四个竹秆变异毛竹变型的全基因组序列分析

Genomic sequence analysis of four culm variants of Moso bamboo(Phyllostachys edulis)on culm

关键词:  毛竹, 变型, 全基因组重测序, 基因注释

Key words:  Moso bamboo(Phyllostachys edulis), variant, whole genome re-sequencing, gene annotation

摘要:

毛竹是我国重要的经济竹种,在长期栽培适应过程中产生了丰富的变异。为揭示毛竹竹秆变异变型的全基因组突变类型,以黄皮毛竹、金丝毛竹、绿皮花毛竹和花毛竹4个毛竹变型为实验材料,采用高通量重测序技术获得全基因组序列,进行单核苷多态性(SNP)、小片段插入缺失(InDel)和结构变异(SV)检测和注释,并将变异基因进行功能注释。结果表明:花毛竹基因组检测得到的基因变异数最多,为12 555个; 金丝毛竹样品变异位点数最少,为11 923个; 4个样品都有7 000多个变异基因得到功能注释。GO注释分类包括细胞组件、分子功能和生物过程三个基因功能分类体系的56个功能组。在细胞组件方面,叶绿素合成相关基因有2 431个; 在生物过程方面,参与类胡萝卜素合成过程的基因有75个,参与花青素合成过程中的调控以及紫外光下组织中花青素积累的相关基因有80个。COG分类表明参与复制、重组和修复的基因数为369个,信号转导机制的基因数为291个,转录的相关基因为222个。通过KEGG数据库系统地分析变异基因参与的黄酮类、类胡萝卜素等物质代谢合成途径。深入研究这些差异基因的调控途径,从DNA水平上解释竹秆的变异机制,可为深入研究毛竹种内丰富的多态性和遗传变异提供数据支持,阐析不同变异类型的基因家族、功能基因等遗传基础。

Abstract:

As an important and economic bamboo species in China, Moso bamboo has performed lots of variations with long-term cultivation conditions. For an overall understanding of the whole genome of four representative culm variations, Phyllostachys edulis f. holochrysa, P. edulis f. gracilis, P. edulis f. nabeshimana and P. edulis f. huamozhu, re-sequencing was used for high-throughput sequencing to detect its variations by molecular data. The single nucleotide polymorphism(SNP), insertion-deletion(InDel)and structure variation(SV)were detected and annotated, and the mutant genes were compared with the functional databases. The results were as follows: Phyllostachys edulis f. gracilis had the lowest number of mutation sites, that was 11 923, andP. edulis f. huamozhu had the highest number 12 555, of which more than 7 000 mutant genes were annotated. GO annotation classification included 56 functional groups of three functional classification systems: cellular component, molecular function and biological processes. In terms of cell components, there were 2 431 genes related to chlorophyll synthesis. In terms of biological processes, there were 75 genes involved in the synthesis of carotenoids and 80 ones involved in the regulation of anthocyanin synthesis and anthocyanin accumulation in tissues under ultraviolet light. COG classification showed that 369 genes involved in replication, recombination and repair, 291 ones in signal transduction mechanism, and 222 ones in transcription. The metabolic pathways of flavonoids, carotenoids and other substances involved in the mutant genes were analyzed by KEGG database. In-depth study of the regulatory pathways and interpretation of the variation mechanism on culm from the DNA level, can provide a data basis for further exploration of the rich polymorphism and genetic variation of Moso bamboo, and elucidate the genetic basis of gene family and functional genes of different variation types.