Bioinformatics analysis of CRM gene family in Brassica rapa

doi:10.14088/j.cnki.issn0439-8114.2021.09.029

Abstract

Abstract: The CRM（Chloroplast RNA splicing and ribosome maturation） genes involve in the splicing of genes containing group Ⅱ introns in mitochondria and chloroplast genome in plants. In the present study, gene number, conserved motif, isoelectric point of amino acids, molecular evolution, and expression pattern of CRM family of Brassica rapa（AA,2n=20） were well analyzed based on the bioinformatic methods. A total of 22 genes belonging to CRM gene family were identified in the B. rapa genome. These genes could be divided into three subgroups, and distributed on all the chromosomes of B. rapa except chromosome A10. The coding sequences of CRM genes ranged from 657 bp to 5 909 bp, and the isoelectric point of amino acids of these genes ranged from 4.42 to 9.89. The CRM genes in B. rapa showed specific expression in different tissues and response to different stresses, and some CRM genes were actively transcribed in leaves and stems. After dealt with Flg22 and Ps stress which can be used to simulate biotic stresses, some CRM genes significantly down-regulated, indicating these genes likely responded to the biotic stresses.

Key words: Brassica rapa, CRM gene family, bioinformatics, biotic stress

CLC Number:

S565.4
Q819

ZHU Bin, WANG Xiao-shuang, LUO Xi, HU Xin. Bioinformatics analysis of CRM gene family in Brassica rapa[J]. HUBEI AGRICULTURAL SCIENCES, 2021, 60(9): 141-146.

References

[1] ASAKURA Y, BARKAN A.A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts[J].Plant cell,2007, 19(12): 3864-3875.
[2] ANDEOL F, IAN D, CLAIRE L.Nuclearly encoded splicing factors implicated in RNA splicing in higher plant organelles[J]. Molecular plant,2010, 3(4):691-705.
[3] ZMUDJAK M, COLAS C, KEREN I, et al.mCSF1, a nucleus-encoded CRM protein required for the processing of many mitochondrial introns, is involved in the biogenesis of respiratory complexes I and IV in Arabidopsis[J]. New phytolgist, 2013, 199:379-394.
[4] LEE K,PARK S J,PARK Y I,et al.CFM9, a mitochondrial CRM protein, is crucial for mitochondrial intron splicing, mitochondria function and Arabidopsis growth and stress responses[J]. Plant and cell physiology, 2019, 60(11): 2538-2548.
[5] ZHANG Q, SHEN L, REN D, et al.Characterization of the CRM gene family and elucidating the function of OsCFM2 in rice[J]. Biomolecules, 2020, 10(2): 327.
[6] DE LONGEVIALLE A F, SMALL I D, LURIN C. Nuclearly encoded splicing factors implicated in RNA splicing in higher plant organelles[J]. Molecula plant, 2010, 3(4): 691-705.
[7] CHENG F, LIU S Y, WU J, et al.BRAD, the genetics and genomics database for Brassica plants[J]. BMC plant biology, 2011, 11(1): 136-141.
[8] 李蒙蒙,崔丽洁,钱忠英,等. DNA分子标记在不结球白菜遗传育种中的应用[J]. 上海师范大学学报(自然科学版),2017,46(5) : 720-728.
[9] 赵敬会,王瑞雪,李荣冲,等. 白菜SAUR基因家族的生物信息学分析[J]. 中国农学通报,2012,28(22):130-137.
[10] 张艺思,刘高峰,刘路平,等. 白菜PLD基因家族全基因组鉴定及对高温胁迫的响应[J]. 西北植物学报,2019,39(8):1361-1370.
[11] 庞文玉,王安,杨宝谊,等. 大白菜ENT基因家族的鉴定与生物信息学分析[J]. 江苏农业科学,2019,47(12):52-57.
[12] LARKIN MA, BLACKSHIELDS G, BROWN NP, et al.Clustal W and Clustal X version 2.0[J]. Bioinformatics, 2007, 23(21): 2947-2948.
[13] KUMAR S, STECHER G, TAMURA K.MEGA7:Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Molecular biology and evolution, 2016, 33(7): 1870-1874.
[14] CHEN C, CHEN H, HE Y,et al.TBtools, a toolkit for biologists integrating various biologicaldata handling tools with a user-friendly interface[J]. Molecular biology and evolution, 2018, 33(7): 1870-1874.
[15] KLEIN A P, SATTELY E S.Two cytochromes P450 catalyze S-heterocyclizations in cabbage phytoalexin biosynthesis[J]. Nature chemical biology, 2015, 11(11):837-839.
[16] KATHARINA M,DELPHINE C,MARKUS A,et al.Contamination risks in work with synthetic peptides:Flg22 as an example of a pirate in commercial peptide preparations[J]. Plant cell,2012,24(8):3193-3197.
[17] NOBUAKI I, HIROFUMI Y.Post-translational regulation of WRKY transcription factors in plant immunity[J]. Current opinion in plant biology, 2012, 15(4):431-437.
[18] 刘艳霞. 两个水稻叶绿体发育相关基因TCD10和OsCRM的功能验证及调控途径[D]. 上海:上海师范大学,2015.
[19] WANG X, WANG H, WANG J, et al.The genome of the mesopolyploid crop species Brassica rapa[J]. Nature genetics, 2011, 43(10): 1035-1039.
[20] ZHANG Q, SHEN L, WANG Z, et al.OsCAF1, a CRM domain containing protein, influences chloroplast development[J]. International journal of molecular science, 2019, 20(18): 4386.
[21] ZHANG Q, WANG Y, SHEN L, et al.OsCRS2 encoding a peptidyl-tRNA hydrolase protein is essential for chloroplast development in rice[J]. Plant growth regulation, 2020, 92(3): 535-545.
[22] LEE K, LEE H J, KIM D H, et al.A nuclear-encoded chloroplast protein harboring a single CRM domain plays an important role in the Arabidopsis growth and stress response[J]. BMC plant biology, 2014, 14(1): 1-11.