Identification of EST-SSRs in Taxus cuspidata based on high-throughput sequencing.
- Author:
Qiong WU
1
;
Xiao-Qun DUAN
;
Xu CHEN
;
Pei-Gen XIAO
Author Information
- Publication Type:Journal Article
- MeSH: DNA Primers; genetics; Expressed Sequence Tags; Gene Expression Profiling; methods; Gene Expression Regulation, Plant; High-Throughput Nucleotide Sequencing; methods; Microsatellite Repeats; genetics; Taxus; genetics; Transcriptome; genetics
- From: China Journal of Chinese Materia Medica 2012;37(24):3728-3733
- CountryChina
- Language:Chinese
-
Abstract:
OBJECTIVETaxus species are highly valued for the production of taxol. Based on high-throughput sequenceing, EST-SSRs were explored and studied in the transcriptome of Taxus cuspidata.
METHODT cuspidata leaf cDNA was extracted and sequenced by 454 GS FLX Titanium. High-quality sequences were assembled using Newbler Assembler Software, which produced unique sequences. SSRs motif was explored using simple sequence repeat identification tool (Perl Script). Primers were designed using PRIMER3.
RESULTA total of 81 148 high-quality reads from the needles of T. cuspidata were produced using the Roche GS FLX Titanium system. A total of 20 557 unique sequences were obtained. There were 753 simple sequence repeat motifs identified. Primers of PCR were obtained for 519 EST-SSRs, randomly selected cloning sequencing revealed that 87.5% of ESTs were the same as the results of Sanger sequencing.
CONCLUSIONThe results provide the first EST-SSRs collection in Taxus and are essential for future efforts of gene discovery, functional genomics, and genome annotation in related species.
