculiarities of the genome of parthenogenesis and provides some clues to the genetic basis for parthenogenetic reproduction. This draft genome should be the basis to elucidate fundamental questions related to parthenogenesis such as its origin and mechanisms through comparative analyses with other nematodes. Furthermore, being the closest outgroup to the genus Caenorhabditis, the draft genome will help to disclose many idiosyncrasies of the model C. elegans and its congeners in future studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3860-x) contains supplementary material, which is available to authorized users. |
| تدمد: | 1471-2164 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1f86619d61751e25c510a1a2e4174df9 https://doi.org/10.1186/s12864-017-3860-x |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....1f86619d61751e25c510a1a2e4174df9 |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 14712164 |
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