姜黄根茎的高通量转录组测序与生物信息学分析

High-throughput Transcriptome Sequencing and Bioinformatics Analysis of Rhizoma of Curcuma longa

为获得姜黄(Curcuma longa)的转录组特征信息,本研究采用Illumina HiSeqΧTen高通量测序平台对姜黄根茎进行高通量转录组测序并进行系统的生物信息学分析。共获得7.18Gb Clean数据,组装了50194条unigenes,平均长度961.3 bp,N50为1339 bp。数据库比对显示,姜黄根茎转录组unigenes在NR、Swiss-Prot、KEGG、KOG、eggNOG、GO、Pfam数据库中分别注释到38802条(77.30%)、27869条(55.52%)、14725条(29.34%)、22225条(44.28%)、37317条(74.35%)、25863条(51.53%)、26137条(52.07%)。注释结果显示,姜黄与野生型马来西亚蕉的同源序列最多,unigenes在GO数据库中注释到参与生物过程、细胞组分和分子功能3个大类50小类,KOG功能分类获得25个不同的功能群,涉及128个KEGG代谢通路,其中包括21个次生代谢通路。在植物抗性基因(PRG)数据库中分别注释到3718条unigenes;借助MISA软件发现7183个SSR,三碱基重复的SSR数量最多,有3615个,占50.33%,其中CCG/CGG类型的比例最高。本研究获得了姜黄根茎转录组序列信息以及SSR信息,为后续开展姜黄功能基因的挖掘、次生代谢途径解析提供了数据资源和理论基础。

To obtain the transcriptome dataset of Curcuma longa,the transcriptome dataset was obtained using the high-throughput sequencing platform Ilumina HiSeq X Ten,followed by systemic bioinformatics analysis.A total of 7.18 Gb high-quality clean reads were obtained by the transcriptome sequencing.Using Trinity de novo assem bling,a total of 50194 unigenes were finally obtained,with an average length of961.3 nt and N50 length of1339 bp.BLAST analysis indicated that 38802(accounting for 77.30%of the total unigenes),27869(55.52%),14725(29.34%),22225(44.28%),37317(74.35%),25863(51.53%),26137(52.07%)unigenes were successfully annotated in the NR,Swiss-port,KEGG,KOG,gNOG,GO,and Pfam databases,respectively.Curcuma longa and Musa acuminata subsp.malaccensis have the most homologous sequences.GO classification contained 50 sub groups with the basic three major groups,including biological process,cellular component,and molecular func tion.KOG functional classification obtains 25 different functional groups,involving 128 KEGG metabolic pathways,including 21 secondary metabolic pathways.Of all unigenes,3718 unigenes were annotated in the plant resistance gene(PRG)database.Using MISA prediction,7183 simple sequence repeats(SSRs)were obtained,and the number of three-nucleotide SSRs was the largest,with 3615(50.33%).Among them,the proportion of CCG/CGG type was the highest.This study obtained a large amount of Curcuma longa transcriptome sequence information and SSR information,which provides a data resource and theoretical foundation for the subsequent mining of turmeric functional genes and analysis of secondary metabolic pathways.