Genome Sequence of the Freshwater Yangtze Finless Porpoise

Yuan Yuan; Peijun Zhang; Kun Wang; Mingzhong Liu; Jing Li; Jingsong Zheng; Ding Wang; Wenjie Xu; Mingli Lin; Lijun Dong; Chenglong Zhu; Qiang Qiu; Songhai Li

doi:10.3390/genes9040213

Genome Sequence of the Freshwater Yangtze Finless Porpoise

Genes (Basel). 2018 Apr 16;9(4):213. doi: 10.3390/genes9040213.

Authors

Yuan Yuan^{1

2}, Peijun Zhang³, Kun Wang^{4

5}, Mingzhong Liu⁶, Jing Li⁷, Jingsong Zheng⁸, Ding Wang⁹, Wenjie Xu¹⁰, Mingli Lin¹¹, Lijun Dong¹², Chenglong Zhu¹³, Qiang Qiu^{14

15}, Songhai Li¹⁶

Affiliations

¹ Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China. 2017203291@mail.nwpu.edu.cn.
² Qingdao Research Institute, Northwestern Polytechnical University, Qingdao 266200, China. 2017203291@mail.nwpu.edu.cn.
³ Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China. pjzhang@idsse.ac.cn.
⁴ Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China. wk8910@gmail.com.
⁵ Qingdao Research Institute, Northwestern Polytechnical University, Qingdao 266200, China. wk8910@gmail.com.
⁶ Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China. liumingzhong@idsse.ac.cn.
⁷ Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China. nwpulijing@163.com.
⁸ Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. zhengjinsong@ihb.ac.cn.
⁹ Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. wangd@ihb.ac.cn.
¹⁰ Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China. 2014303644@mail.nwpu.edu.cn.
¹¹ Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China. mingli@idsse.ac.cn.
¹² Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China. donglj@idsse.ac.cn.
¹³ Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China. Long9602@mail.nwpu.edu.cn.
¹⁴ Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China. qiuqiang@lzu.edu.cn.
¹⁵ Qingdao Research Institute, Northwestern Polytechnical University, Qingdao 266200, China. qiuqiang@lzu.edu.cn.
¹⁶ Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China. lish@idsse.ac.cn.

Abstract

The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina HiSeq 2000 platform. After filtering the low-quality and duplicated reads, we assembled a draft genome of 2.22 Gb, with contig N50 and scaffold N50 values of 46.69 kilobases (kb) and 1.71 megabases (Mb), respectively. We identified 887.63 Mb of repetitive sequences and predicted 18,479 protein-coding genes in the assembled genome. The phylogenetic tree showed a relationship between the Yangtze finless porpoise and the Yangtze River dolphin, which diverged approximately 20.84 million years ago. In comparisons with the genomes of 10 other mammals, we detected 44 species-specific gene families, 164 expanded gene families, and 313 positively selected genes in the Yangtze finless porpoise genome. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information under BioProject accession number PRJNA433603.

Keywords: Yangtze finless porpoise; annotation; endangered species; genome; genome assembly; genome evolution.