摘要
本研究利用Illumina HiSeqTM 2000对马蓝转录组进行高通量测序,使用软件MicroSAtellite(MISA)分析转录组中的SSR位点信息。通过组装马蓝转录组数据获得了51381条Unigene,并对获得的Unigene进行SSR检测,共检测到8471个SSR位点,其分布在6782条Unigene中,出现的频率为16.49%。SSR中以二核苷酸和三核苷酸重复类型为主,其中二核苷酸以重复单元AT/TA为主,占18.14%,其余类型的重复单元相对较少。SSR所在序列功能注释结果显示在Nr和SwissProt中分别有5932和4285条序列被注释,同时SSR所在序列还被注释到47个GO分类,25个KOG分类和29个KEGG代谢通路中。通过设计、筛选,共获得5819对引物组合,随机挑选的18对引物中有13对引物扩增出符合预期大小的条带。马蓝SSR出现的频率高,重复种类丰富,为研究马蓝遗传多样性、基因定位和品质改良等提供了科学依据。
In this research,the Illumina HiSeqTM 2000 was used for high-throughput sequenceing of Baphicacanthus cusia,and the distribution frequency of SSR and basic characteristics of repeat motifs were analyzed by using MicroSAtellite software.51381 Unigene were obtained by assembling transcriptome data of Baphicacanthus cusia,following detected by SSR.The results showed that a total of 8471 SSR loci were detected,which were distributed in 6782 Unigenes with a frequency of 16.49%.The SSR was dominated by dinucleotide and trinucleotide repeat types,in which the dinucleotide is mainly composed of repeating units AT/TA,accounting for 18.14%,and the remaining types of repeating units are relatively few.The sequence function annotation results of SSR showed that 5932 and 4285 sequences were annotated in Nr and SwissProt,respectively,and the sequence of SSR was also annotated into 47 GO classifications,25 KOG classifications,and 29 KEGG metabolic pathways.A total of 5819 pairs of primer combinations were obtained through design and screening,and 13 pairs of primers amplified bands of the expected size among 18 randomly selected primers.SSR of Baphicacanthus cusia has a high frequency and abundant repeat types,which provides a necessary reference for studying genetic diversity,gene mapping and quality improvement of Baphicacanthus cusia.
作者
公培民
宁书菊
叶齐
于剑
赵璇璇
沈继伟
马小毛
蔡国倩
胡永乐
魏道智
Gong Peimin;Ning Shuju;Ye Qi;Yu Jian;Zhao Xuanxuan;Shen Jiwei;Ma Xiaomao;Cai Guoqian;Hu Yongle;Wei Daozhi(Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring,College of Life Science,Fujian Agriculture and Forestry University,Fuzhou,350002;Key Laboratory of Crop Ecology and Molecular Physiology,Fujian Province Universities,College of Crop Science,Fujian Agriculture and Forestry University,Fuzhou,350002;Ecology and Engineering College,Wuyi University,Wuyishan,354300)
出处
《分子植物育种》
CAS
CSCD
北大核心
2020年第12期4000-4008,共9页
Molecular Plant Breeding
基金
国家自然科学基金面上项目(81573517)
福建省自然科学基金面上项目(2019J01827)共同资助。
