SSR loci information analysis in transcriptome of Cordyceps sinensis.
10.19540/j.cnki.cjcmm.20190829.102
- Author:
Han ZHANG
1
;
Fang WANG
1
;
Jing BAI
1
;
Qiang DONG
1
;
Xin-Xin TONG
1
;
Yuan YUAN
2
;
Jin-Lin GUO
1
Author Information
1. Key Laboratory of Standardization of Chinese Medicine,Ministry of Education,Key Laboratory of Systematic Research,Development and Utilization of Chinese Medicine,Resources Breeding Base of Co-founded by Sichuan Province and MOST,Chengdu University of Traditional Chinese Medicine Chengdu 611137,China.
2. Chinese Medicine Resource Center,China Academy of Chinese Medical Sciences Beijing 100700,China.
- Publication Type:Journal Article
- Keywords:
Cordyceps sinensis;
SSR loci information;
transcriptome
- MeSH:
Cordyceps/genetics*;
Expressed Sequence Tags;
Microsatellite Repeats;
Polymorphism, Genetic;
Transcriptome
- From:
China Journal of Chinese Materia Medica
2019;44(21):4605-4611
- CountryChina
- Language:Chinese
-
Abstract:
To analysis the SSR loci information in the transcriptome of Cordyceps sinensis and develop SSR molecular markers,MISA(MicroSatellite) software was used to analyze the microsatellites information from 16 875 unigene sequences and SSR primer designed by Primer 3. 0. In total,5 899 SSRs were detected in 4 252 unigene with the distribution frequency of 34. 99%,which was represented by 74 repeat motifs and SSR loci occurred per 7 952 bp in length. In the SSRs,the mono-nucleotide was the most abundant repeat motif(42. 5%),followed by tri-nucleotide(34. 48%),C/G and CCG/CGG were the dominant repeat motifs,respectively. The number of repetitions of the six SSR repeat types was concentrated on 5 to 12 times,and the length was mostly less than 24 bp. A total of 12 282 pairs of primers were screened and selected 20 pairs of primers for validity detection randomly,10 pairs of primers amplified the expected specific bands,and primer P1 has significant polymorphism. Moreover,it was found that unigene containing SSR loci is mainly related to genetic and environmental functions after GO and KEGG annotation. In conclusion,these SSR loci in the transcriptome of O. sinensis are high in frequency,rich in primitive types,high in polymorphism,and highly available,which will provides abundant candidate molecular markers for its genetic diversity analysis,resource identification protection,and gene function research.
