龙眼RDRP基因家族的全基因组鉴定与功能预测

Genome-wide identification and functional prediction of the RDRP gene family in Dimocarpus longan Lour.

为了解龙眼RNA依赖的RNA聚合酶基因(RDRP)家族的生物学功能,采用生物信息学分析方法对龙眼RDRP家族基因成员进行鉴定,并且对其染色体定位、分子进化树、启动子顺式作用元件、蛋白质结构域、蛋白质二级和三级结构、蛋白质互作、可变剪接类型以及在体胚发生过程中差异表达的FPKM值进行分析.结果显示:龙眼RDRP家族基因包括10位成员,分别定位在1、8、9、11、15号共5条染色体上.通过龙眼与拟南芥、水稻构建的进化树分析,将其分为4类,分别为DlRDR1、DlRDR2、DlRDR4、DlRDR6.龙眼RDRP成员启动子包含多种植物激素以及低温、干旱等非生物胁迫的元件.龙眼RDRP家族均含有RDRP保守结构域,其蛋白质家族成员二级、三级结构较为相似,并且与特异性核酸内切酶(DCL)蛋白互作关系密切,同时也与基因沉默蛋白抑制剂3(SGS3)、依赖DNA的RNA聚合酶(NRPD1A)发生互作.不同体细胞胚发生阶段与不同组织部位的可变剪接事件以内含子剪接为主.龙眼体细胞胚不同阶段的表达模式分析中,龙眼RDRP在非胚性阶段显著上调.本研究表明龙眼RDRP家族成员能够响应植物激素的应答并且参与龙眼体胚和不同组织部位生长发育调控.

Bioinformatics analysis was used to clarify the biological functions of RNA-dependent RNA polymerase(RDRP)gene families in longan,and their chromosomal locations;molecular evolutionary tree;cisacting promoter element;protein domain,secondary and tertiary structure,and interaction;alternative splicing types;and FPKM values were analyzed in somatic embryos.The results showed that the RDRP family in longan consisted of 10 members located on a total of 5 chromosomes,namely chromosomes 1,8,9,11,and 15.By analyzing an evolutionary tree constructed using Dimocarpus longan Lour.,Arabidopsis,and Oryza sativa,the genes were divided into four categories:DlRDR1,DlRDR2,DlRDR4,and DlRDR6.The RDRP family in longan contains an RDRP conserved domain while its protein family members have similar secondary and tertiary structures that can be associated with SGS3 and NRPD1A;this is particularly true of DCL proteins.Intron retention was the main splicing event at different stages of the somatic embryo and at different tissue sites.The analysis of gene expression patterns at different stages of somatic embryo development in the longan showed that RDRP was significantly upregulated in the non-embryonic stage.This study clarified how RDRP family members respond to plant hormones and participate in the growth and regulatory development of somatic embryos and different tissue parts in longan.