Identification and codon bias of NBS-LRR gene family in Brassica napus

FENG Shu-yan,CHEN Hui-long,LI Qiang,WANG Li-xia,ZHANG Wei-meng,WANG Tong,CUI Chun-lin,LI Miao-miao,YU Ying,NIE Fu-lei*,SONG Xiao-ming*

CHINESE JOURNAL OF OIL CROP SCIENCES ›› 2019, Vol. 41 ›› Issue (6) : 858.

PDF(8208 KB)
Welcome to CHINESE JOURNAL OF OIL CROP SCIENCES, May. 10, 2025
PDF(8208 KB)
CHINESE JOURNAL OF OIL CROP SCIENCES ›› 2019, Vol. 41 ›› Issue (6) : 858. DOI: 10.19802/j.issn.1007-9084.2019017

Identification and codon bias of NBS-LRR gene family in Brassica napus

Author information +
History +

Abstract

NBS-LRR (nucleotide binding site and leucine rich repeat) is a large complex gene family playing important role in plant disease resistance. For better understanding of NBS-LRR gene family in Brassica napus (L.), bioinformatics analyses were conducted in B. napus and other 4 species (B. oleracea, B. rapa and Arabidopsis thali? ana and Oryza sativa). As a whole, family identification, phylogenetic analysis, conserved motif, gene structure, chromosome localization and codon bias were analyzed. Results showed that 463 NBS-LRR members were identi? fied in B. napus. Referenced by A. thaliana, the members were divided into 2 groups, TIR-NBS-LRR and CCNBS- LRR, which were further divided into 4 and 8 subgroups respectively. All 19 chromosomes contained NBSLRR genes. Among them, 53 genes distributed on ChrC09. The NBS-LRR genes were mostly presented in clusters. Large-scale fragment replication of the genes was speculated. Results of codon bias analysis of the family in the 5 species showed that ENC (effective number of codon) of B. napus genes was 37.76 to 61.00, which was similar to B. oleracea in their preference. Codon bias features by preference of collinear homologous relationship showed more similarity between B. napus and B. oleracea.

Key words

Brassica napus / NBS-LRR gene family / phylogenetic evolution / chromosome localization / synte?ny / codon bias

Cite this article

Download Citations
FENG Shu-yan,CHEN Hui-long,LI Qiang,WANG Li-xia,ZHANG Wei-meng,WANG Tong,CUI Chun-lin,LI Miao-miao,YU Ying,NIE Fu-lei*,SONG Xiao-ming* . Identification and codon bias of NBS-LRR gene family in Brassica napus[J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2019, 41(6): 858 https://doi.org/10.19802/j.issn.1007-9084.2019017

References

[1] 刘云飞,万红建,李志邈,等. 植物NBS-LRR抗病基因的结构、功能、进化起源及其应用[J]. 分子植物育种,2014,12(2):377-389.
[2] Meyers B C,Kozik A,Griego A,et al. Genome-wideanalysis of NBS-LRR-encoding genes in Arabidopsis [J]. Plant Cell,2003,15(4):809-834.
[3] Ameline-Torregrosa C,Wang B B,O'Bleness M S,et al. Identification and characterization of nucleotide-bind? ing site-leucine-rich repeat genes in the model plant Medicago truncatula[J]. Plant Physiol,2008,146(1): 5-21.
[4] Tan X P,Meyers B C,Kozik A,et al. Global expression analysis of nucleotide binding site-leucine rich repeatencoding and related genes in Arabidopsis[J]. BMC Plant Biol,2007,7(1):56.
[5] Shao Z Q,Xue J Y,Wu P,et al. Large-scale analyses of angiosperm nucleotide-binding site-leucine-rich re? peat genes reveal three anciently diverged classes with distinct evolutionary patterns[J]. Plant Physiol,2016, 170(4):2095-2109.
[6] Zhang Y,Xia R,Kuang H H,et al. The diversification of plant NBS-LRR defense genes directs the evolution of microRNAs that target them[J]. Mol Biol Evol,2016, 33(10):2692-2705.
[7] Mondragon-Palomino M. Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thali? ana[J]. Genome Res,2002,12(9):1305-1315.
[8] Yu J Y,Tehrim S,Zhang F Q,et al. Genome-wide com? parative analysis of NBS-encoding genes between Brassi? ca species and Arabidopsis thaliana[J]. BMC Genom, 2014,15(1):3.
[9] Wu P,Shao Z Q,Wu X Z,et al. Loss/retention and evo? lution of NBS-encoding genes upon whole genome tripli? cation of Brassica rapa[J]. Gene,2014,540(1):54- 61.
[10] Zhang Y M,Shao Z Q,Wang Q,et al. Uncovering the dynamic evolution of nucleotide-binding site-leucinerich repeat(NBS-LRR)genes in Brassicaceae[J]. J In? tegr Plant Biol,2016,58(2):165-177.
[11] Lozano R,Hamblin M T,Prochnik S,et al. Identifica? tion and distribution of the NBS-LRR gene family in the cassava genome[J]. BMC Genom,2015,16:360.
[12] Liu W,Ghouri F,Yu H,et al. Genome wide re-se? quencing of newly developed rice lines from common wild rice(Oryza rufipogon Griff.)for the identification of NBS-LRR genes[J]. Plos One, 2017, 12(7) : ENC e0180662.
[13] Zhu H Y,Cannon S B,Young N D,et al. Phylogeny and genomic organization of the TIR and non-TIR NBSLRR resistance gene family in Medicago truncatul[J]. Mol Plant - Microbe Inter,2002,15(6):529-539.
[14] Song W,Wang B Q,Li X H,et al. Identification of im? mune related LRR-containing genes in maize(Zea mays L.) by genome-wide sequence analysis[J]. Int J Ge? nom,2015,2015:1-11.
[15] Yang X P,Wang J P. Genome-wide analysis of NBSLRR genes in Sorghum genome revealed several events contributing to NBS-LRR gene evolution in grass species [J]. Evol Bioinform,2016,12(12):9.
[16] Habachi-Houimli Y,Khalfallah Y,Mezghani-Khemak? hem M,et al. Genome-wide identification,characteriza? tion,and evolutionary analysis of NBS-encoding resis? tance genes in barley[J]. 3 Biotech,2018,8(11):453.
[17] Li N Y,Zhou L,Zhang D D,et al. Heterologous expres? sion of the cotton NBS-LRR gene GbaNA1 enhances ver? ticillium wilt resistance in Arabidopsis[J]. Front Plant Sci,2018,9:119.
[18] Cao J Y,Xu Y P,Zhao L,et al. Tight regulation of the interaction between Brassica napus and Sclerotinia sclero? tiorum at the microRNA level[J]. Plant Mol Biol,2016, 92(1/2):39-55.
[19] 续晨,蔡小宁,钱保俐,等. 葡萄基因组密码子使用偏好模式研究[J]. 西北植物学报,2012,32(2):409- 415.
[20] 王云,彭丽云,苏立遥,等. 龙眼Hsf基因家族密码子使用模式分析[J/OL].分子植物育种:1-15[2019-08-27]. http://kns. cnki. net/kcms/detail/46.1068. S.20181210.1119.009.html.
[21] 黄赛花,袁瑗,王成坤,等. 大豆花叶病毒CP基因密码子使用偏性分析[J]. 中国油料作物学报,2015,37 (2):148-153.
[22] Alamery S,Tirnaz S,Bayer P,et al. Genome-wide iden? tification and comparative analysis of NBS-LRR resis? tance genes in Brassica napus[J]. Crop Pasture Sci, 2018,69(1):72.
[23] Cheng F,Liu S Y,Wu J,et al. BRAD,the genetics and genomics database for Brassica plants[J]. BMC Plant Bi? ol,2011,11(1):136.
[24] Chalhoub B,Denoeud F,Liu S,et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Bras? sica napus oilseed genome[J]. Science, 2014, 345 (6199):950-953.
[25] Liu S,Liu Y,Yang X,et al. The Brassica oleracea ge? nome reveals the asymmetrical evolution of polyploid ge? nomes[J]. Nat Commun,2014,5(3930). doi:10.1038/ ncomms4930.
[26] 李春金,郭媛媛,杨启航,等. 甘蓝型油菜HMG基因家族的生物信息学分析[J]. 中国油料作物学报, 2018,40(3):318-325.
[27] Finn R D,Bateman A,Clements J,et al. Pfam:the pro? tein families database[J]. Nucl Acids Res,2014,42 (D1):D222-D230.
[28] Xu Q,Dunbrack R L. Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB[J]. Bioinformatics,2012,28(21): 2763-2772.
[29] Larkin M A,Blackshields G,Brown N P,et al. Clustal W and Clustal X version 2.0[J]. Bioinformatics,2007, 23(21):2947-2948.
[30] Shimada M K,Nishida T. A modification of the PHYLIP program:A solution for the redundant cluster problem, and an implementation of an automatic bootstrapping on trees inferred from original data[J]. Mol Phylogenetics Evol,2017,109:409-414.
[31] 王岩,李兆阳,唐心龙,等. 拟南芥基因组NBS-LRR 类基因家族的生物信息学分析[J]. 中国农学通报, 2009,25(15):40-45.
[32] Wang Y,Tang H,DeBarry J D,et al. MCScanX:a tool? kit for detection and evolutionary analysis of gene synte? ny and collinearity[J]. Nucleic Acids Res,2012,40 (7):e49.
[33] Krzywinski M,Schein J,Birol I,et al. Circos:An infor? mation aesthetic for comparative genomics[J]. Genome Res,2009,19(9):1639-1645.
[34] 陈哲,胡福初,王祥和,等. 菠萝密码子使用偏好性分析[J]. 果树学报,2017,34(8):946-955.
[35] Campbell W H,Gowri G. Codon usage in higher plants, green algae, and Cyanobacteria[J]. Plant Physiol, 1990,92(1):1-11.
[36] Chiapello H,Lisacek F,Caboche M,et al. Codon usage and gene function are related in sequences of Arabidopsis thaliana[J]. Gene,1998,209(1/2):GC1-GC38.
[37] Paul P,Malakar A K,Chakraborty S. Compositional bi? as coupled with selection and mutation pressure drives codon usage in Brassica campestris genes[J]. Food Sci Biotechnol,2018,27(3):725-733.
[38] 宋辉,王鹏飞,马登超,等. 蒺藜苜蓿WRKY转录因子密码子使用偏好性分析[J]. 农业生物技术学报, 2015,23(2):203-212.
[39] 方辉,曲俊杰,孙嘉曼,等. 香蕉全基因组NBS抗病基因密码子使用偏好性分析[J]. 分子植物育种, 2017,15(3):883-889.
[40] Song X M,Duan W K,Huang Z N,et al. Comprehen? sive analysis of the flowering genes in Chinese cabbage 867 and examination of evolutionary pattern of CO-like genes in plant kingdom[J]. Sci Rep,2015,5:14631.
[41] Song X M,Wang J P,Ma X,et al. Origination,expan? sion, evolutionary trajectory, and expression bias of AP2/ERF superfamily in Brassica napus[J]. Front Plant Sci,2016,7:1186.
[42] Song X M,Li Y,Hou X L. Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage(Brassica rapa ssp. pekinensis)[J]. BMC Ge? nom,2013,14(1):573.
[43] Song X M,Huang Z N,Duan W K,et al. Genome-wide analysis of the bHLH transcription factor family in Chi? nese cabbage(Brassica rapa ssp. pekinensis)[J]. Mol Genet Genomics,2014,289(1):77-91.
[44] Song X M,Ma X,Li C J,et al. Comprehensive analyses of the BES1 gene family in Brassica napus and examina? tion of their evolutionary pattern in representative species [J]. BMC Genom,2018,19:346.
[45] Song X M,Liu T K,Duan W K,et al. Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis)[J]. Genomics,2014, 103(1):135-146.
[46] Duan W K,Song X M,Liu T K,et al. Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage)[J]. Mol Genet Genomics,2015,290 (1):239-255.
[47] Song X M,Liu G F,Duan W K,et al. Genome-wide identification,classification and expression analysis of the heat shock transcription factor family in Chinese cab? bage[J]. Mol Genet Genomics,2014,289(4):541- 551.
PDF(8208 KB)

1383

Accesses

0

Citation

Detail

Sections
Recommended

/