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Genes 2018, 9(4), 213; doi:10.3390/genes9040213

Genome Sequence of the Freshwater Yangtze Finless Porpoise

1
Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an 710072, China
2
Qingdao Research Institute, Northwestern Polytechnical University, Qingdao 266200, China
3
Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
4
Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 26 February 2018 / Revised: 6 April 2018 / Accepted: 11 April 2018 / Published: 16 April 2018
(This article belongs to the Special Issue Conservation Genetics and Genomics)
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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. View Full-Text
Keywords: Yangtze finless porpoise; endangered species; genome; genome assembly; annotation; genome evolution Yangtze finless porpoise; endangered species; genome; genome assembly; annotation; genome evolution
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Yuan, Y.; Zhang, P.; Wang, K.; Liu, M.; Li, J.; Zheng, J.; Wang, D.; Xu, W.; Lin, M.; Dong, L.; Zhu, C.; Qiu, Q.; Li, S. Genome Sequence of the Freshwater Yangtze Finless Porpoise. Genes 2018, 9, 213.

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