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Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale
Song, Hao1,2,3,4; Zhang, Yi-Xin5; Yang, Mei-Jie1,2,3; Sun, Jing-Chun1,2,4; Zhang, Tao1,2,4; Wang, Hai-Yan1,2,4
2018-12-01
Source PublicationJOURNAL OF GENETICS
ISSN0022-1333
Volume97Pages:79-86
Corresponding AuthorZhang, Tao(tzhang@qdio.ac.cn) ; Wang, Hai-Yan(haiyanwang@qdio.ac.cn)
AbstractThe veined rapa whelk (Rapana venosa) is an economically important gastropod in China, but is considered as an invasive species globally. Only a few studies have examined the R. venosa genome, a genomewide survey is necessary for improving our understanding of the genome structure and size of this organism. Microsatellite markers are powerful tools for characterizing germplasms, genetic diversity and kinship among individuals. The resultant data are applicable to breeding efforts in commercial aquaculture or for understanding invasion mechanisms. Here, we investigated the genome structure of R. venosa on an Illumina Hi-seq platform with 92x sequencing depth. We performed a K-mer analysis to estimate genome size, repeat sequences and heterozygosity. Clean reads were de novo assembled for the identification of simple-sequence repeat (SSR) loci that are suitable as markers. The estimated genome size of R. venosa was 2200.07 Mb, with a 1.41% heterozygosity rate and 67.04% repeats. We detected 5,477,450 simple-sequence repeats (SSRs), with 3,400,602 loci present as pure tandem repeats and 2,076,848 as compound motifs. We further selected and characterized 28 polymorphic markers in 78 individuals from Dandong, Laizhou, Weihai and Zhoushan in China. The range of alleles was 2-28 and the observed heterozygosity was 0.2857-0.8676. The data obtained from our genomic survey will aid the design of R. venosa whole-genome sequencing projects and advance the identification of SSR markers. Both these developments are valuable for further studies on ecological, evolutionary and genetic breeding in R. venosa.
Keywordnext-generation sequencing simple-sequence repeats gastropod Rapana venosa
DOI10.1007/s12041-018-0975-z
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000451438500010
PublisherINDIAN ACAD SCIENCES
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/156193
Collection海洋生态与环境科学重点实验室
Corresponding AuthorZhang, Tao; Wang, Hai-Yan
Affiliation1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao 266071, Shandong, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao 266071, Peoples R China
3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdoa 266071, Peoples R China
5.Qingdao 2 Middle Sch Shandong Prov, Qingdao 266071, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Song, Hao,Zhang, Yi-Xin,Yang, Mei-Jie,et al. Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale[J]. JOURNAL OF GENETICS,2018,97:79-86.
APA Song, Hao,Zhang, Yi-Xin,Yang, Mei-Jie,Sun, Jing-Chun,Zhang, Tao,&Wang, Hai-Yan.(2018).Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale.JOURNAL OF GENETICS,97,79-86.
MLA Song, Hao,et al."Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale".JOURNAL OF GENETICS 97(2018):79-86.
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