木荷基因组SSR位点开发及初步分析

Development and Preliminary Analysis of SSR Locus in Schima superba Genome

为开发木荷分子标记,采用高通量测序技术获得木荷基因组原始数据,经生物信息学软件对木荷基因组序列进行序列拼接、组装和对比,共获得308 418条Contig序列和459 984条Scafford序列。采用MISA软件搜索木荷基因组序列中微卫星(Microsatellite)位点,共得到334 843个SSR序列,总长度5 074 708 bp,占木荷基因组大小的0.98%,木荷基因组SSR序列平均长度为15.2 bp,平均分布频率为644个/Mb。木荷SSR序列中,单核苷酸序列数量最多,共188 217个,占木荷SSR序列总数的56.21%,其次是二核苷酸(23%)>三核苷酸(13%)>四核苷酸(5%)>五核苷酸(2%)>六核苷酸(1%)。木荷全基因组SSR序列中共包括400种重复基元,其中单核苷酸重复基元A和二核苷酸重复基元AT是主要重复基元,分别占总SSR的56%和11%,SSR基元的重复次数分布在4~40次,主要分布在4~25次。本研究丰富了木荷分子标记类型,为进一步群体遗传结构和遗传多样性分析提供了基础数据。

In order to develop the molecular marker of Schima superba, high-throughput sequencing was used to obtain the original data of S. superba. Bioinformatics softwares were used to sequence, assemble and compare the S. superba genomic sequences. A total of 308 418 contig sequences and 459 984 scafford sequences were obtained. In total, 334 843 SSR sequences were obtained by using the bioinformatics analysis software MISA. The total length of the SSR was 5 074 708 bp, accounting for 0.98% of the genome size of S. superba, with an average length of 15.2 bp. The mean distribution frequency was 644/Mb. Among the SSR of S. superba genome, the number of single nucleotides was the largest, with a total number of 188 217, accounting for 56.21% of the total SSR of S. superba, followed by dinucleotide（23%） trinucleotides（13%） teranucleotides（5%） pentanucleotides（2%） hexanucleotide（1%）. The SSR sequences of S. superba genome was consisted of 400 repeat motifs, in which mononucleotide repeat A and dinucleotide repeat AT were the major repeat motifs, accounting for 56% and 11% of the total SSR respectively. The number of repetitions of SSR motifs was distributed from 4 to 40, mainly between 4 and 25 times. This study would provide basic data for further genetic diversity analysis of S. superba.