摘要
【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。
【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.
作者
王硕
葛秀秀
孔维一
陈洪伟
刘克锋
王红利
WANG Shuo;GE Xiuxiu;KONG Weiyi;CHEN Hongwei;LIU Kefeng;WANG Hongli(College of Biological Science and Engineering,Beijing University of Agriculture,Beijing 102206,China;Key Laboratory of Urban Agriculture(North)Ministry of Agriculture, Beijing University of Agriculture,Beijing 102206,China;Plant Science and Technology College, Beijing University of Agriculture,Beijing 102206,China;College of Urban&Rural Development,Beijing University of Agriculture,Beijing 102206,China;College of Landscap Architecture, Beijing University of Agriculture,Beijing 102206,China)
出处
《北京农学院学报》
2018年第2期15-22,共8页
Journal of Beijing University of Agriculture
基金
北京市教育委员会科技计划面上项目(KM201510020001)
2017年农业部华北都市农业重点试验室开放课题(kf2017014)
