水杉基因组微卫星分析及标记开发

doi:10.11707/j.1001-7488.20130623

Abstract

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

CLC Number:

S718.46

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

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