Biology and genome of a newly discovered sibling species of Caenorhabditis elegans

Creators: Kanzaki, Natsumi; Tsai, Isheng J.; Tanaka, Ryusei; Hunt, Vicky L.; Liu, Dang; Tsuyama, Kenji; Maeda, Yasunobu; Namai, Satoshi; Kumagai, Ryohei; Tracey, Alan; Holroyd, Nancy; Doyle, Stephen R.; Woodruff, Gavin C.; Murase, Kazunori; Kitazume, Hiromi; Chai, Cynthia; Akagi, Allison; Panda, Oishika; Ke, Huei-Mien; Schroeder, Frank C.; Wang, John; Berriman, Matthew; Sternberg, Paul W.; Sugimoto, Asako; Kikuchi, Taisei

Abstract

A 'sibling' species of the model organism Caenorhabditis elegans has long been sought for use in comparative analyses that would enable deep evolutionary interpretations of biological phenomena. Here, we describe the first sibling species of C. elegans, C. inopinata n. sp., isolated from fig syconia in Okinawa, Japan. We investigate the morphology, developmental processes and behaviour of C. inopinata, which differ significantly from those of C. elegans. The 123-Mb C. inopinata genome was sequenced and assembled into six nuclear chromosomes, allowing delineation of Caenorhabditis genome evolution and revealing unique characteristics, such as highly expanded transposable elements that might have contributed to the genome evolution of C. inopinata. In addition, C. inopinata exhibits massive gene losses in chemoreceptor gene families, which could be correlated with its limited habitat area. We have developed genetic and molecular techniques for C. inopinata; thus C. inopinata provides an exciting new platform for comparative evolutionary studies.

Additional Information

© The Author(s) 2018. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Received 08 December 2017; Accepted 19 July 2018; Published 10 August 2018. This work was supported by Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Numbers 26292178, 16H04722, and 15K14503. V.L.H. was supported by JSPS International Research Fellowship, A.T., N.H., S.R.D., and M.B. by the core funding at the Wellcome Trust Sanger Institute (grant no. 206194), P.W.S. by Howard Hughes Medical Institute. Genome data analyses were partly performed using the DDBJ supercomputer system. We thank Akemi Yoshida, Mark Bligh, Mohammad-Masum Billah, Tanzila Afrin, Aya Adachi, Shakhinur Islam Mondal, Arzuba Akter, Haruhiko Maruyama, Tzu-hao Kuo, Karen Brooks, Michelle Smith for assistance and comments. Author Contributions: T.K. and N.K. conceived the study. P.W.S., A.S., F.S., I.J.T., N.K., and T.K. contributed to study design. V.L.H., A.S., I.J.T., P.W.S., N.K., and T.K. wrote the manuscript with inputs from others. N.K., R.T., K.T., S.N., R.K., H.K., H.T., C.C., A.A., O.P., and J.W. conducted experiments. N.K. and G.C.W. provided the strains. I.J.T., A.T., S.R.D., N.H., T.K., and M.B. completed genome assembly. V.L.H., Y.M., K.M., D.L., I.J.T., and T.K. analysed genome data. The authors declare no competing interests. Data availability: All sequence data from the C. elegans sibling genome project have been deposited at DDBJ/ENA/GenBank under BioProject accession PRJDB5687. Taxonomic descriptions were deposited at Zoobank. Nematode specimen and strains are available from T. Kikuchi or N. Kanzaki on request. All relevant data are available from the corresponding authors upon reasonable request.

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