茶树PPR基因家族全基因组鉴定及白化相关基因表达分析

doi:10.13305/j.cnki.jts.2021.02.002

茶叶科学 ›› 2021, Vol. 41 ›› Issue (2): 159-172.doi: 10.13305/j.cnki.jts.2021.02.002

茶树PPR基因家族全基因组鉴定及白化相关基因表达分析

刘丁丁^1,2, 王君雅^1,2, 汤榕津^1,2, 陈亮^1,*, 马春雷^1,*

1.中国农业科学院茶叶研究所/国家茶树改良中心/农业部茶树生物学与资源利用重点实验室,浙江杭州 310008;
2.中国农业科学院研究生院,北京 100081

收稿日期:2020-07-13 修回日期:2020-09-15 出版日期:2021-04-15 发布日期:2021-04-13
通讯作者: *liangchen@tricaas.com;malei220@tricaas.com
作者简介:刘丁丁,女,硕士研究生,主要从事茶树资源育种与遗传改良研究。
基金资助:
中国农业科学院科技创新工程（CAAS-ASTIP-2017-TRICAAS）、现代农业产业技术体系（CARS-19）、浙江省农业（茶树）新品种选育重大科技专项子课题（2016C02053-5）、中国农业科学院茶叶研究所基本科研业务费（1610212017008、1610212019004）

Genome-wide Identification of PPR Gene Family and Expression Analysis of Albino Related Genes in Tea Plants

LIU Dingding^1,2, WANG Junya^1,2, TANG Rongjin^1,2, CHEN Liang^1,*, MA Chunlei^1,*

1. Tea Research Institute of the Chinese of Agricultural Sciences, National Center for Tea Improvement, Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Hangzhou 310008, China;
2. Graduate School of Chinese Academy of Agriculture Science, Beijing 100081, China

Received:2020-07-13 Revised:2020-09-15 Online:2021-04-15 Published:2021-04-13

摘要/Abstract

摘要： 三角状五肽（PPR）蛋白作为一类靶向定位于半自主细胞器的序列特异性RNA结合蛋白,在植物的生长发育过程中具有重要的作用。本研究基于茶树基因组数据,利用生物信息学方法对茶树CsPPR基因家族进行系统鉴定,并对其蛋白质理化性质、结构域保守性、亚细胞定位、基因结构、染色体定位与分布等进行了分析。结果表明,在茶树基因组数据中共鉴定到858个CsPPR基因,分属于P和PLS两个亚家族;结构域分析表明各个结构域在茶树中比较保守;亚细胞定位结果显示超过一半的CsPPR蛋白定位于叶绿体;基因结构分析表明茶树CsPPR基因家族中共有31%的CsPPR基因不具有内含子结构,并且家族成员在进化过程中发生过多次基因复制事件。另外,为探究茶树CsPPR基因家族在调控茶树白化相关基因表达过程中的作用,对正常叶色品种舒茶早和安吉黄茶等5个白化茶树品种进行转录组测序,共筛选到24个差异共表达CsPPR基因,并利用实时荧光定量PCR技术对其在不同品种和不同组织中的表达模式进行了分析,结果显示大多数CsPPR基因在新梢、成熟叶和茎中高表达,但在花和根中痕量表达。本研究结果可为茶树CsPPR家族成员的基因克隆和功能研究提供参考。

关键词: 茶树, PPR基因家族, 转录组, 生物信息学, 实时荧光定量PCR

Abstract: Pentatricopeptide repeat (PPR) proteins are a kind of sequence-specific RNA binding proteins and targeted at semi-autonomous organelles, which play essential roles in play growth and development. In this study, the CsPPR genes were systematically identified by bioinformatics analysis based on the tea genome data. Then, their subcellular localization, physicochemical properties, gene structures, the chromosome locations and distribution were analyzed. The results show that a total of 858 putative CsPPR members were obtained from the genome data, which belong to P and PLS subfamilies. Domain analysis shows that each domains were relatively conservative in tea plants. Subcellular localization prediction indicates more than half of CsPPR proteins were located in the chloroplasts. Gene structure analysis shows that 31% of CsPPR genes lacked intron and the gene family had undergone extensive gene duplication events in the process of evolution. Subsequently, In order to investigate the role of CsPPR gene family in regulating the gene expressions of albino tea plants, transcriptome analysis was performed on the normal leaf color cultivar ‘Shuchazao’ and five albino tea cultivars such as ‘Anji Huangcha’. And 24 differential co-expressed CsPPR genes were identified from transcriptome data of five groups, and the real-time quantitative PCR technology was used to analysis the expression pattern of the 24 CsPPR genes in different cultivars and tissues of tea plants, and the results show that the majority of them were highly expressed in shoots, mature leaves and stems. The research results would provide a basis for CsPPR gene cloning and functional research.

Key words: tea plants, PPR gene family, transcriptome, bioinformatics, real-time quantitative PCR

中图分类号:

刘丁丁, 王君雅, 汤榕津, 陈亮, 马春雷. 茶树PPR基因家族全基因组鉴定及白化相关基因表达分析[J]. 茶叶科学, 2021, 41(2): 159-172. doi: 10.13305/j.cnki.jts.2021.02.002.

LIU Dingding, WANG Junya, TANG Rongjin, CHEN Liang, MA Chunlei. Genome-wide Identification of PPR Gene Family and Expression Analysis of Albino Related Genes in Tea Plants[J]. Journal of Tea Science, 2021, 41(2): 159-172. doi: 10.13305/j.cnki.jts.2021.02.002.

参考文献

[1] Claire L, Charles A, Sebastien A, et al.Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis[J]. The Plant Cell, 2004, 16(8): 2089-2103.
[2] Small I D, Peeters N.The PPR motif-a TPR-related motif prevalent in plant organellar proteins[J]. Trends Biochem Sci, 2000, 25(2): 46-47.
[3] Dipnarayan S, Prasad A M, Ramamurthy S.Pentatricopeptide repeat proteins and their emerging roles in plants[J]. Plant Physiology and Biochemistry, 2007, 45(8): 521-534.
[4] Barkan A, Waller M, Nolasco M.A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms[J]. EMBO J, 1994, 13(13): 3170-3181.
[5] Sam M.An overview of pentatricopeptide repeat proteins and their applications[J]. Bochimine, 2015, 113: 93-99.
[6] Schmitz-Linneweber C, Small I.Pentatricopeptide repeat proteins: a socket for organelle gene expression[J]. Trends Plant Sci, 2008, 13(12): 663-670.
[7] 陈龙. 水稻淡绿叶基因PGL12的克隆与功能分析[D]. 武汉: 华中农业大学, 2019: 40-42.
Chen L.Cloning and functional analysis of PALE-GREEN LEAF 12 in rice [D]. Wuhan: Huazhong Agricultural University, 2019: 40-42.
[8] 陈璐. 水稻低温条件下叶绿体发育必需基因TCM8的克隆与功能分析[D]. 上海: 上海师范大学, 2019: 27-29.
Chen L.Cloning and functional analysis of essential gene TCM8 for chloroplast development under low temperature conditions in rice (Oryza sativa L.) [D]. Shanghai: Shanghai Normal University, 2019: 27-29.
[9] 葛生珍. 水稻黄化突变体xnt7的生理特性和基因精细定位[D]. 重庆: 西南大学, 2014: 28-33.
Ge S Z.Physiological characteristics of a xanthic mutant and fine-mapping of its related gene xnt7 in rice [D]. Chongqing: Southwest University, 2014: 28-33.
[10] 简磊, 王仲康, 曾冬冬, 等. 水稻白化转绿突变体albg的鉴定和基因精细定位[J]. 核农学报, 2017, 31(12): 2289-2297.
Jian L, Wang Z K, Zeng D D, et al.Characterization and fine mapping of a green-revertible albino (albg) mutant in rice[J]. Journal of Nuclear Agricultural Sciences, 2017, 31(12): 2289-2297.
[11] 尚丽娜, 陈新龙, 米胜南, 等. 水稻温敏型叶片白化转绿突变体tsa2的表型鉴定与基因定位[J]. 作物学报, 2019, 45(5): 662-675.
Shang L N, Chen X L, Mi S N, et al.Phenotypic identification and gene mapping of temperature-sensitive green revertible albino mutant tsa2 in rice (Oryza sativa L.)[J]. Acta Agronomica Sinica, 2019, 45(5): 662-675.
[12] 何鹏, 张丽华, 牟亚楠, 等. 棉花叶片黄化基因GhYL1的筛选、鉴定及功能分析[C]//中国农学会棉花分会2017年年会暨第九次会员代表大会论文汇编. 安阳: 棉花学报, 2017: 38.
He P, Zhang L H, Mou Y N, et al.Dentification and functional analysis of yellow variegated leaf gene GhYL1 in cotton[C]//2017 Annual Meeting of the Cotton Branch of Chinese Agricultural Association and the Ninth Member Congress. Anyang: Cotton Science, 2017: 38.
[13] 袁玲. 白叶1号阶段性返白过程中差异表达基因的分离及部分基因全长cDNA克隆[D]. 长沙: 湖南农业大学, 2012: 29-39.
Yuan L.Separation of differentially expressed genes and full length cDNA cloning of selective genes during periodic albinism in Anjibaicha(Camellia sinensis) [D]. Changsha: Hunan Agricultural University, 2012: 29-39.
[14] Punta M, Coggill P C, Eberhardt R Y.The pfam protein families database[J]. Nucleic Acids Research, 2012, 40(1): 290-301.
[15] Simon C P, Aurelien L, Sean R.E, et al. HMMER web server: 2018 update[J]. Nucleic Acids Research, 2018, 46: 200-204.
[16] Finn R D, Clements J, Eddy SR.HMMER web server: interactive sequence similarity searching[J]. Nucleic Acids Res, 2011, 39: 29-37.
[17] Xia E H, Zhang H B, Sheng J, et al.The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis[J]. Molecular Plant, 2017, 10(6): 866-877.
[18] Wei C L, Yang H, Wang S B, et al.Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality[J]. PNAS, 2018, 115(18): E4151-E4158.
[19] Chen J D, Zheng C, Ma J Q, et al.The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization ebent in tea plant[J]. Horticulture Research, 2020, 7: 63. doi: 10.1038/s41438-020-0288-2.
[20] Xia E H, Tong W, Hou Y, et al.The reference genome of tea plant and resequencing of 18 diverse accessions provide insights into genome evolution and adaptation of tea plants[J]. Molecular Plant, 2020, 13(6/7): 1013-1026.
[21] Zhang Q J, Li W, Li K, et al.The chromosome-level reference genome of tea tree unveils recent bursts of non-autonomous LTR retrotransposons to drive genome size evolution[J]. Molecular Plant, 2020, 13(7): 935-938.
[22] 韦雪芳, 王冬梅, 刘思, 等. 信号肽及其在蛋白质表达中的应用[J]. 生物技术通报, 2006(6): 38-42.
Wei X F, Wang D M, Liu S, et al.Signal sequence and its application to protein expression[J]. Journal of Biotechnology, 2006(6): 38-42.
[23] 谭晖, 官春云. 甘蓝型油菜PPR家族生物信息学分析与新疆野生油菜候选育性基因克隆[J]. 作物研究, 2017, 31(3): 246-255.
Tan H, Guan C Y.Bioinformatics analysis of PPR family in Brassica napus L. and cloning of candidate restorer gene of Xinjiang wild rapeseed[J]. Crop Research, 2006, 31(3): 246-255.
[24] Nicholas O, Mitsuru H, Charles A, et al.On the expansion of the pentatricopeptide repeat gene family in plants[J]. Society of Molecular Biology and Evolution, 2008, 25: 1120-1128.
[25] 丁安明. 番茄与烟草PPR基因家族分析及育性相关基因功能研究[D]. 北京: 中国农业科学院, 2014.
Ding A M.Identification of PPR gene family in N.tomentosiformis and tomato and function analysis of Rf-related genes in tobacco [D]. Beijing: Chinese Academy of Agricultural Sciences, 2014.
[26] Xing H T, Fu X K, Yang C.et al.Genome-wide investigation of pentatricopeptide repeat gene family in poplar and their expression analysis in response to biotic and abiotic stresses[J]. Scientific Reports, 2018, 8: 2817. doi: 10.1038/s41598-018-21269-1.
[27] 郭彩娟, 公杰, 刘永杰, 等. 全基因组小麦PPR基因家族鉴定及表达分析[J]. 生物技术通报, 2019, 35(8): 1-8.
Guo C J, Gong J, Liu Y J, et al.Genome-wide bioinformatics identification of PPR gene family and expression profiles analysis in wheat[J]. Journal of Biotechnology, 2019, 35(8): 1-8.
[28] Liu J M, Xu Z S, Lu P P, et al.Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet[J]. BMC Genomics. 2016, 17(1): 840. doi: 10.1186/s12864-016-3184-2.
[29] Chen G, Zou Y, Hu J, et al.Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments[J]. BMC Genomics, 2018, 19(1): 720. doi: 10.1186/s12864-018-5088-9.
[30] 倪晨子. 水稻PPR基因OsPGL1功能的初步分析[D]. 武汉: 武汉大学, 2017: 38-39.
Ni C Z.An initial function analysis of the PPR gene OsPGL1 in rice (Oryza sativa L.) [D]. Wuhan: Wuhan University, 2017: 38-39.
[31] 高媛媛. 水稻PPR蛋白基因TCD34的克隆与功能分析[D]. 上海: 上海师范大学, 2020: 27-36.
Gao Y Y.Cloning and functional analysis of PPR gene TCD34 in rice (Oryza sativa L.) [D]. Shanghai: Shanghai Normal University, 2020: 27-36.
[32] Du L, Zhang J, Qu S F, et al.The pentratricopeptide repeat protein pigment-defective mutant2 is involved in the regulation of chloroplast development and chloroplast gene expression in Arabidopsis[J]. Plant and Cell Physiology, 2017, 4(58): 747-759.
[33] Cushing D A, Forsthoefel N R, Gestaut D R, et al.Arabidopsis emb175 and other ppr knockout mutants reveal essential roles for pentatricopeptide repeat (PPR) proteins in plant embryogenesis[J]. Planta, 2005, 221: 424-436.
[34] Karin M, Susanne F, Takahiro N, et al.HCF152, an Arabidopsis RNA Binding Pentatricopeptide Repeat Protein Involved in the Processing of Chloroplast psbB-psbT-psbH-petB-petD RNAs[J]. Plant Cell, 2003, 15(6): 1480-1495.

茶树PPR基因家族全基因组鉴定及白化相关基因表达分析

Genome-wide Identification of PPR Gene Family and Expression Analysis of Albino Related Genes in Tea Plants

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