目的 分析茯苓转录组中简单重复序列(SSR)信息,以及含SSR的基因功能,为开发茯苓新型分子标记奠定基础。方法 利用MISA软件搜索转录组Unigene及基因组scaffold中SSR,对含SSR的Unigene使用BlastX比对nr及KEGG数据库,注释其功能,并聚类分析。结果 在转录组序列中发现4.57%的Unigene序列含有2 075个SSR,平均17 010条Unigene出现1个SSR,SSR的平均长度19.59 bp;而基因组中SSR的平均密度54.00个/Mb,平均长度20.74 bp。在转录组中发现的241种碱基重复模式中,以 (CG/CG)_n比例最高(10.97%);以六核苷酸类重复数量最多(35.64%),以 (ACCACG/CGTGGT)₁₄最长(84 bp)。在1 887条含SSR的Unigene中,115条能被基因本体(GO)分类注释到细胞代谢进程、核酸结合等;1 223条Unigene能被注释到219个KEGG通路图中,其中314条注释到新陈代谢,297条注释到遗传信息处理。结论 茯苓转录组SSR的类型丰富、多态性潜能较高,关联功能相关基因的SSR开发对茯苓目的性状的分子标记辅助育种具有巨大潜力。

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.

国家“十二五”科技支撑计划项目(2011BAI06B03)