Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction

BMC Genomics

Research Article

Yumiko Ueta¹  Hideaki Hiraki¹  Yuji Kohara¹  Hiroshi Kagoshima²  Michael Kroiher³  Einhard Schierenberg³  Philipp H. Schiffer³  Christopher Kraus³ 

[1] Genome Biology Laboratory, National Institute of Genetics, Mishima, Japan;Genome Biology Laboratory, National Institute of Genetics, Mishima, Japan;Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo, Japan;Zoologisches Institut, Universität zu Köln, Cologne, NRW, Germany;

关键词: Genome assembly;    Allelic expression;    Nematode;    Parthenogenesis;    Meiosis;    Cohesin;   

DOI  :  10.1186/s12864-017-3860-x

 received in 2016-12-09, accepted in 2017-06-13,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundSexual 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.ResultsWe 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© The Author(s). 2017