Honglin Luo1,2, Guanghua Huang1, Jianbin Li1, Qiong Yang1, Jiajie Zhu1, Bin Zhang1, Pengfei Feng1, Yongde Zhang3, Xueming Yang4. 1. Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, People's Republic of China. 2. Guangxi Medical University, Nanning, 530021, People's Republic of China. 3. Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, People's Republic of China. yondar@126.com. 4. Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, People's Republic of China. nnyxming@126.com.
Abstract
BACKGROUND: Holothuria scabra is a costly gourmet and traditional Chinese tonic medicine. However, the lack of high-quality genome information hinders the genetic, phylogenetic, and bioactivator researches. OBJECTIVE: To construct high-quality genomic data of H. scabra and conduct genome-wide phylogenetic analysis. METHODS: The whole genome of a male H. scabra was sequenced based on Nanopore MinION platform, and the sequence was assembled by wtdbg2. Transcriptome sequencing was used to aid the gene annotation. Repeat sequences, non-coding RNA, pseudogene and gene functional annotation were analyzed. 750 single-copy gene families from ten species were applied to construct phylogenetic tree for evolutionary analysis by using the ML method. RESULTS: The H. scabra genome of 1.18 Gb (N50 = 1557,492 bp) with 500.42 Mb of putative repetitive sequences was assembled from a male H. scabra individual, and 16,642 protein-coding genes, 951 pseudogenes, 1791 motifs and 45,400 domains from the generated assembly were identified. The divergence time between H. scabra and its ancestor was estimated approximately 192.6 million years ago. H. scabra and A. japonicas joined together while sea urchin and sea star diverged about 440 Mya ago. Some key genes involved in notochord and gill slits development, skeleton degeneration and nervous system, as well as homeobox genes differ between H. scabra and Apostichopus japonicas. CONCLUSION: We report the first whole genome of H. scabra with expectation that this will be a valuable resource for genetic, phylogenetic, breading, molecular biology and bioactivator studies of sea cucumbers and other invertebrates.
BACKGROUND: Holothuria scabra is a costly gourmet and traditional Chinese tonic medicine. However, the lack of high-quality genome information hinders the genetic, phylogenetic, and bioactivator researches. OBJECTIVE: To construct high-quality genomic data of H. scabra and conduct genome-wide phylogenetic analysis. METHODS: The whole genome of a male H. scabra was sequenced based on Nanopore MinION platform, and the sequence was assembled by wtdbg2. Transcriptome sequencing was used to aid the gene annotation. Repeat sequences, non-coding RNA, pseudogene and gene functional annotation were analyzed. 750 single-copy gene families from ten species were applied to construct phylogenetic tree for evolutionary analysis by using the ML method. RESULTS: The H. scabra genome of 1.18 Gb (N50 = 1557,492 bp) with 500.42 Mb of putative repetitive sequences was assembled from a male H. scabra individual, and 16,642 protein-coding genes, 951 pseudogenes, 1791 motifs and 45,400 domains from the generated assembly were identified. The divergence time between H. scabra and its ancestor was estimated approximately 192.6 million years ago. H. scabra and A. japonicas joined together while sea urchin and sea star diverged about 440 Mya ago. Some key genes involved in notochord and gill slits development, skeleton degeneration and nervous system, as well as homeobox genes differ between H. scabra and Apostichopus japonicas. CONCLUSION: We report the first whole genome of H. scabra with expectation that this will be a valuable resource for genetic, phylogenetic, breading, molecular biology and bioactivator studies of sea cucumbers and other invertebrates.
Authors: Chen-Shan Chin; Paul Peluso; Fritz J Sedlazeck; Maria Nattestad; Gregory T Concepcion; Alicia Clum; Christopher Dunn; Ronan O'Malley; Rosa Figueroa-Balderas; Abraham Morales-Cruz; Grant R Cramer; Massimo Delledonne; Chongyuan Luo; Joseph R Ecker; Dario Cantu; David R Rank; Michael C Schatz Journal: Nat Methods Date: 2016-10-17 Impact factor: 28.547
Authors: R D Burke; L M Angerer; M R Elphick; G W Humphrey; S Yaguchi; T Kiyama; S Liang; X Mu; C Agca; W H Klein; B P Brandhorst; M Rowe; K Wilson; A M Churcher; J S Taylor; N Chen; G Murray; D Wang; D Mellott; R Olinski; F Hallböök; M C Thorndyke Journal: Dev Biol Date: 2006-08-10 Impact factor: 3.582