药用植物益智的基因组调研及SSR分子标记开发

Genome Survey and SSR Molecular Marker Development of Medicinal Plant Alpinia oxyphylla Miq.

益智是中国著名的“四大南药”之一,也是海南省道地药材。本研究以Illumina高通量测序技术为基础,通过益智样品的基因组DNA构建350 bp文库,采用Kmer分析方法分析益智基因组大小、重复序列比例和杂合率;采用MISA方法分析可能的SSR分子标记;利用与NT库(Nucleotide Database)进行BLAST比对,分析益智物种多样性。结果显示:益智的基因组大小为2.06 Gb,重复序列比例为77.94%,基因组杂合度为0.38%;在基因组序列中,进行SSR分子标记分析,共鉴定出了409474个SSR,其中,单、双、三核苷酸重复模体的比例较高,分别占比68.16%、19.66%、10.68%;为分析益智的物种多样性,在测序构建的350 bp小文库中,任意筛选10000条单端reads与NCBI核酸数据库比对,发现在已公布的序列信息的物种中,小豆蔻(Elettaria cardamomum)和艳山姜(Alpinia zerumbet)上的reads匹配率较高,分别占比15.96%和10.44%。该研究表明,南药益智的基因组属于大基因组,高重复的复杂基因组结构特征;同时,也为益智的资源保护和遗传多样性分析及品种选育提供了遗传信息支撑。

Alpinia oxyphylla Miq.is one of the Four Famous Southern Medicines in China and the genuine medicinal materials of Hainan Province.This study was based on Illumina high-throughput sequencing technology,350 bp library from genomic DNA of Alpinia oxyphylla Miq.was constructed and Kmer analysis was applied to estimate its genome size,repeat sequence ratio and heterozygosity rate;simple sequence repeat(SSR)loci that are suitable as markers were identified by MISA software;its species diversity was analyzed by blasting with the Nucleotide Database.Results showed that the estimated genome size of Alpinia oxyphylla Miq.was 2.06 Gb,with a77.94%repeat sequence ratio and 0.38%heterozygosity rate.In the genome sequence,409474 simple sequence repeats(SSRs)were detected by SSR molecular marker analysis,among which mono-nucleotide,di-nucleotide and tri-nucleotide repetitive motifs ranked the higher percentages of 68.16%、19.66%and 10.68%.In order to analyze the species diversity of Alpinia oxyphylla Miq.,we selected 10000 single-end reads randomly from the 350 bp small library and blasted it with Nucleotide Database in NCBI,results showed that Elettaria cardamomum and Alpinia zerumbet were blasted with the reads of 15.96%and 10.44%among the species with published sequence information.This study demonstrated that the genome of Alpinia oxyphylla Miq.belongs to the complex genome structure characteristics of high repetition and large genome and it provides ge netic information support for resource protection,genetic diversity analysis and breeding variety.