水杉基因组微卫星分析及标记开发

doi:10.11707/j.1001-7488.20130623

林业科学 ›› 2013, Vol. 49 ›› Issue (6): 160-166.doi: 10.11707/j.1001-7488.20130623

水杉基因组微卫星分析及标记开发

张新叶¹, 张亚东¹, 彭婵¹, 宋丛文², 杨彦伶¹

1. 湖北省林业科学研究院武汉 430075;
2. 湖北生态工程职业技术学院武汉 430200

收稿日期:2012-09-14 修回日期:2012-11-22 出版日期:2013-06-25 发布日期:2013-07-16
通讯作者: 杨彦伶
基金资助:
湖北省自然科学基金项目(2011CDB115); 湖北省林业科学研究院青年基金水杉项目。

Analysis of Genomic Microsatellite Sequence and Development of SSR Markers in Metasequoia glyptostroboides

Zhang Xinye¹, Zhang Yadong¹, Peng Chan¹, Song Congwen², Yang Yanling¹

1. Hubei Forestry Academy Wuhan 430075;
2. Hubei Ecology Vocational College Wuhan 430200

Received:2012-09-14 Revised:2012-11-22 Online:2013-06-25 Published:2013-07-16

摘要/Abstract

关键词: 水杉, 基因组, 微卫星, 标记开发

Abstract:

In this paper, the partial genome of Metasequoia glyptostroboides, a rare plant, was sequenced by using the ROCHE-454 GLX high-throughput sequencing platform. Through sequence assembly and microsatellite finding, 1 965 microsatellite loci were obtained in the sequence and the repeat unit length was 2-5 base pairs, by which 921 pairs of primer were designed with the Primer 3 Plus software. Analysis of these microsatellite sequences showed that tetranucleotide microsatellite was the most abundant, accounting for 38.8% of the total repeat sequences, followed by dinucleotide (31.8%), trinucleotide (22%) and pentanucleotide (7.4%) in the M. glyptostroboides genome. Among the dinucleotide repeat types, AG type was the most, accounting for 13.9% of total repeats and 43.8% of dinucleotide repeats. In the eight trinucleotide repeat types, AAG type accounted for 8.3% of total repeats and 37.7% of trinucleotide repeats, followed by ATG (23.1%), AAC (16.7%) and AAT (13.0%). The analysis of different lengths of the microsatellite repeat unit showed that the most abundant variants were dinucleotide microsatellite and there were 23 different types of repeat lengths, followed by the tetranucleotide repeat (10 types), trinucleotide repeat (8 types) and pentanucleotide repeat (3 types). The validation of SSR markers showed that, 87 pairs brought about clear products and 46 pairs had polymorphic products, accounting for 62.14% and 32.86% out of the 140 primer pairs,respectively.

Key words: Metasequoia glyptostroboides, genome, microsatellites, marker development

中图分类号:

S718.46

张新叶, 张亚东, 彭婵, 宋丛文, 杨彦伶. 水杉基因组微卫星分析及标记开发[J]. 林业科学, 2013, 49(6): 160-166.

Zhang Xinye, Zhang Yadong, Peng Chan, Song Congwen, Yang Yanling. Analysis of Genomic Microsatellite Sequence and Development of SSR Markers in Metasequoia glyptostroboides[J]. Scientia Silvae Sinicae, 2013, 49(6): 160-166.

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水杉基因组微卫星分析及标记开发

Analysis of Genomic Microsatellite Sequence and Development of SSR Markers in Metasequoia glyptostroboides

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