Development of Saccharina japonica genomic SSR markers using next-generation sequencing
Development of Saccharina japonica genomic SSR markers using next-generation sequencing
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使用下一代测序开发日本糖精基因组 SSR 标记
DOI：
10.1007/s10811-015-0643-0
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发表时间：
2016-04-01
影响因子：
3.3
通讯作者：
Duan, Delin
中科院分区：
文献类型：
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作者：
Li, Qiuying;Zhang, Jie;Duan, Delin
Illumina HiSeq 2000下一代测序（NGS）用于日本稻瘟病菌标本以从高质量基因组序列开发SSR。利用MISA程序共检测到181，595个SSR位点。SSR重复序列在S.其中以单核苷酸（54%）和三核苷酸（26%）最为丰富。从19，658对引物中筛选出600对引物，在3个参试材料中共扩增出166个多态性位点，多态性位点占28%. japonica个体对24个S.每个位点有2 ~ 7个等位基因，平均3.7个，观察杂合度0~0.625，期望杂合度0.082~0.745。多态性信息含量（PIC）值范围为0.08至0.69。16个基因座被归类为信息标记（PIC 0.5）。
Illumina HiSeq 2000 next-generation sequencing (NGS) was used on Saccharina japonica specimens to develop SSRs from high-quality genomic sequences. There were 181,595 SSR loci identified using the MISA program. SSR repeat types are plentiful in genomic sequences of S. japonica, with the most abundant types being mononucleotides (54 %) and trinucleotides (26 %). Six hundred primer pairs were selected and synthesized from 19,658 primer pairs, showing 166 polymorphic SSR loci (28 %) in three selected S. japonica individuals. Sixty polymorphic SSRs were further analyzed in 24 S. japonica individuals, showing two to seven alleles for each locus (average 3.7 alleles), with observed heterozygosities of 0~0.625 and expected heterozygosities of 0.082~0.745. Polymorphism information content (PIC) values ranged from 0.08 to 0.69. Sixteen loci were classified as informative markers (PIC > 0.5).