摘要
目的:分析夏枯草转录组中简单重复序列(SSR)信息,为开发夏枯草新的分子标记奠定基础。方法:使用Micro SAtelite(MISA)软件对转录组序列进行SSR位点搜索并利用Primer3软件设计引物。结果:发现4248条Unigenes序列中含有5450个SSR位点,发生频率为27.50%,平均每5933 bp含1个SSR位点;二核苷酸、三核苷酸和单核苷酸重复是其优势重复类型,分别占总SSR数量的44.59%、28.44%、24.75%;在夏枯草转录组中共发现160种重复基元,其中以AG/CT比例最高,约25%,其次是A/T,约占24.26%;夏枯草转录组SSR以5~11次重复为主,其中75.97%的基序长度集中在12~20 bp;共得到4228对SSR位点特异性引物。结论:夏枯草转录组SSR位点出现频率高、重复类型丰富、密度大、多态性较高,通过对夏枯草转录组资源SSR信息的研究,为进一步开发夏枯草SSR分子标记奠定了基础。
Objective： In order to establish new molecular markers and design SSR primers, the SSR information was analyzed in the transcriptome of Prunella vulgaris. Methods： MicroSAtelite （MISA） software was used to search for the SSR site of the P. vulgaris L. transcriptome and the primers were designed by Primer3 software. Results： 5450 SSRs were dis- tributed in 4248 Unigenes which accounted for 27.50% , each 5933 bp contains one SSR loci, dinucleotide, trinucleotide and mono nucleotide repeat was the main type of repetition, for 44. 59%, 28.44% 24. 75% of the total number of SSR. We found in the transcriptome of 160 kinds of variation pattern, the highest percentage was AG/CT, about 25%, followed by A/T, a- bout 24. 26%. The SSR of P. vulgaris transcript was mainly 5 to 11 replicates, 75.97% of the motif length concentrated in the 12-20 bp; 4228 SSR locus specific primers were obtained. Conclusion： The SSR site in the transcriptome of P. vulgaris have the characteristics of high frequency of occurrences, type richness, high density and high potential of polymorphism. With the study of SSR information of P. vulgaris transcriptome, it will lay a foundation for the further development of P. vulgaris SSR mo- lecular markers.
作者
王会敏
苏秀红
董诚明
朱畇昊
WANG Hui-min;SU Xiu-hong;DONG Cheng-ming;ZHU Yun-hao(School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China;Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment ＆ Chinese Medicine Development of Henan Province, Zhengzhou 450046, China)
出处
《中国现代中药》
CAS
2018年第1期29-33,38,共6页
Modern Chinese Medicine
关键词
夏枯草
转录组
SSR信息分析
Prunella vulgaris L.
transcriptome
SSR bioinfomlatic analysis
