Development of 11 Ecklonia radicosa (Phaeophyceae, Laminariales) SSRs markers using next-generation sequencing and intra-genus amplification analysis
Development of 11 Ecklonia radicosa (Phaeophyceae, Laminariales) SSRs markers using next-generation sequencing and intra-genus amplification analysis
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DOI：
10.1007/s10811-018-1406-5
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发表时间：
2018-06
影响因子：
3.3
通讯作者：
Shingo Akita;K. Koiwai;T. Hanyuda;Syou Kato;R. Nozaki;Tsubasa Uchino;T. Sakamoto;H. Kondo;I. Hirono;D. Fujita
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文献类型：
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作者：
Shingo Akita;K. Koiwai;T. Hanyuda;Syou Kato;R. Nozaki;Tsubasa Uchino;T. Sakamoto;H. Kondo;I. Hirono;D. Fujita
利用Illumina MiSeq下一代测序技术（NGS），构建了一对具有多态性的短重复序列（SSR）标记。使用MISA perl脚本，从61.5 Mb组装的基因组DNA中总共鉴定出3112个SSR（重复超过6次的二至六核苷酸基序）。其中，二核苷酸（853个，占27.4%）和三核苷酸（1813个，占58.3%）占优势，四核苷酸（172个，占5.5%）、五核苷酸（175个，占5.6%）和六核苷酸（99个，占3.2%）不常见。通过对75个位点（重复8次以上）的特异性扩增和多态性检测，成功开发了11个SSR标记（Eradic 01 -11）。11个标记的等位基因数、观测杂合度和期望杂合度的范围分别为3-13、0.200-0.683和0.258-0.864。多态信息含量（PIC）分析表明，8个标记（Eradic 01、02、04、05、06、08、09和11）具有较高的信息量（PIC > 0.5），3个标记具有较好的信息量（PIC < 0.25）。此外，在除Eradic 02、08和11之外的所有标记中获得属内扩增。这些标记有助于揭示E.根
Polymorphic simple sequence repeat (SSR) markers ofEcklonia radicosawere developed using Illumina MiSeq next-generation sequencing (NGS) analysis. In total, 3112 SSRs (di- to hexanucleotide motifs repeated more than six times) were identified from 61.5-Mb assembled genomic DNA using MISA perl script. Among the SSRs, di- (853 loci, 27.4%) and trinucleotides (1813 loci, 58.3%) were dominant, while tetra- (172 loci, 5.5%), penta- (175 loci, 5.6%), and hexanucleotides (99 loci, 3.2%) were not common. After specific amplification and polymorphic tests of 75 selected loci (tri- to hexanucleotide motifs repeated more than eight times), 11 SSR markers (Eradic01–11) were successfully developed. The range of the number of alleles, observed heterozygosity, and expected heterozygosity in the 11 markers was 3–13, 0.200–0.683, and 0.258–0.864, respectively. Polymorphic information content (PIC) analysis indicated that eight markers (Eradic01, 02, 04, 05, 06, 08, 09, and 11) were highly informative (PIC > 0.5) and the other three were reasonably informative (0.5 < PIC < 0.25). In addition, intra-genus amplification was obtained in all markers except for Eradic02, 08, and 11. These markers could help to reveal the genetic diversity and population structure ofE. radicosa.