一串红全基因组调研及SSR特征分析

【目的】为了制定更好的一串红全基因组denovo测序策略及筛选SSR标记。【方法】利用Illumina测序平台对一串红基因组大小进行测定,通过生物信息学分析对一串红基因组的重复序列、杂合度等基本信息进行了预估,并进行了初步组装,在此基础上对一串红全基因组进行了SSR查找。【结果】(1)一串红全基因组大小预估为841Mbp;(2)一串红基因组杂合度较低,有一定的重复序列;(3)共获得95 982个重复单元长度为1~6碱基及复合型的SSR重复序列,其中单碱基重复的SSR单元最为丰富,共39 903个,占41.6%;其次是二碱基重复类型(24 820个)和复合型(13 281个),所占比例分别为25.9%和13.8%。【结论】为一串红全基因组denovo测序和SSR标记的筛选提供了依据,对于一串红后续的分子水平上的研究及遗传多样性、遗传图谱构建、品种鉴定等提供了应用价值。

Genome survey and characteristic analysis of SSR in Salvia splendens

Obsjective]In order to develop a better sequence strategy of S.splendens genome denovo and screening SSR makers,the survey of whole genome and the search for SSR were carried out.Methods]This is the first study on the genome size of S.splendens and that were measured using next-generation sequencing technology (Illumina).The basic information of S.splendens including repeat sequence and heterogeneity percentage were estimated by bioinformatics.Then,preliminary genome assembly was conducted and SSR was detected.Results](1) the genome size was about 841 Mbp,(2) the homozygosity of the genome was good and there is a certain repeat sequence,(3) there were 95 982 microsatellites (SSRs) repeat sequence which ranged from 1 to 6 bp and compound SSR.Among them,the most were mononucleotide repeats (39 903) and it accounted for 41.6％ of the total;secondly,dinucleotide repeats were 24 820 and compound repeats were 13 281,and they accounted for 25.9％ and 13.8％,respectively.Conclusion]This study provides a basis for genome denove of S.splendens and the selection of SSR makers.It is also valuable for the study of molecular level,genetic diversity,genetic map construction,variety identification and so on.