A genome survey sequence (GSS) analysis and microsatellite marker development for Indian mackerel, Rastrelliger kanagurta, using Ion Torrent technology

被引：7

作者：

Adelyna, M. A. Noor ^{[1
]}

Jung, H. ^{[2
]}

Chand, V. ^{[3
]}

Mather, P. B. ^{[4
]}

Azizah, M. N. Siti ^{[5
,6
]}

机构：

[1] Univ Sains Malaysia, Ctr Global Sustainabil Studies, George Town, Malaysia

[2] Queensland Univ Technol, Ctr Trop Crops & Biocommod, Brisbane, Qld, Australia

[3] Queensland Univ Technol, Inst Future Environm, Brisbane, Qld, Australia

[4] Queensland Univ Technol, Fac Sci & Engn, Earth Environm & Biol Sci, Brisbane, Qld, Australia

[5] Univ Sains Malaysia, Sch Biol Sci, George Town, Malaysia

[6] Univ Sains Malaysia, Ctr Marine & Coastal Studies, George Town, Malaysia

来源：

META GENE | 2016年 / 10卷

关键词：

Rastrelliger kanagurta; Microsatellite markers; GSS; Ion Torrent; Indian mackerel;

D O I：

10.1016/j.mgene.2016.10.005

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

A next generation sequencing platform (Ion Torrent PG (TM)) was used to generate a partial genome survey sequence (GSS) dataset to develop microsatellite markers from R. kanagurta genomic DNA. Data generated included a total of 399,794 sequence reads (81.29 Mbp) with 16,209 sequence reads successfully assembled. This produced 327 contigs averaging 677 bp in length in addition to the SSR markers. Results based on GSS BLASTx and BLASTn possessed significant similarity (E value < 10(-6)) with available data in public databases, with the majority matching well to previously reported fish sequences. A total of 7891 SSR-containing motif repeats of which 1688 qualified for primer design were generated. After optimization and testing for reproducibility and polymorphism, eight microsatellite markers were deemed suitable for future population genetic analysis in the target species.

引用

页码：67 / 72

页数：6

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