陆地棉MIKCC基因家族的全基因组分析

doi:10.11963/1002-7807.znhy.20170913

摘要/Abstract

摘要： 【目的】MIKC^C是1类保守的转录因子家族，参与调控植物的开花时间和花器官发育。通过对MIKC^C家族进行全基因组学分析，为深入研究MIKC^C在棉花开花及花器官发育的分子调控机理提供基础。【方法】利用HMMER 3.0及pfam种子文件鉴定棉花全基因组MIKC^C基因，结合其表达量进行偏向表达及聚类分析。【结果】在陆地棉基因组中共鉴定发现100个MIKC^C基因，分为11个亚类。表达聚类分析显示，棉花MIKC^C基因的表达模式大致可分为4个不同的类群，说明这类基因在棉花进化中出现了功能分化。100个MIKC^C基因中，有12个基因具有miRNA靶位点。【结论】研究结果显示MIKC^C家族基因在棉花纤维中存在功能分化，而且可能受到miRNA的调控，这为进一步研究该家族基因的功能提供信息参考。

关键词: 陆地棉; MIKC^C基因; 功能分化; miRNA

Abstract: [Objective] In plants, floral organ identity and the process of the transition from vegetative to reproductive development is regulated by MIKC^Cgene family. Whole genome analysis is helpful to understand the evolutionary history of MIKC^C genes and provides the basis for an in-depth analysis of molecular mechanism of MIKC^Cfamily in flowering and floral organ development in cotton. [Method] Whole genome identification of MIKC^C genes were carried by HMMER 3.0 and pfam gene bias expression and were clustered based on the RNA-seq data. [Result] We identified 100 MIKC^C genes and classified them into 11 subfamilies, according to their phylogenetic relationships to the Arabidopsis and Vitis vinifera MIKC_Cgenes. According to their expression profiles, MIKC^C genes were classified into four types. The MIKC^C genes of C/D and E subfamily were particularly highly expressed during cotton fiber elongation stage, indicating gene functional differentiation in cotton evolution. 12 of the 100 MIKC^Cgenes contains miRNA target sites, indicating that the flower development and the transition from vegetative to reproductive development of cotton may be regulated by miRNAs. [Conclusion] This study not only showed the functional differentiation of MIKCC genes in cotton fiber development, but also found that MIKC^Cfamily genes may be regulated by miRNAs in the growth and development of cotton, which provided the useful information for further functional studies of MIKC^Cgenes in cotton.

Key words: upland cotton; MIKC^C gene; functional differentiation; miRNA

中图分类号:

S562.03

周娜, 汪露瑶, 张天真, 胡艳. 陆地棉MIKC^C基因家族的全基因组分析[J]. 棉花学报, 2017, 29(6): 495-503.

Zhou Na, Wang Luyao, Zhang Tianzhen, Hu Yan. Genome-Wide Analysis of MIKC^C Gene Family in Cotton[J]. Cotton Science, 2017, 29(6): 495-503.

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链接本文: http://journal.cricaas.com.cn/Jweb_mhxb/CN/10.11963/1002-7807.znhy.20170913

http://journal.cricaas.com.cn/Jweb_mhxb/CN/Y2017/V29/I6/495

参考文献

[1] Alvarez-Buylla E R, Liljegren S J, Pelaz S, et al. MADS-box gene evolution beyond flowers: Expression in pollen, endosperm, guard cells, roots and trichomes[J]. Plant Journal, 2000, 24(4): 457-466.
[2] Liu Y, Cui S, Wu F, et al. Functional conservation of MIKC*-type MADS box genes in Arabidopsis and rice pollen maturation[J]. Plant Cell, 2013, 25(4): 1288-1303
[3] Kofuji R, Sumikawa N, Yamasaki M, et al. Evolution and divergence of the MADS-box gene family based on genome-wide analyses[J]. Molecular Biology & Evolution, 2003, 20(12):1963-1977.
[4] Kaufmann K, Melzer R, Theissen G. MIKC-type MADS-domain proteins: Structural modularity, protein interactions and network evolution in land plants[J]. Gene, 2005, 347(2): 183-198.
[5] Henschel K A. Strukturelle und funktionelle charakterisierung von MADS-Box-genen aus dem laubmoos Physcomitrella patens (Hedw.) B. S. G.[D]. Cologne: University of Cologne, 2002.
[6] Gramzow L, Theiβen G. Phylogenomics of MADS-Box genes in plants - Two opposing life styles in one gene family[J]. Biology, 2013, 2(3): 1150-1164.
[7] Duan W, Song X, Liu T, et al. Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage)[J]. Molecular Genetics and Genomics, 2015, 290(1): 239-255.
[8] Moon J, Suh S S, Lee H, et al. The SOC1 MADS-box gene integrates vernalization and gibberellin signals for flowering in Arabidopsis[J]. Plant Journal, 2003, 35(5): 613-623.
[9] Tapia-López R, García-Ponce B, Dubrovsky J G, et al. An AGAMOUS-related MADS-box gene, XAL1 (AGL12), regulates root meristem cell proliferation and flowering transition in Arabidopsis[J]. Plant Physiology, 2008, 146(3): 1182-1192.
[10] Nesi N, Debeaujon I, Jond C, et al. The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat[J]. Plant Cell, 2002, 14(10): 2463-2479.
[11] Zahn L M, Leebens-Mack J H, Arrington J M, et al. Conservation and divergence in the AGAMOUS, subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events[J]. Evolution & Development, 2006, 8(1): 30-45.
[12] Pa enicová L, Folter S D, Kieffer M, et al. Molecular and phylogenetic analyses of the complete MADS-Box transcription factor family in Arabidopsis: New openings to the MADS world[J]. Plant Cell, 2003, 15(7): 1538-1551.
[13] Liu C, Chen H, Hong L E, et al. Direct interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis[J]. Development (Cambridge, England), 2008, 135(8): 1481-1491.
[14] Ratcliffe O J, Kumimoto R W, Wong B J, et al. Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold[J]. Plant Cell, 2003, 15(5): 1159-1169.
[15] Adamczyk B J, Lehtishiu M D, Fernandez D E. The MADS domain factors AGL15 and AGL18 act redundantly as repressors of the floral transition in Arabidopsis[J]. Plant Journal, 2007, 50(6): 1007-1019.
[16] Michaels S D, Amasino R M. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering[J]. Plant Cell, 1999, 11(5): 949-956.
[17] Lee J H, Yoo S J, Park S H, et al. Role of SVP in the control of flowering time by ambient temperature in Arabidopsis[J]. Genes & Development, 2007, 21(4): 397-402.
[18] Hu J Y, Meaux J D. miR824-regulated AGAMOUS-LIKE16 contributes to flowering time repression in Arabidopsis[J]. The Plant cell, 2014, 26(5): 2024-2037.
[19] Yu F, Huaxia Y, Lu W, et al. GhWRKY15, a member of the WRKY transcription factor family identified from cotton (Gossypium hirsutum L.), is involved in disease resistance and plant development[J]. BMC Plant Biology, 2012, 12(1): 144.
[20] Zheng S Y, Guo Y L, Xiao Y H, et al. Cloning of a MADS box protein gene (GhMADS1) from cotton (Gossypium hirsutum L.)[J]. Acta Genetica Sinica, 2004, 31(10): 1136-1141.
[21] Guo Y, Zhu Q, Zheng S, et al. Cloning of a MADS box gene (GhMADS3) from cotton and analysis of its homeotic role in transgenic Tobacco[J]. Journal of Genetics & Genomics, 2007, 34(6): 527-535.
[22] Li Y, Ning H, Zhang Z, et al. A cotton gene encoding novel MADS-box protein is preferentially expressed in fibers and functions in cell elongation[J]. Acta Biochimica Et Biophysica Sinica, 2011, 43(8): 607-617.
[23] Yang Z, Li C, Ye W, et al. GhAGL15s, preferentially expressed during somatic embryogenesis, promote embryogenic callus formation in cotton (Gossypium hirsutum L.)[J]. Molecular Genetics and Genomics, 2014, 289(5): 873-883.
[24] Zhang W, Fan S, Pang C, et al. Molecular cloning and function analysis of two SQUAMOSA-Like MADS-box genes from Gossypium hirsutum L.[J]. Journal of Integrative Plant Biology, 2013, 55(7): 597-607.
[25] Zhang T, Hu Y, Jiang W, et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement[J]. Nature Biotechnology, 2015, 33(5): 531- 537.
[26] Li F, Fan G, Wang K, et al. Genome sequence of the cultivated cotton Gossypium arboreum[J]. Nature Genetics, 2014, 46(6): 567-72.
[27] Wang K, Wang Z, Li F, et al. The draft genome of a diploid cotton Gossypium raimondii[J]. Nature Genetics, 2012, 44(10): 1098-1103.
[28] Finn R D, Clements J, Arndt W, et al. HMMER web server: 2015 update.[J]. Nucleic Acids Research, 2015, 43(1): 30-38.
[29] Edgar R C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput[J]. Nucleic Acids Research, 2004, 32(5):1792-1797.
[30] Tamura K, Peterson D, Peterson N, et al. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods[J]. Molecular Biology & Evolution, 2011, 28(10): 2731-2739.
[31] Altschul S F, Madden T L, Schäffer A A, et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs[J]. Nucleic Acids Research, 1997, 25(17):3389-3402.
[32] Cox M P, Peterson D A, Biggs P J. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data[J]. BMC Bioinformatics, 2010, 11(1): 485.
[33] Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript analysis of RNA-seq experiments with TopHat and Cufflinks[J]. Nature Protocols, 2014, 7(3): 562-578.
[34] Dai X, Zhao P X. psRNATarget: a plant small RNA target analysis server[J]. Nucleic Acids Research, 2011, 39 (web server issue): 155-159.
[35] 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.
[36] Gramzow L, Theissen G. A hitchhiker's guide to the MADS world of plants[J]. Genome Biology, 2010, 11(6): 214.
[37] Wei B, Zhang R Z, Guo J J, et al. Genome-wide analysis of the MADS-box gene family in Brachypodium distachyon[J]. PLoS One, 2014, 55: 245-256.
[38] Pnueli L, Abu-Abeid M, Zamir D, et al. The MADS box gene family in tomato: Temporal during floral development, conserved secondary structures and homology with homeotic genes from Antirrhinum and Arabidopsis[J]. Plant Journal, 1991, 1(2): 255-266.
[39] Müller F, Frentzen M. Phosphatidylglycerophosphate synthases from Arabidopsis thaliana[J]. Febs Letters, 2001, 509(2): 298- 302.
[40] Jiang W, Chang S, Li H, et al. Liquid hot water pretreatment on different parts of cotton stalk to facilitate ethanol production[J]. Bioresource Technology, 2015, 176: 175-180.
[41] Gregis V, Sessa A, Colombo L, et al. AGL24, SHORT VEGETATIVE PHASE, and APETALA1 redundantly control agamous during early stages of flower development in Arabidopsis[J]. Plant Cell, 2006, 18(6): 1373-1382.
[42] Liu C, Zhou J, Brachadrori K, et al. Specification of Arabidopsis floral meristem identity by repression of flowering time genes[J]. Development, 2007, 134(10): 1901-1910.
[43] Cubas P, Martínez-Zapater J M, Carmona M J. Floral meristem identity genes are expressed during tendril development in grapevine[J]. Plant Physiology, 2004, 135(3): 1491-1501.
[44] Zhou Y, Li B Y, Li M, et al. A MADS-box gene is specifically expressed in fibers of cotton (Gossypium hirsutum) and influences plant growth of transgenic Arabidopsis in a GA-dependent manner[J]. Plant Physiology & Biochemistry, 2014, 75(2):70-79.
[45] Kutter C, SchÖb H, Stadler M, et al. MicroRNA-mediated regulation of stomatal development in Arabidopsis[J]. Journal of the American Statistical Association, 2007, 19(8):2417-2429.
[46] Wang H, Jiao X, Kong X, et al. A signaling cascade from miR444 to RDR1 in rice antiviral RNA silencing pathway[J]. Plant Physiology, 2016, 170(4): 2365-2377.
[47] Yan Y, Wang H, Hamera S, et al. miR444a has multiple functions in the rice nitrate-signaling pathway[J]. Plant Journal, 2014, 78(1): 44-55.
[48] Fernandez D E, Wang C T, Zheng Y, et al. The MADS-domain factors agamous-like15 and agamous-like18, along with short vegetative phase and agamous-like24, are necessary to block floral gene during the vegetative phase[J]. Plant Physiology, 2014, 165(4): 1591-1603.