Characterization and gene function analysis of SSR sequences in Poria cocos transcriptome / 中草药

ABSTRACT

Objective: To develop new molecular markers for Poria cocos, and to characterize the SSR in P. cocos transcriptome. Methods: The transcriptome Ungenes and genomic scaffolds were examined by the tool of MISA. The gene annotation and gene function cluster were obtained by blasting the Unigenes which contained SSR to the nr and KEGG databases with BlastX. Results: A total of 2 075 SSRs were identified in 4.57% Unigene sequences, the density of distribution was average one SSR per 17.01 kb, and the average length of SSR was 19.59 bp. Meanwhile, those were 54.00 SSRs per Mb, and 20.74 bp in genomic sequences. Among all 241 SSR motifs found in transcriptome, (CG/CG)n which accounted for 10.97% was the most frequent repeat motif. And hexa-nucleotide repeats which accounted for 35.64% was the most group among mono- to hexa-nucleotide repeats. (ACCACG/CGTGGT)14 with the length of 84 bp was the longest SSR. Only 115 Unigenes of 1 887 Unigenes containing SSR were annotated to cellular metabolic process or nucleotide binding, etc, with GO classification. On the other hand, 1 223 Unigenes containing SSR annotated into 219 KEGG pathway maps. 314 and 297 Unigenes of them were annotated into metabolism pathways and genetic information processing pathways, respectively. Conclusion: The SSR in the transcriptome of P. cocos is rich in type, and has a high potential of polymorhpism. Associating gene function, SSR might be applied in marker-assisted breeding with the aim of specific traits.