日本落叶松木质部发育相关基因筛选及其共表达网络构建

Screening and Co-Expression Network Building of Xylem Development-Related Genes in Larix kaempferi

【目的】鉴定日本落叶松木质部发育相关基因,构建核心基因与木质部发育相关基因的共表达网络,为后期开展日本落叶松木材形成相关研究提供参考。【方法】对日本落叶松木质部、韧皮部和针叶3个组织进行二代和三代转录组测序,利用R软件的DEseq2包筛选木质部相对韧皮部和木质部相对针叶的差异表达基因,通过整合2组差异基因获得木质部特异表达基因,借助GO、KEGG及BLASTN等生物信息学分析手段探索基因功能,利用WGCNA分析构建木质部特异表达基因共表达网络。【结果】共获得2596个木质部特异的高表达和低表达基因;GO分析结果显示这些基因在代谢过程、细胞过程、定位膜、细胞、细胞组件、催化活性、位点结合和转运活性等分类中显著富集;KEGG分析结果显示这些基因在淀粉和蔗糖代谢、类黄酮生物合成和代谢途径通路中显著富集,在苯丙烷代谢途径及淀粉和蔗糖代谢途径中分别富集到38个和196个基因;鉴定出木材形成相关基因,包括木质素合成相关基因PAL4、CCR1、C4H、HCT、COMT1、PER12、PER52、CYP98A3、LAC12和LAC17等,纤维素和半纤维素合成相关基因DEC、CEL1、Csl、CTL2和SPS3等;2596个木质部特异的高表达和低表达基因经WGCNA分析后筛选出与木质部发育相关基因关联度较高的17个核心基因。【结论】筛选的日本落叶松木质部发育相关基因参与半乳甘露聚糖合成、木葡聚糖合成、纤维素微纤丝形成、细胞壁纤维素合成、次生细胞壁形成过程、纤维伸长过程、调控合成木质素的碳代谢流、木质素生物合成及降解、木质素单体聚合、木质素单体甲基化和细胞程序化死亡等木材形成相关生物学过程;在共表达网络中筛选出的17个核心基因可作为今后研究的重点来探索其在木材形成过程中的具体功能。

【Objective】In this study,we identified xylem development-related genes in differentiating xylem of Larix kaempferi and built a gene co-expression network among hub genes and xylem development-related genes,aiming to provide reference for wood formation-related studies in L.kaempferi in future.【Method】Illumia-seq and SMRT-seq were used to sequence xylem,phloem and needles of L.kaempferi;The differential expressed genes(DEGs)between xylem and phloem and between xylem and needles were identified by DEseq2 package in R software.The specifically expressed genes in differentiating xylem were obtained by comparing DEGs in the two parallel groups.The functions of these xylem-specific genes were predicted using GO,KEGG and BLASTN method.WGCNA method was used to build a co-expression network.【Result】We obtained 2596 genes in total that were specifically up or down regulated in the differentiating xylem of L.kaempferi;GO analysis showed that these genes were mainly enriched in metabolic process,cellular process,localization,membrane,cell,cell part,catalytic activity,binding and transporter activity.KEGG analysis showed that these genes were significantly enriched in starch and sucrose metabolism,flavonoid biosynthesis and metabolic pathways.38 and 196 genes were enriched in phenylpropanoid biosynthesis and starch and sucrose metabolism pathway,respectively;In the differentiating xylem of L.kaempferi,lignin formation-related genes were identified including PAL4,CCR1,C4H,HCT,COMT1,PER12,PER52,CYP98A3,LAC12 and LAC17,and cellulose and hemicellulose formation-related genes were identified including DEC,CEL1,Csl,CTL2 and SPS3.All 2596 up or down regulated genes were analysed by WGCNA method,17 hub genes having close relationship with wood formation-related genes were obtained.【Conclusion】Xylem development-related genes in Larix kaempferi participate in biological processes of wood formation such as galactomannan biosynthesis,xyloglucan biosynthesis,microfibrils formation,fiber biosynthesis in cell wall,secondary cell wall formation,fiber elongation,carbon flux to lignins,biosynthesis and degradation of lignin,monolignol polymerization,monolignol methylation and programmed cell death;the 17 hub genes in gene co-expression network are candidates for function exploration during wood formation in future.