|Table of Contents|

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

Chinese Journal of Applied & Environmental Biology[ISSN:1006-687X/CN:51-1482/Q]

Issue:
2021 05
Page:
1364-1371
Research Field:
Articles
Publishing date:

Info

Title:
Genome-wide identification and functional prediction of the RDRP gene family in Dimocarpus longan Lour.
Author(s):
LIN Yiling XU Xiaoping ZHANG Chunyu CHEN Xiaohui ZHANG Zihao & LAI Zhongxiong?
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Keywords:
Dimocarpus longan Lour. RNA-dependent RNA polymerase gene (RDRP) gene family genome-wide identification function analysis
CLC:
-
PACS:
DOI:
10.19675/j.cnki.1006-687x.2020.06063
DocumentCode:

Abstract:
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; cis-acting 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.

References

1 丁超, 张兰, 曹洁, 于文强. RNA依赖的RNA聚合酶(RdRP)与非编码RNA(ncRNA)调控的研究进展[J]. 复旦学报医学版, 2015, 42 (2): 256-261 [Ding C, Zhang L, Cao J, Yu WQ. Research progress on regulation of RNA-dependent RNA polymerase (RdRP) and non-coding RNA (ncRNA) [J]. J Fudan Univ Med Sci, 2015, 42 (2): 256-261]
2 De Farias ST, Junior AP, Rego TG, Jose MV. Origin and evolution of RNA-Dependent RNA Polymerase [J]. Front Genet, 2017, 8: 125
3 Ng KK, Arnold JJ, Cameron CE. Structure-Function relationships among RNA-dependent RNA polymerases [J]. Curr Topics Microbiol Immunol, 2008, 320:137-156
4 Astiermanifacier S, Cornuet P. RNA-dependent RNA polymerase in Chinese cabbage [J]. Biochim Biophysi Acta, 1971, 232 (3): 484-493
5 Mansilla C, Sanchez F, Padgett HS, Pogue GP, Ponz F. Chimeras between oilseed rape mosaic virus and tobacco mosaic virus highlight the relevant role of the tobamoviral RdRp as pathogenicity determinant in several hosts [J]. Mol Plant Pathol, 2009, 10 (1): 59-68
6 Xiao BY,?Li D,?Hui Z,?Chen GD,?Quan SD,?Dian QL,?Yuan YF,?Garcia JA,?Rong XF,?Hui SG. RNA-dependent RNA polymerase 1 from Nicotiana tabacum suppresses RNA silencing and enhances viral infection in Nicotiana benthamiana [J]. Plant Cell, 2010, 22 (4): 1358-1372
7 Mourrain P, Béclin C, Elmayan T, Feuerbach F, Godon C,?Morel J,?Jouette D,?Lacombe A,?Nikic S,?Picault N,?Remoue K,?Sanial M,?Vo T,?Vaucheret H. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance [J]. Cell, 2000, 101 (5): 533-542
8 Deng S, Xu J, Liu J, Kim S,?Shi SH,?Chua N. JMJ24 binds to RDR2 and is required for the basal level transcription of silenced loci in Arabidopsis [J]. Plant J, 2015, 83 (5): 770-782
9 Lam P, Zhao L, Mcfarlane HE, Aiga M,?Lam V,?Hooker TS,?Kunst L. RDR1 and SGS3, Components of RNA-mediated gene silencing, are required for the regulation of cuticular wax biosynthesis in developing inflorescence stems of arabidopsis [J]. Plant Physiol, 2012, 159 (4): 1385-1395
10 和琼姬, 燕飞, 陈剑平. RNA干扰机制及其主要蛋白因子研究进展[J]. 浙江农业学报, 2011, 23 (2): 415-420 [He QJ, Yan F, Chen JP. advances in RNA interference mechanisms and their major protein factors [J]. Acta Agric Zhejiangensis, 2011, 23 (2): 415-420]
11 Qin L, Mo N, Muhammad T,?Liang Y. Genome-Wide analysis of DCL, AGO, and RDR gene families in pepper (Capsicum annuum L.) [J]. Intern Journal Mol Sci, 2018, 19 (4): 1038
12 Adkar-Purushothama CR , Perreault JP . Suppression of RNA-dependent RNA polymerase 6 favors the accumulation of potato spindle tuber viroid in Nicotiana benthamiana [J]. Viruses, 2019, 11 (4): 345
13 Liu Y, Gao Q, Wu B, Ai T, Guo X. NgRDR1, an RNA-dependent RNA polymerase isolated from Nicotiana glutinosa, was involved in biotic and abiotic stresses [J]. Plant Physiol Biochem, 2009, 47 (5): 359-368
14 Rakhshandehroo F, Rezaee S, Palukaitis P. Silencing the tobacco gene for RNA-dependent RNA polymerase 1 and infection by potato virus Y cause remodeling of cellular organelles [J]. Virology, 2017, 510: 127-136
15 Willmann MR, Endres MW, Cook RT, Gregory BD. The functions of RNA-Dependent RNA polymerases in arabidopsis [J]. Arabidopsis Book, 2001, 9:e0146
16 王冕. 棉花RNA依赖的RNA聚合酶6(GhRDR6)基因的分离及功能分析[D]. 泰安: 山东农业大学, 2011 [Wang MY. Isolation and functional analysis of cotton RNA-dependent RNA polymerase 6 (GhRDR6) gene [D]. Tai’an: Shandong Agricultural University, 2011]
17 Zhang K, Shi X, Zhao X, Ding D, Tang JH, Niu JX. Investigation of miR396 and growth-regulating factor regulatory network in maize grain filling [J]. Acta Physiol Plant, 2015, 37 (2): 1-12
18 Campos L, Granell P, Susana Tárraga,?Lopezgresa P, Conejero V, Belles J M, Rodrigo I, Lison P. Salicylic acid and gentisic acid induce RNA silencing-related genes and plant resistance to RNA pathogens [J]. Plant Physiol Biochem, 2014, 77 (2): 35-43
19 Jue D, Sang X, Liu L,Shu B,?Wang YH,?Liu CM,?Xie JH,?Shi SY. Identification of WRKY gene family from Dimocarpus longan and its expression analysis during flower induction and abiotic stress responses [J]. IntJ Mol Sci, 2018, 19 (8): 2169
20 郑炜旋. 龙眼RDR家族全基因组鉴定及其表达分析[D]. 福州: 福建农林大学, 2020 [Zheng WX. Whole-genome identification and expression analysis of RDR family in longan [D]. Fuzhou: Fujian Agriculture and Forestry University, 2020]
21 Lai Z, Lin Y. Analysis of the global transcriptome of longan (Dimocarpus longan Lour.) embryogenic callus using llumina paired-end sequencing [J]. BMC Genomics, 2013, 14 (1): 561
22 ?Lin YL,?Min JM,?Lai RL,?Wu ZY,?Chen YK,?Yu LL,?Cheng CZ,?Jin YC,?Tian QL,?Liu QF,?Liu WH,? Zhang CG,?Lin LX,?Hu Y,?Zhang DM,?Thu MY,?Zhang ZH,?Liu SC,?Zhong CS,?Fang XD,?Wang J, Yang HM,?Varshney RK,?Yin Y,?Lai ZX. Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics [J]. Gigascience, 2017, 6 (5): 1-14
23 Chen CJ,?Chen H,?Zhang Y,?Thomas H R,?Frank?M H,?He?YH,?Xia?R. TBtools - an integrative toolkit developed for interactive analyses of big biological data. Mol Plant, 2020, 13 (8): 1194-1202
24 王云, 彭丽云, 孙雪丽, 高玉莹, 陈晓慧, 陈裕坤, 林玉玲, 赖钟雄. 龙眼Hsf基因家族全基因组鉴定及体胚发生过程中的表达分析[J]. 应用与环境生物学报, 2019, 25 (2): 420-431[Wang Y, Peng LY, Sun XL, Gao YY, Chen XH, Chen YQ, Lin YL, Lai ZX. Genomic identification of the longan Hsf family and expression analysis during somatic embryogenesis [J]. Chin J Appl Environ Biol, 2019, 25 (2): 420-431]
25 高梅, 辛健康, 姜山. 小立碗藓LysM型类受体激酶基因家族生物信息学分析[J]. 广西植物, 2021, 41 (6): 979-988 [Gao M, Xin JK, Jiang S. Bioinformatic analysis of the Lysm-like receptor kinase gene family of Moss sphagnum [J]. Plants Guangxi, 2021, 41 (6): 979-988]
26 罗旭东, 丁莉, 叶祥东, 李珊, 陈宗运. Swiss-PDB Viewer软件在蛋白质结构与功能教学中的应用[J]. 基础医学教育, 2019, 21 (7): 562-564 [Luo XD, Ding L, Ye XD, Li S, Chen ZY. Application of swiss-pdb Viewer in protein structure and function teaching [J]. Basic Med Educ, 2019, 21 (7): 562-564]
27 Li FF, Wang YQ, Zhou XP. SGS3 Cooperates with RDR6 in triggering geminivirus-induced gene silencing and in suppressing geminivirus infection in Nicotiana benthamiana [J]. Viruses, 2017, 9 (9): 247
28 冯雅岚, 熊瑛, 张均, 原佳乐, 蔡艾杉, 马超. 可变剪切在植物发育和非生物胁迫响应中的作用[J]. 核农学报, 2020, 34 (1): 62-70 [Feng YL, Xiong Y, Zhang J, Yuan JL, Cai AS, Ma C. Effects of variable shear on plant development and abiotic stress response [J]. J Nucl Agric, 2020, 34 (1): 62-70.?]
29 Kapoor M, Arora R, Lama T, Nijhawan A, Khurana JP, Tyagi AK, Kapoor S. Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analysis during reproductive development and stress in rice [J]. BMC Genomics, 2008, 9 (1): 451-451
30 Sabbione A, Daurelio LD, Vegetti AC. Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis [J]. BMC Plant Biol, 2019, 19 (1): 1-13
31 Gan D, Liang D, Wu J, Talon M, Tadeo FR, Dotto MC. Genome-Wide identification of the Dicer-like, Argonaute, and RNA-dependent RNA polymerase gene families in cucumber (Cucumis sativus L.) [J]. J Plant Growth Regul, 2016, 35 (1): 135-150
32 Bai M, Yang G, Chen W, Mao ZC,?Kang HX,?Chen GH,?Yang YH,?Xie BY. Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum [J]. Gene, 2012, 501 (1): 52-62
33 逯晓明, 于成明, 王国鲁, 王德亚, 耿国伟, 刘珊珊, 师科荣, 原雪峰. 烟草丛顶病毒RNA依赖RNA聚合酶(RdRp)介导的体外复制体系[J]. 植物病理学报, 2017, 47 (6): 790-796 [Lu XM, Yu CM, Wang GL, Wang DY, Geng GW, Liu SS, Shi KR, Yuan XF. In vitro replication system mediated by RdRp-dependent RNA polymerase of tobacco Plexus topiruses [J]. J Plant Pathol, 2017, 47 (6): 790-796]
34 Hunter LJ, Brockington SF, Murphy AM, Pate AE,?Gruden K,?Macfarlane SA,?Palukaitis P,?Carr JP. RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases [J]. Sci Rep, 2016, 6 (1): 23082-23082
35 Garciaruiz H, Takeda A, Chapman EJ, Sullivan CM,?Fahlgren N,?Brempelis KJ,?Carrington JC. Arabidopsis RNA-dependent RNA polymerases and Dicer-like proteins in antiviral defense and small interfering RNA biogenesis during turnip mosaic virus infection [J]. Plant Cell, 2010, 22 (2): 481-496
36 Jia Y, Lisch D, Ohtsu K, Scanlon MJ,?Nettleton D,?Schnable PS. Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs [J]. PLOS Genet, 2009, 5 (11):?e1000737
37 Cao JY, Xu YP, Li W, Li SS. Genome-wide identification of Dicer-Like, Argonaute, and RNA-dependent RNA polymerase gene families in brassica species and functional analyses of their Arabidopsis homologs in resistance to Aclerotinia sclerotiorum [J]. Front Plant Sci, 2016, 7 (1): 1614
38 Dong XZ, Spiering MJ, Nuss DL. Characterizing the roles of Cryphonectria parasitica RNA-dependent RNA polymerase-like genes in antiviral defense, viral recombination and transposon transcript accumulation [J]. PLoS ONE, 2014, 9 (9): e108653
39 Jauvion V, Rivard M, Bouteiller N, Elmayan T, Vaucheret H. RDR2 partially antagonizes the production of RDR6-dependent siRNA in sense transgene-mediated PTGS [J].?PLoS ONE, 2012, 7 (1): e29785
40 Bouche N, Lauressergues D, Gasciolli V, Vaucheret H. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs [J]. EMBO J, 2006, 25 (14): 3347-3356
41 Yang H, Wang M, Gao Z, Zhu C, Guo X. Isolation of a novel RNA-dependent RNA polymerase 6 from Nicotiana glutinosa, NgRDR6, and analysis of its response to biotic and abiotic stresses [J]. Mol Biol Rep, 2011, 38 (2): 929-937
42 王娜. 苹果YTH结构域RNA结合蛋白基因MhYTP1和MhYTP2的功能研究[D]. 咸阳: 西北农林科技大学, 2017 [Wang N. Functional study of apple YTH domain RNA-binding protein genes MhYTP1 and MhYTP2 [D]. Xianyang: Northwest A&F University, 2017]
43 肖畅, 彭婷. 植物应答非生物胁迫的信号转导途径研究进展[J]. 陕西农业科学, 2020, 66 (2): 72-81 [Xiao C, Peng T. Advances in signal transduction pathways in plant response to abiotic stress [J]. Shaanxi Agric Sci, 20, 66 (2): 72-81]
44 Makeyev EV, Bamford DH. Cellular RNA-dependent RNA polymerase involved in posttranscriptional gene silencing has two distinct activity modes [J]. Mol Cell, 2002, 10 (6): 1417-1427
45 吴冰月, 宋普文, 陈华涛, 崔瑾, 许晓明, 陈新. 2个大豆RNA依赖的RNA聚合酶基因GmRDR6a和GmRDR6b的克隆与分析[J]. 南京农业大学学报, 2014, 37 (3): 27-34 [Wu BY, Song PW, Chen HT, Cui J, Xu XM, Chen X. Cloning and analysis of two RNA polymerase genes GMRDR6A and GMRDR6B in soybean [J]. J Nanjing Agric Univ, 2014, 37 (3): 27-34]
46 李永红, 彭坚, 鲁朝辉, 许柏球, 俞征瑶, 房远林. 四季花龙眼冬梢结果母枝花芽分化过程中内源激素含量变化研究[J]. 中国果树, 2013 (4): 15-18 [Li YH, Peng J, Lu QH, Xu BC, Yu ZY, Fang YL. Changes of endogenous hormone content in the differentiation of flower buds in the mother branch of winter shoot of longan [J]. China Fruiting Tree, 2013 (4): 15-18]
47 牟望舒. 脱落酸及脱落酸-乙烯互作调控番茄果实成熟的效应与机理[D]. 杭州: 浙江大学, 2019 [Mou WS. Effect and mechanism of abscisic acid and abscisic acid-ethylene interaction on tomato fruit ripening [D]. Hangzhou: Zhejiang University, 2019]
48 Xu L,?Yang L,?Pi LM,?Liu QL,?Ling QH,?Wang H,?Poethig RS,?Huang H. Genetic interaction between the AS1-AS2 and RDR6-SGS3-AGO7 pathways for leaf morphogenesis [J]. Plant Cell Physiol, 2006, 47 (7): 853-863
49 Li ZF,?Li DN,?Li BY,?Liu YH,?Niu XP,?Aslam M,?Cai HY,?Su ZS,?Qin Y. Genome-wide identification, characterization of RDR genes and their expression analysis during reproductive development and stress in Pineapple [J]. Trop Plant Biol, 2020, 13 (1): 1-10
50 陈晓慧. 龙眼体胚发生过程中DlDCLs的克隆与功能分析[D]. 福州: 福建农林大学, 2018 [Chen XH. Cloning and functional analysis of DlDCLs during somatic embryo development in longan [D]. Fuzhou: Fujian Agriculture and Forestry University, 2018]

Memo

Memo:
-
Last Update: 2021-10-25