粘虫 Mythimna separata（Walker）是一种迁飞性害虫，严重危害玉米、水稻、小麦等粮食作物。 SSR 是指以1～6个核苷酸为基本重复单位的串联重复 DNA 序列。 SSR 位点的信息分析为粘虫扩散、迁飞和交配等行为分子机制的研究以及粘虫的...粘虫 Mythimna separata（Walker）是一种迁飞性害虫，严重危害玉米、水稻、小麦等粮食作物。 SSR 是指以1～6个核苷酸为基本重复单位的串联重复 DNA 序列。 SSR 位点的信息分析为粘虫扩散、迁飞和交配等行为分子机制的研究以及粘虫的综合防治奠定理论基础。本研究基于高通量测序获得的粘虫转录组数据，利用软件 msatcom‐mander 发掘粘虫 SSR 位点。结果从20776条转录组 Unigenes 中共搜索出400个 SSR ，分布于372条 Unigenes 中。在粘虫转录组 SSR 中，三核苷酸重复的数量最为丰富，有271个；其次是二核苷酸和单核苷酸重复，分别是70个和49个；四至六核苷酸重复的数量都很少，共10个。粘虫转录组 SSR 共包含24种重复基元，其中 CCG／CGG 是优势重复基元类型，有69个；其次是 AAG／CTT ，有57个。 CG／CG 有18个，在二核苷酸重复基元中所占的比例达到25.7％。此研究发掘到的 SSR 位点将为粘虫遗传图谱的构建、遗传多样性分析、亲缘关系分析等提供丰富的分子标记。展开更多
The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. T...The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. To provide tools for addressing both population genetics studies and gene mapping, dito pentanucleotide simple sequence repeat (SSR) markers were developed using 454 pyrosequencing. Among the 1466 SSR markers developed, 1244 primer sets produced strong PCR products, of which 905 (72.7%) were polymorphic in kelp grouper. Cross-species utility of the 905 polymorphic SSR markers was tested in four additional Epinephelinae species of Hyporthodus septemfasciatus, Plectropomus leopardus, Epinephelus lanceolatus and Epinephelus coioides. Results revealed that, respectively, 401 (44.3%), 136 (15.0%), 434 (49.0%) and 538 (59.4%) SSRs showed specific polymorphic products. Of these, 40 SSR markers (33 di-, 1 tri- and 6 tetra-nucleotides) showed polymorphism in all species tested. Additionally, three AGAT SSR motifs which accounted for 42.9% of the nondi-nucleotide markers were found in the 40 SSR markers. This indicates that the AGAT SSR motif has a high potential as a highly versatile SSR marker in grouper Epinephelinae. The SSR markers developed in this study can be employed to obtain reliable genetic variability estimates for groupers (Epinephelinae).展开更多
文摘粘虫 Mythimna separata（Walker）是一种迁飞性害虫，严重危害玉米、水稻、小麦等粮食作物。 SSR 是指以1～6个核苷酸为基本重复单位的串联重复 DNA 序列。 SSR 位点的信息分析为粘虫扩散、迁飞和交配等行为分子机制的研究以及粘虫的综合防治奠定理论基础。本研究基于高通量测序获得的粘虫转录组数据，利用软件 msatcom‐mander 发掘粘虫 SSR 位点。结果从20776条转录组 Unigenes 中共搜索出400个 SSR ，分布于372条 Unigenes 中。在粘虫转录组 SSR 中，三核苷酸重复的数量最为丰富，有271个；其次是二核苷酸和单核苷酸重复，分别是70个和49个；四至六核苷酸重复的数量都很少，共10个。粘虫转录组 SSR 共包含24种重复基元，其中 CCG／CGG 是优势重复基元类型，有69个；其次是 AAG／CTT ，有57个。 CG／CG 有18个，在二核苷酸重复基元中所占的比例达到25.7％。此研究发掘到的 SSR 位点将为粘虫遗传图谱的构建、遗传多样性分析、亲缘关系分析等提供丰富的分子标记。
文摘The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. To provide tools for addressing both population genetics studies and gene mapping, dito pentanucleotide simple sequence repeat (SSR) markers were developed using 454 pyrosequencing. Among the 1466 SSR markers developed, 1244 primer sets produced strong PCR products, of which 905 (72.7%) were polymorphic in kelp grouper. Cross-species utility of the 905 polymorphic SSR markers was tested in four additional Epinephelinae species of Hyporthodus septemfasciatus, Plectropomus leopardus, Epinephelus lanceolatus and Epinephelus coioides. Results revealed that, respectively, 401 (44.3%), 136 (15.0%), 434 (49.0%) and 538 (59.4%) SSRs showed specific polymorphic products. Of these, 40 SSR markers (33 di-, 1 tri- and 6 tetra-nucleotides) showed polymorphism in all species tested. Additionally, three AGAT SSR motifs which accounted for 42.9% of the nondi-nucleotide markers were found in the 40 SSR markers. This indicates that the AGAT SSR motif has a high potential as a highly versatile SSR marker in grouper Epinephelinae. The SSR markers developed in this study can be employed to obtain reliable genetic variability estimates for groupers (Epinephelinae).
