TIFY Gene Family in Sugar Beet: Whole Genome Identification and Bioinformatics Analysis

doi:10.11924/j.issn.1000-6850.casb2021-0831

Abstract

Abstract:

TIFY transcription factors play an important role in regulating plant growth and development as well as stress response, therefore, the purpose of this study is to identify and analyze TIFY transcription factors in sugar beet (Beta vulgaris L.). Based on the genome data of sugar beet, bioinformatics techniques were used to identify and analyze the members of sugar beet TIFY family at the whole genome level. The results showed that there were 21 TIFY genes in sugar beet with low sequence similarity. Collinearity analysis showed that only BvTIFY15 and BvTIFY18 had gene replication events. The family of BvTIFY transcription factors included 2 TIFY proteins, 8 JAZ proteins, 6 ZML proteins and 5 PPD proteins. Protein-protein interaction prediction showed that members of the JAZ family played an important role in the regulation of JA signaling. This study analyzed the structure and function of BvTIFY genes and discovered the salt stress responsive genes BvTIFY13 and BvTIFY15 in sugar beet roots. It can provide a theoretical basis for subsequent functional studies on BvTIFY genes.

Key words: sugar beet, transcription factors, TIFY family, whole genome identification, bioinformatics

CLC Number:

S566.3

GONG Yongyong, DUANMU Huizi. TIFY Gene Family in Sugar Beet: Whole Genome Identification and Bioinformatics Analysis[J]. Chinese Agricultural Science Bulletin, 2022, 38(8): 17-24.

Figures/Tables 8

References 13

[14]	WHITE D W. PEAPOD regulates lamina size and curvature in rabidopsis[J]. Proc. natl. acad. sci. USA, 2006, 103(35):13238-13243. doi: 10.1073/pnas.0604349103 URL
[15]	BAI Y H, MENG Y J, HUANG D L, et al. Origin and evolutionary analysis of the plant-specific TIFY transcription factor family[J]. Genomics, 2011, 98(2):128-136. doi: 10.1016/j.ygeno.2011.05.002 URL
[16]	刘蕊, 刘乃新, 吴玉梅, 等. 甜菜MYB转录因子生信分析及种子萌发期差异表达[J]. 中国农学通报, 2019, 35(25):54-65.
[17]	刘乃新, 吴玉梅. 甜菜ARF基因家族生信分析及种子萌发期差异表达[J]. 中国农学通报, 2020, 36(26):22-28.
[18]	韩秉进, 朱向明. 中国甜菜生产发展历程及现状分析[J]. 土壤与作物, 2016, 5(2):91-95.
[19]	CHEN C J, CHEN H, ZHANG Y, et al. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data[J]. Molecular plant, 2020, 13(8):1194-1202. doi: 10.1016/j.molp.2020.06.009 URL
[20]	KIMOTHO R N, BAILLO E H, ZHANG Z. Transcription factors involved in abiotic stress responses in Maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era[J]. Peerj, 2019, 7(1):e7211. doi: 10.7717/peerj.7211 URL
[21]	BOWERS J E, CHAPMAN B A, RONG J, et al. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events[J]. Nature, 2003, 422(6930):433-438. doi: 10.1038/nature01521 URL
[22]	WANG Y, TANG H, DEBARRY J D, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity[J]. Nucleic acids research, 2012, 40(7):e49. doi: 10.1093/nar/gkr1293 URL
[23]	ZHAO P, WANG D, WANG R, et al. Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress[J]. BMC genomics, 2018, 19(1):61. doi: 10.1186/s12864-018-4443-1 URL
[24]	YANG L, SU D, CHANG X, et al. Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling[J]. Plant communications, 2020, 1(2):100027. doi: 10.1016/j.xplc.2020.100027 URL
[25]	LONG M. Gene Duplication and Evolution[J]. Science, 2001, 293(5535):1551. doi: 10.1126/science.293.5535.1551a URL
[26]	胡利宗, 李超琼, 张雯露, 等. 菜豆TIFY基因的全基因组鉴定与系统进化分析[J]. 分子植物育种, 2020, 18(10):32-40.
[27]	WASTERNACK C. Action of jasmonates in plant stress responses and development -Applied aspects[J]. Biotechnology advances, 2014, 32(1):31-39. doi: 10.1016/j.biotechadv.2013.09.009 URL
[28]	SHEARD L B, XU T, MAO H, et al. Jasmonate perception by inositol-phosphate-potentiated COI1-AZ co-receptor[J]. Nature, 2010, 468(7322):400-405. doi: 10.1038/nature09430 URL
[29]	ACOSTA I F, GASPERINI D, CHETELAT A, et al. Role of NINJA in root jasmonate signaling[J]. Proc natl acad sci USA, 2013, 110(38):15473-15478. doi: 10.1073/pnas.1307910110 URL
[30]	HUANG H, HUA G, LIU B, et al. bHLH13 Regulates Jasmonate-Mediated Defense Responses and Growth[J]. Evolutionary Bioinformatics online, 2018, 14:1-8.
[31]	SCHULER M A. Functional genomics of P450s[J]. Annual review of plant biology, 2003, 54(1):629-667. doi: 10.1146/arplant.2003.54.issue-1 URL
[1]	VANHOLME B, GRUNEWALD W, BATEMAN A, et al. The tify family previously known as ZIM[J]. Trends in plant science, 2007, 12(6):239-244. doi: 10.1016/j.tplants.2007.04.004 URL
[2]	杨锐佳, 张中保, 吴忠义. 植物转录因子TIFY家族蛋白结构和功能的研究进展[J]. 生物技术通报, 2020, 36(12):121-128. doi: 10.13560/j.cnki.biotech.bull.1985.2020-0307
[3]	NISHII A, TAKEMURA M, FUJITA H, et al. Characterization of a Novel Gene Encoding a Putative Single Zinc-finger Protein, ZIM, Expressed during the Reproductive Phase in Arabidopsis thaliana[J]. Journal of the agricultural chemical society of Japan, 2000, 64(7):1402-1409.
[4]	YE H Y, DU H, TANG N, et al. Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice[J]. Plant molecular biology, 2009, 71(3):291-305. doi: 10.1007/s11103-009-9524-8 URL
[5]	ZHANG Y, GAO M, SINGER S D, et al. Genome-Wide Identification and Analysis of the TIFY Gene Family in Grape[J]. PLoS one, 2012, 7(9):e44465. doi: 10.1371/journal.pone.0044465 URL
[6]	ZHU D, BAI X, LUO X, et al. Identification of wild soybean (Glycine soja) TIFY family genes and their expression profiling analysis under bicarbonate stress[J]. Plant cell reports, 2013, 32(2):263-272. doi: 10.1007/s00299-012-1360-7 URL
[7]	EBEL C, BENKEFI A, HANIN M, et al. Characterization of wheat (Triticum aestivum) TIFY family and role of Triticum Durum TdTIFY11a in salt stress tolerance[J]. PloS one, 2018, 13(7):e0200566. doi: 10.1371/journal.pone.0200566 URL
[8]	HEIDARI P, FARAJI S, AHMADIZADEH M, et al. New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis[J]. Frontiers in genetics, 2021, 12:657970. doi: 10.3389/fgene.2021.657970 URL
[9]	AMPARO C P, ASTRID N D, ROBIN V B, et al. The Non-JAZ TIFY Protein TIFY8 from Arabidopsis thaliana Is a Transcriptional Repressor[J]. PLoS one, 2014, 9(1):e84891. doi: 10.1371/journal.pone.0084891 URL
[10]	魏昕, 刘雨恒, 刘宇阳, 等. 植物JAZ蛋白家族研究进展[J]. 植物生理学报, 2021, 57(5):1039-1046.
[11]	STASWICK P E. JAZing up jasmonate signaling[J]. Trends in plant science, 2008, 13(2):66-71. doi: 10.1016/j.tplants.2007.11.011 URL
[12]	CHINI A, FONSECA S, FERNANDEZ G, et al. The JAZ family of repressors is the missing link in jasmonate signalling[J]. Nature, 2007, 448(7154):666-671. doi: 10.1038/nature06006 URL
[13]	CHUNG H Y, SUNTER G. Interaction between the transcription factor AtTIFY4B and begomovirus AL2 protein impacts pathogenicity[J]. Plant molecular biology, 2014, 86(1):185-200. doi: 10.1007/s11103-014-0222-9 URL

基因名	转录本编号	染色体	基因组位置	编码区/bp	蛋白质/aa	分子量/kDa	等电点pI
BvTIFY1	XM_010693544.2	1	177868-181625	1047	348	35.97	9.47
BvTIFY2	XM_010693545.2	1	177868-181625	1047	348	35.97	9.47
BvTIFY3	XM_010673165.2	1	6039574-6047256	1041	346	37.72	5.74
BvTIFY4	XM_019248305.1	1	6039574-6047256	1041	346	37.72	5.74
BvTIFY5	XM_010673216.2	1	6072808-6079282	894	297	32.88	5.94
BvTIFY6	XM_010673225.2	1	6072808-6079282	888	295	32.64	5.94
BvTIFY7	XM_010672448.2	2	39383795-39388815	1119	372	39.43	8.71
BvTIFY8	XM_010695474.2	3	1037984-1064949	1059	352	38.47	8.49
BvTIFY9	XM_010695475.2	3	1037984-1064949	1056	351	38.32	8.5
BvTIFY10	XM_010695476.2	3	1037984-1064949	1050	349	38.14	8.49
BvTIFY11	XM_010695477.2	3	1037984-1064949	1047	348	38.01	8.49
BvTIFY12	XM_010695478.2	3	1037984-1064949	999	332	36.2	8.78
BvTIFY13	XM_010684365.2	6	53385701-53390451	597	198	22.26	8.61
BvTIFY14	XM_010697784.2	7	241127-253491	900	299	32.87	5.94
BvTIFY15	XM_010686977.2	7	36091600-36094215	777	258	29.34	9.24
BvTIFY16	XM_010688927.2	8	19534025-19540778	1050	349	36.08	8.53
BvTIFY17	XM_010688928.2	8	19534025-19540778	1047	348	36.01	8.53
BvTIFY18	XM_010689246.2	8	27921059-27923721	756	251	26.84	9.9
BvTIFY19	XM_010690498.1	9	2254102-2256859	375	124	14.16	9.18
BvTIFY20	XM_010693082.2	9	42035878-42046926	1062	353	38.85	4.97
BvTIFY21	XM_010668415.1	Unknown	29321-30954	372	123	13.71	9.21

基因名	转录本编号	染色体	基因组位置	编码区/bp	蛋白质/aa	分子量/kDa	等电点pI
BvTIFY1	XM_010693544.2	1	177868-181625	1047	348	35.97	9.47
BvTIFY2	XM_010693545.2	1	177868-181625	1047	348	35.97	9.47
BvTIFY3	XM_010673165.2	1	6039574-6047256	1041	346	37.72	5.74
BvTIFY4	XM_019248305.1	1	6039574-6047256	1041	346	37.72	5.74
BvTIFY5	XM_010673216.2	1	6072808-6079282	894	297	32.88	5.94
BvTIFY6	XM_010673225.2	1	6072808-6079282	888	295	32.64	5.94
BvTIFY7	XM_010672448.2	2	39383795-39388815	1119	372	39.43	8.71
BvTIFY8	XM_010695474.2	3	1037984-1064949	1059	352	38.47	8.49
BvTIFY9	XM_010695475.2	3	1037984-1064949	1056	351	38.32	8.5
BvTIFY10	XM_010695476.2	3	1037984-1064949	1050	349	38.14	8.49
BvTIFY11	XM_010695477.2	3	1037984-1064949	1047	348	38.01	8.49
BvTIFY12	XM_010695478.2	3	1037984-1064949	999	332	36.2	8.78
BvTIFY13	XM_010684365.2	6	53385701-53390451	597	198	22.26	8.61
BvTIFY14	XM_010697784.2	7	241127-253491	900	299	32.87	5.94
BvTIFY15	XM_010686977.2	7	36091600-36094215	777	258	29.34	9.24
BvTIFY16	XM_010688927.2	8	19534025-19540778	1050	349	36.08	8.53
BvTIFY17	XM_010688928.2	8	19534025-19540778	1047	348	36.01	8.53
BvTIFY18	XM_010689246.2	8	27921059-27923721	756	251	26.84	9.9
BvTIFY19	XM_010690498.1	9	2254102-2256859	375	124	14.16	9.18
BvTIFY20	XM_010693082.2	9	42035878-42046926	1062	353	38.85	4.97
BvTIFY21	XM_010668415.1	Unknown	29321-30954	372	123	13.71	9.21