Universität zu Köln

Hiraki, Hideaki, Kagoshima, Hiroshi, Kraus, Christopher, Schiffer, Philipp H., Ueta, Yumiko, Kroiher, Michael, Schierenberg, Einhard and Kohara, Yuji (2017). Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction. BMC Genomics, 18. LONDON: BMC. ISSN 1471-2164

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Abstract

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 N-50 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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Hiraki, Hideaki UNSPECIFIED UNSPECIFIED UNSPECIFIED Kagoshima, Hiroshi UNSPECIFIED UNSPECIFIED UNSPECIFIED Kraus, Christopher UNSPECIFIED UNSPECIFIED UNSPECIFIED Schiffer, Philipp H. UNSPECIFIED UNSPECIFIED UNSPECIFIED Ueta, Yumiko UNSPECIFIED UNSPECIFIED UNSPECIFIED Kroiher, Michael UNSPECIFIED UNSPECIFIED UNSPECIFIED Schierenberg, Einhard UNSPECIFIED UNSPECIFIED UNSPECIFIED Kohara, Yuji UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-227457
DOI:	10.1186/s12864-017-3860-x
Journal or Publication Title:	BMC Genomics
Volume:	18
Date:	2017
Publisher:	BMC
Place of Publication:	LONDON
ISSN:	1471-2164
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language CAENORHABDITIS-ELEGANS; SEQUENCE ALIGNMENT; HOLOCENTRIC CHROMOSOMES; SEX DETERMINATION; FLOW-CYTOMETRY; OPEN SOFTWARE; CD-HIT; MEIOSIS; PROTEIN; EVOLUTION Multiple languages Biotechnology & Applied Microbiology; Genetics & Heredity Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/22745