棉花SRS基因家族的全基因组鉴定及生物信息学分析

doi:10.11963/cs20210060

摘要/Abstract

摘要：

【目的】短链相关序列（SHI-related sequence, SRS）家族是一类植物特有的转录因子,在调节植物生长发育和逆境胁迫反应中发挥重要作用。鉴定和分析棉花SRS基因家族成员。【方法】结合拟南芥相关信息,以陆地棉和海岛棉为主要研究对象,对棉花SRS基因进行全基因组鉴定和系统进化研究,并分析其在不同器官、不同发育时期的胚珠和纤维、以及在非生物胁迫下棉苗中的表达模式。【结果】在陆地棉和海岛棉中分别鉴定出27个和26个SRS基因,系统进化分析将棉花SRS基因家族成员划分为3个分支,不同分支都具有相似的保守基序。每个分支都存在多对同源基因。一些SRS基因在胚珠发育时期表达量较高,并响应多种非生物胁迫。【结论】分析预测了棉花SRS基因的家族成员进化关系与潜在功能,为棉花SRS基因的功能研究提供初步的理论基础。

关键词: 棉花; SRS; 系统进化; 表达模式; 基因家族

Abstract:

[Objective] SHI-related sequence (SRS) family is a group of plant-specific transcription factors that play important roles in regulating plant development and response to adversity stress. However, the function of SRS gene family in cotton has not been well characterized. [Method] Based on the published genomic data of Gossypium hirsutum, G. barbadense and Arabidopsis thaliana, the genome-wide identification and phylogenetic analysis of SRS genes in cotton were conducted. And the expression pattern of SRS genes in ovule and fiber at different developmental stages, in different organs and under different abiotic stress conditions were analyzed. [Result] In total, 27 and 26 SRS genes were identified in G. hirsutum and G. barbadense, respectively. According to the phylogenetic analysis, SRS genes in cotton could be divided into three groups, and different groups had similar conserved motifs. There were multiple pairs of homologous genes in each subgroup. Some SRS genes were highly expressed in ovules at different developmental stages, and were also responsive to various abiotic stresses. [Conclusion]The evolution and potential functions of SRS gene family were analyzed and predicted, which provided a theoretical basis for the functional analysis of SRS genes in cotton.

Key words: cotton; SRS; phylogeny; expression pattern; gene family

张雪, 孙瑞斌, 马聪聪, 马丹, 张晓睿, 刘志红, 刘传亮. 棉花SRS基因家族的全基因组鉴定及生物信息学分析[J]. 棉花学报, 2022, 34(2): 107-119.

Zhang Xue, Sun Ruibin, Ma Congcong, Ma Dan, Zhang Xiaorui, Liu Zhihong, Liu Chuanliang. Genome-wide identification and bioinformatic analysis of SRS gene family in cotton[J]. Cotton Science, 2022, 34(2): 107-119.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://journal.cricaas.com.cn/Jweb_mhxb/CN/10.11963/cs20210060

https://journal.cricaas.com.cn/Jweb_mhxb/CN/Y2022/V34/I2/107

图/表 8

表1

表2

陆地棉和海岛棉中SRS基因家族成员鉴定"

基因编号 Gene ID	染色体 Chromosome	氨基酸数量 Number of amino acid	蛋白质分子质量 Protein molecular weight/ku	等电点 Isoelectric point
Ghir_A01G010130	A01	306	33.886	6.501
Ghir_A02G018470	A02	269	29.042	5.197
Ghir_A03G009170	A03	194	22.116	5.630
Ghir_A03G021640	A03	213	23.519	8.560
Ghir_A05G007390	A05	341	36.219	8.568
Ghir_A05G019280	A05	309	34.127	8.249
Ghir_A06G000610	A06	296	32.807	6.503
Ghir_A07G012780	A07	352	37.128	8.086
Ghir_A08G001440	A08	337	34.887	8.349
Ghir_A09G011760	A09	356	37.006	7.970
Ghir_A10G019020	A10	278	29.951	6.946
Ghir_A11G018900	A11	391	42.601	5.407
Ghir_A13G002830	A13	197	22.333	8.894
Ghir_D01G010870	D01	218	23.826	8.018
Ghir_D02G009920	D02	204	23.303	6.758
Ghir_D02G023130	D02	213	23.485	8.488
Ghir_D03G001140	D03	286	31.235	6.234
Ghir_D05G007440	D05	339	35.881	8.568
Ghir_D05G019290	D05	314	34.751	8.309
Ghir_D06G000460	D06	307	34.094	8.136
Ghir_D07G012950	D07	344	35.953	8.132
Ghir_D08G001480	D08	433	45.074	8.522
Ghir_D09G011300	D09	356	36.994	7.786
Ghir_D10G020600	D10	219	23.916	8.562
Ghir_D11G019050	D11	341	36.511	5.393
Ghir_D13G003130	D13	195	21.959	8.933
Ghir_Scaffold3053G000010	Scaffold3053	312	33.111	8.437
Gbar_A01G010490	A01	306	33.904	6.501
Gbar_A02G018040	A02	283	30.919	7.050
Gbar_A03G009180	A03	204	23.289	6.758
Gbar_A03G021720	A03	214	23.742	8.416
Gbar_A05G006860	A05	536	57.555	8.358
Gbar_A05G043260	Scaffold372	312	34.495	8.309
Gbar_A06G000430	A06	307	34.108	7.690
Gbar_A07G012670	A07	344	35.807	8.429
Gbar_A08G001400	A08	336	34.750	8.347
Gbar_A09G011810	A09	353	36.639	8.137
Gbar_A10G019930	A10	278	29.951	6.946
Gbar_A11G018450	A11	341	36.738	6.722
Gbar_A13G003030	A13	203	23.149	9.095
Gbar_D01G010960	D01	308	34.303	6.976
Gbar_D02G010370	D02	209	23.798	7.660
Gbar_D02G023660	D02	207	22.898	8.485
Gbar_D03G001180	D03	287	31.304	6.758
Gbar_D05G019300	D05	311	34.402	8.467
Gbar_D05G007350	D05	339	35.881	8.568
Gbar_D06G000550	D06	307	34.080	8.136
Gbar_D07G013070	D07	378	40.550	7.727
Gbar_D08G001380	D08	428	44.348	8.545
Gbar_D09G011580	D09	356	36.978	7.786
Gbar_D10G020120	D10	277	29.809	7.578
Gbar_D11G019330	D11	341	36.573	6.267
Gbar_D13G025970	Scaffold1673	195	21.944	8.933

表2

图1

图2

图3

图4

图6

图5

参考文献 46

[1]	Fridborg I, Kuusk S, Robertson M, et al. The Arabidopsis protein SHI represses gibberellin responses in Arabidopsis and barley[J/OL]. Plant Physiology, 2001, 127(3): 937-948[2021-10-01]. https://doi.org/10.1104/pp.127.3.937.
[2]	Kuusk S, Sohlberg J J, Eklund D M, et al. Functionally redundant SHI family genes regulate Arabidopsis gynoecium development in a dose-dependent manner[J/OL]. The Plant Journal, 2006, 47(1): 99-111[2021-10-01]. https://doi.org/10.1111/j.1365-313X.2006.02774.x.
[3]	Eklund D M, Stldal V, Valsecchi I, et al. The Arabidopsis thaliana STYLISH1 protein acts as a transcriptional activator regulating auxin biosynthesis[J/OL]. The Plant Cell, 2010, 22(2): 349-363[2021-10-01]. https://doi.org/10.1105/tpc.108.064816.
[4]	Smith D L, Fedoroff N V. LRP1, a gene expressed in lateral and adventitious root primordia of Arabidopsis[J/OL]. The Plant Cell, 1995, 7(6): 735-745[2021-10-01]. https://doi.org/10.1105/tpc.7.6.735.
[5]	Singh S, Yadav S, Singh A, et al. Auxin signaling modulates LATERAL ROOT PRIMORDIUM1 (LRP1) expression during lateral root development in Arabidopsis[J/OL]. The Plant Journal, 2020, 101(1): 87-100[2021-10-01]. https://doi.org/10.1111/tpj.14520.
[6]	Rybel B D, Audenaert D, Xuan W, et al. A role for the root cap in root branching revealed by the non-auxin probe naxillin[J/OL]. Nature Chemical Biology, 2012, 8(9): 798-805[2021-10-01]. https://doi.org/10.1038/nchembio.1044.
[7]	Eklund D M, Cierlik I, Stldal V, et al. Expression of Arabidopsis SHORT INTERNODES/STYLISH family genes in auxin biosynthesis zones of aerial organs is dependent on a GCC box-like regulatory element[J/OL]. Plant Physiology, 2011, 157(4): 2069-2080[2021-10-01]. https://doi.org/10.1104/pp.111.182253.
[8]	Stldal V, Cierlik I, Song C, et al. The Arabidopsis thaliana transcriptional activator STYLISH1 regulates genes affecting stamen development, cell expansion and timing of flowering[J/OL]. Plant Molecular Biology, 2012, 78(6): 545-559[2021-10-01]. https://doi.org/10.1007/s11103-012-9888-z.
[9]	Fridborg I, Kuusk S, Moritz T, et al. The Arabidopsis dwarf mutant shi exhibits reduced gibberellin responses conferred by overexpression of a new putative zinc finger protein[J/OL]. The Plant Cell, 1999, 11(6): 1019-1032[2021-10-01]. https://doi.org/10.2307/3870795.
[10]	Baylis T, Cierlik I, Sundberg E, et al. SHORT INTERNODES/STYLISH genes, regulators of auxin biosynthesis, are involved in leaf vein development in Arabidopsis thaliana[J/OL]. New Phytologist, 2013, 197(3): 737-750[2021-10-01]. https://doi.org/10.1111/nph.12084.
[11]	Kuusk S, Sohlberg J J, Long J A, et al. STY1 and STY2 promote the formation of apical tissues during Arabidopsis gynoecium development[J/OL]. Development, 2002, 129(20): 4707-4717[2021-10-01]. https://doi.org/10.1242/dev.129.20.4707.
[12]	Gomariz-Fernández A, Sánchez-Gerschon V, Fourquin C, et al. The role of SHI/STY/SRS genes in organ growth and carpel development is conserved in the distant eudicot species Arabidopsis thaliana and Nicotiana benthamiana[J/OL]. Frontiers in Plant Science, 2017, 8: 814[2021-10-01]. https://doi.org/10.3389/fpls.2017.00814.
[13]	Yuan T T, Xu H H, Zhang Q, et al. The COP1 target SHI-RELATED SEQUENCE 5 directly activates photomorphogenesis-promoting genes[J/OL]. The Plant Cell, 2018, 30(10): 2368-2382[2021-10-01]. https://doi.org/10.1105/tpc.18.00455.
[14]	Zhang Y X, von Behrens I, Zimmermann R, et al. LATERAL ROOT PRIMORDIA 1 of maize acts as a transcriptional activator in auxin signaling downstream of the Aux/IAA gene rootless with undetectable meristem 1[J/OL]. Journal of Experimental Botany, 2015, 66(13): 3855-3863[2021-10-01]. https://doi.org/10.1093/jxb/erv187.
[15]	Sohlberg J J, Myrens M, Kuusk S, et al. STY1 regulates auxin homeostasis and affects apical-basal patterning of the Arabidopsis gynoecium[J/OL]. The Plant Journal, 2006, 47(1): 112-123[2021-10-01]. https://doi.org/10.1111/j.1365-313X.2006.02775.x.
[16]	Lütken H, Jensen L S, Topp S H, et al. Production of compact plants by overexpression of AtSHI in the ornamental Kalancho[J/OL]. Plant Biotechnology Journal, 2010, 8(2): 211-222[2021-10-01]. https://doi.org/10.1111/j.1467-7652.2009.00478.x.
[17]	Islam M A, Lütken H, Haugslien S, et al. Overexpression of the AtSHI gene in poinsettia, Euphorbia pulcherrima, results in compact plants[J/OL]. PLoS One, 2013, 8(1): e53377[2021-10-01]. https://doi.org/10.1371/journal.pone.0053377.
[18]	Kim S G, Lee S, Kim Y S, et al. Activation tagging of an Arabidopsis SHI-RELATED SEQUENCE gene produces abnormal anther dehiscence and floral development[J/OL]. Plant Molecular Biology, 2010, 74(4/5): 337-351[2021-10-01]. https://doi.org/10.1007/s11103-010-9677-5.
[19]	Duan E, Wang Y, Li X, et al. OsSHI1 regulates plant architecture through modulating the transcriptional activity of IPA1 in rice[J/OL]. The Plant Cell, 2019, 31(5): 1026-1042[2021-10-01]. https://doi.org/10.1105/tpc.19.00023.
[20]	Zhao S P, Song X Y, Guo L L, et al. Genome-wide analysis of the Shi-Related Sequence family and functional identification of GmSRS18 involving in drought and salt stresses in soybean[J/OL]. International Journal of Molecular Sciences, 2020, 21(5): 1810[2021-10-01]. https://doi.org/10.3390/ijms21051810.
[21]	Youssef H M, Eggert K, Koppolu R, et al. VRS2 regulates hormone-mediated inflorescence patterning in barley[J/OL]. Nature Genetics, 2016, 49(1): 157-161[2021-10-01]. https://doi.org/10.1038/ng.3717.
[22]	Yuo T, Yamashita Y, Kanamori H, et al. A SHORT INTERNODES(SHI) family transcription factor gene regulates awn elongation and pistil morphology in barley[J/OL]. Journal of Experimental Botany, 2012, 63(14): 5223-5232[2021-10-01]. https://doi.org/10.1093/jxb/ers182.
[23]	Zawaski C, Kadmiel M, Ma C, et al. SHORT INTERNODES-like genes regulate shoot growth and xylem proliferation in Populus[J/OL]. New Phytologist, 2011, 191(3): 678-691[2021-10-01]. https://doi.org/10.1111/j.1469-8137.2011.03742.x.
[24]	Li F G, Fan G Y, Lu C R, et al. Genome sequence of cultivated upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution[J]. Nature Biotechnology, 2015, 33(5): 524-530[2021-10-01]. https://doi.org/10.1038/nbt.3208. doi: 10.1038/nbt.3208
[25]	Zhu T, Liang C Z, Meng Z G, et al. CottonFGD: an integrated functional genomics database for cotton[J/OL]. BMC Plant Biology, 2017, 17: 101[2021-10-01]. https://doi.org/10.1186/s12870-017-1039-x.
[26]	Wang M J, Tu L L, Yuan D, et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense[J/OL]. Nature Genetics, 2019, 51(2): 224-229[2021-10-01]. https://doi.org/10.1038/s41588-018-0282-x.
[27]	El-Gebali S, Mistry J, Bateman A, et al. The Pfam protein families database in 2019[J/OL]. Nucleic Acids Research, 2019(D1):D427-D432 [2021-10-01]. https://doi.org/10.1093/nar/gky995.
[28]	Finn R D, Clements J, Eddy S R. HMMER web server: interactive sequence similarity searching[J/OL]. Nucleic Acids Research, 2011, 39:W29-W37 [2021-10-01]. https://doi.org/10.1093/nar/gkr367.
[29]	Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications[J/OL]. BMC Bioinformatics, 2009, 10(1): 421[2021-10-01]. https://doi.org/10.1186/1471-2105-10-421.
[30]	Jones P, Binns D, Chang H Y, et al. InterProScan 5: genome-scale protein function classification[J/OL]. Bioinformatics, 2014, 30(9): 1236-1240[2021-10-01]. https://doi.org/10.1093/bioinformatics/btu031.
[31]	Edgar R C. MUSCLE: multiple sequence alignment with high accuracy and high throughput[J]. Nucleic Acids Research, 2004, 32(5): 1792-1797[2021-10-01]. https://doi.org/10.1093/nar/gkh340. doi: 10.1093/nar/gkh340
[32]	Trifinopoulos J, Nguyen L T, von Haeseler A, et al. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis[J/OL]. Nucleic Acids Research, 2016(W1):W232-W235[2021-10-01]. https://doi.org/10.1093/nar/gkw256.
[33]	Bailey T L, Boden M, Buske F A, et al. MEME SUITE: tools for motif discovery and searching[J/OL]. Nucleic Acids Research, 2009, 37:W202-W208 [2021-10-01]. https://doi.org/10.1093/nar/gkp335.
[34]	Chen C, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data[J/OL]. Molecular Plant, 2020, 13(8): 1194-1202[2021-10-01]. https://doi.org/10.1016/j.molp.2020.06.009.
[35]	Hao Z, Lv D, Ge Y, et al. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms[J/OL]. PeerJ. Computer Science, 2020, 6:e251 [2021-10-01]. https://doi.org/10.7717/peerj-cs.251.
[36]	Wang Y, Tang H, Debarry J D, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity[J/OL]. Nucleic Acids Research, 2012, 40(7):e49 [2021-10-01]. https://doi.org/10.1093/nar/gkr1293.
[37]	Krzywinski M, Schein J, Birol I, et al. Circos: an information aesthetic for comparative genomics[J/OL]. Genome Research, 2009, 19: 1639-1645[2021-10-01]. https://doi.org/10.1101/gr.092759.109.
[38]	Hao P B, Wu A M, Chen P Y, et al. GhLUX1 and GhELF3 are two components of the circadian clock that regulate flowering time of Gossypium hirsutum[J/OL]. Frontiers in Plant Science, 2021, 12: 691489[2021-10-01]. https://doi.org/10.3389/FPLS.2021.691489.
[39]	Cheng S S, Chen P Y, Su Z Z, et al. High-resolution temporal dynamic transcriptome landscape reveals a GhCAL-mediated flowering regulatory pathway in cotton (Gossypium hirsutum L.)[J/OL]. Plant Biotechnology Journal, 2021, 19(1): 153-166[2021-10-01]. https://doi.org/10.1111/pbi.13449.
[40]	Cai D, Liu H, Sang N, et al. Identification and characterization of CONSTANS-like (COL) gene family in upland cotton (Gossypium hirsutum L.)[J/OL]. PLoS One, 2017, 12(6):e0179038 [2021-10-01]. https://doi.org/10.1371/journal.pone.0179038.
[41]	Lacape J M, Claverie M, Vidal R O, et al. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton[J/OL]. PLoS One, 2012, 7(11):e48855 [2021-10-01]. https://doi.org/10.1371/journal.pone.0048855.
[42]	Sun W J, Gao Z Y, Wang J, et al. Cotton fiber elongation requires the transcription factor GhMYB212 to regulate sucrose transportation into expanding fibers[J/OL]. New Phytologist, 2019, 222(2): 864-881 [2021-10-01]. https://doi.org/10.1111/nph.15620.
[43]	Zhao B, Cao J F, Hu G J, et al. Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation[J/OL]. New Phytologist, 2018, 218(3): 1061-1075[2021-10-01]. https://doi.org/10.1111/nph.15063.
[44]	He B, Shi P, Lv Y, et al. Gene coexpression network analysis reveals the role of SRS genes in senescence leaf of maize (Zea mays L.)[J/OL]. Journal of Genetics, 2020, 99(1): 3[2021-10-01]. https://doi.org/10.1007/s12041-019-1162-6.
[45]	Eklund D M, Thelander M, Landberg K, et al. Homologues of the Arabidopsis thaliana SHI/STY/LRP1 genes control auxin biosynthesis and affect growth and development in the moss Physcomitrella patens[J/OL]. Development, 2010, 137(8): 1275-1284[2021-10-01]. https://doi.org/10.1242/dev.039594.
[46]	Liu X, Zhao B, Zheng H J, et al. Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites[J/OL]. Scientific Reports, 2015, 5(1): 14139[2021-10-01]. https://doi.org/10.1038/srep14139.

基因编号 Gene ID	正向引物 Forward primer	反向引物 Reverse primer
Ghir_A02G018470	GGCGGTGAACATTGGTGGA	AACGGTGTCGTAGATGAAGGAGAAG
Ghir_A05G007390	ATCAAACGGCTGTAAACATCGC	TGTGCCTGGATTGCTGGAAG
Ghir_A08G001440	CCCACTCCTAACAGCGTCTCCTT	GCTACCTCCACCCATTCCACC
Ghir_D03G001140	GGCGGTGAACATTGGTGGA	AACGGTGTCGTAGATGAAGGAGAAG
Ghir_D05G019290	GAACCAGCTGGCAAGGTAACCA	GGGGTGATCTCATCTCACGAAGC
Ghir_D06G000460	GGTGCGTGAAAGTAAGTGCTATGGA	GAGATTCAGGTCCTTGGTCATAGAGTA
GhHis3	TCAAGACTGATTTGCGTTTCCA	GCGCAAAGGTTGGTGTCTTC