Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda

Handle URI:
http://hdl.handle.net/10754/621897
Title:
Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda
Authors:
Nozawa, Masafumi; Onizuka, Kanako; Fujimi, Mai; Ikeo, Kazuho; Gojobori, Takashi ( 0000-0001-7850-1743 )
Abstract:
Y chromosomes often degenerate via the accumulation of pseudogenes and transposable elements. By contrast, little is known about X-chromosome degeneration. Here we compare the pseudogenization process between genes on the neo-sex chromosomes in Drosophila miranda and their autosomal orthologues in closely related species. The pseudogenization rate on the neo-X is much lower than the rate on the neo-Y, but appears to be higher than the rate on the orthologous autosome in D. pseudoobscura. Genes under less functional constraint and/or genes with male-biased expression tend to become pseudogenes on the neo-X, indicating the accumulation of slightly deleterious mutations and the feminization of the neo-X. We also find a weak trend that the genes with female-benefit/male-detriment effects identified in D. melanogaster are pseudogenized on the neo-X, implying the masculinization of the neo-X. These observations suggest that both X and Y chromosomes can degenerate due to a complex suite of evolutionary forces.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC); Environmental Science and Engineering Program
Citation:
Nozawa M, Onizuka K, Fujimi M, Ikeo K, Gojobori T (2016) Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda. Nature Communications 7: 13659. Available: http://dx.doi.org/10.1038/ncomms13659.
Publisher:
Springer Nature
Journal:
Nature Communications
Issue Date:
29-Nov-2016
DOI:
10.1038/ncomms13659
Type:
Article
ISSN:
2041-1723
Sponsors:
We thank Chie Iwamoto and Miu Kubota for helping with our experiments and Masanori Toda for species identification. We are also grateful to Junichi Imoto, Yukako Katsura, Sonoko Kinjo, Norikazu Kitamura, Kaoru Matsumoto, Masatoshi Nei, Masa-aki Yoshida and Ikuko Yuyama for their comments on earlier versions of the manuscript. This work was supported by grants from the National Institute of Genetics and JSPS KAKENHI (Grant Numbers 25711023 and 15K14585) to M.N.
Additional Links:
http://www.nature.com/articles/ncomms13659
Appears in Collections:
Articles; Environmental Science and Engineering Program; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorNozawa, Masafumien
dc.contributor.authorOnizuka, Kanakoen
dc.contributor.authorFujimi, Maien
dc.contributor.authorIkeo, Kazuhoen
dc.contributor.authorGojobori, Takashien
dc.date.accessioned2016-11-30T08:43:10Z-
dc.date.available2016-11-30T08:43:10Z-
dc.date.issued2016-11-29en
dc.identifier.citationNozawa M, Onizuka K, Fujimi M, Ikeo K, Gojobori T (2016) Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda. Nature Communications 7: 13659. Available: http://dx.doi.org/10.1038/ncomms13659.en
dc.identifier.issn2041-1723en
dc.identifier.doi10.1038/ncomms13659en
dc.identifier.urihttp://hdl.handle.net/10754/621897-
dc.description.abstractY chromosomes often degenerate via the accumulation of pseudogenes and transposable elements. By contrast, little is known about X-chromosome degeneration. Here we compare the pseudogenization process between genes on the neo-sex chromosomes in Drosophila miranda and their autosomal orthologues in closely related species. The pseudogenization rate on the neo-X is much lower than the rate on the neo-Y, but appears to be higher than the rate on the orthologous autosome in D. pseudoobscura. Genes under less functional constraint and/or genes with male-biased expression tend to become pseudogenes on the neo-X, indicating the accumulation of slightly deleterious mutations and the feminization of the neo-X. We also find a weak trend that the genes with female-benefit/male-detriment effects identified in D. melanogaster are pseudogenized on the neo-X, implying the masculinization of the neo-X. These observations suggest that both X and Y chromosomes can degenerate due to a complex suite of evolutionary forces.en
dc.description.sponsorshipWe thank Chie Iwamoto and Miu Kubota for helping with our experiments and Masanori Toda for species identification. We are also grateful to Junichi Imoto, Yukako Katsura, Sonoko Kinjo, Norikazu Kitamura, Kaoru Matsumoto, Masatoshi Nei, Masa-aki Yoshida and Ikuko Yuyama for their comments on earlier versions of the manuscript. This work was supported by grants from the National Institute of Genetics and JSPS KAKENHI (Grant Numbers 25711023 and 15K14585) to M.N.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.nature.com/articles/ncomms13659en
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleAccelerated pseudogenization on the neo-X chromosome in Drosophila mirandaen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentEnvironmental Science and Engineering Programen
dc.identifier.journalNature Communicationsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCenter for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japanen
dc.contributor.institutionDepartment of Genetics, SOKENDAI, 1111 Yata, Mishima, Shizuoka 411-8540, Japanen
dc.contributor.institutionDepartment of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0397, Japanen
kaust.authorGojobori, Takashien
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