Data mining of simple sequence repeats in transcriptome sequences of Tibetan medicinal plant Zangyinchen Swertia mussotii / 中国中药杂志
China Journal of Chinese Materia Medica
;
(24): 2068-2076, 2015.
Article
in Chinese
| WPRIM
| ID: wpr-337981
ABSTRACT
MISA (MicroSAtelite) software was employed to screen SSRs in 68 787 contigs of Swertia mussotii transcriptome sequences. 5 610 SSRs were distributed in 5 099 contigs which accounted for 7.41% of 68 787 contigs. There are 220 kinds of SSR motifs existing in S. mussotii transcriptome. On average, SSRs occurred every 12.60 kb in length. In the SSRs, the tri-nucleotide repeat motif was the most abundant (45.99%), followed by the di-nucleotide (41.62%). AT/TA and AAT/TTA were the main types of motif in di-, tri-nucleotide repeats. The repeat numbers of SSRs which from S. mussotii transcriptome SSRs were mainly from 5 to 10 and motif length of them mostly ranged from 12 bp to 30 bp. A total of 30 651 contigs were annotated, and only 1 447 SSRs were occurred in protein-coding regions. In the six repeat motifs, tri-nucleotide repeats were the most abundant in coding regions (928). There are abundant SSRs in S. mussotii transcriptome with high frequency and various types, indicating their usefulness in theory. This research may lay the foundation for designing the targeted SSR primers and developing SSR molecular markers by mining the information of SSRs loci in S. mussotii transcriptome sequences data.
Full text:
Available
Index:
WPRIM (Western Pacific)
Main subject:
Plants, Medicinal
/
Microsatellite Repeats
/
Swertia
/
Medicine, Tibetan Traditional
/
Data Mining
/
Transcriptome
/
Genetics
Language:
Chinese
Journal:
China Journal of Chinese Materia Medica
Year:
2015
Type:
Article
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