棉花EXO70基因家族全基因组的鉴定及种间比较

doi:10.3864/j.issn.0578-1752.2023.23.005

摘要/Abstract

摘要：

【目的】当前四倍体棉花的主栽品种是陆地棉与海岛棉，陆地棉产量高且适应性好，海岛棉纤维品质优异但产量一般。EXO70是胞外分泌体（exocyst complex）中的关键亚基，在植物生长发育、胁迫响应等方面发挥重要作用。通过全基因组水平鉴定和分析陆地棉与海岛棉EXO70基因家族成员，并研究其在纤维发育、环境适应等方面的功能，有助于揭示陆地棉与海岛棉种间性状差异形成的分子基础。【方法】从拟南芥数据库（TAIR）获取EXO70家族蛋白序列作为参考序列，采用HMMER、ExPASy、MEME、TBtools等分析工具对陆地棉TM-1和海岛棉Hai7124基因组中EXO70家族成员进行鉴定与分析，系统比较该家族在基因表达模式、重要农艺性状的相关性、逆境响应等方面的异同点。【结果】通过对陆地棉和海岛棉的基因组水平分析，均鉴定出54个EXO70家族成员，根据系统进化发育可将其分为8个分支。陆地棉和海岛棉同源基因可一一对应，分布在陆地棉与海岛棉的20条染色体上，绝大多数成员为单外显子，但是两者间有12对同源基因在阅读框序列上存在较大差异。陆地棉与海岛棉大部分同源基因表达模式类似，但在同一纤维发育时期表达量存在差异，如分支A中的GH_A04G1208与同源基因GB_A04G1253。重要农艺性状关联分析中发现，海岛棉有16个EXO70基因与纤维品质性状显著相关，多于陆地棉；陆地棉有13个基因与产量性状衣分显著相关，多于海岛棉。发现部分性状关联的差异可能由海陆种间的基因结构差异造成，如GH_A11G3714和GB_A11G3791。在不同逆境胁迫下，陆地棉中有25个基因受诱导，显著多于海岛棉中10个受诱导基因。【结论】在棉花四倍体形成、分化与驯化过程中，陆地棉与海岛棉EXO70家族基因序列结构相对保守，基因表达模式也保持较高的一致性。海岛棉有更多的EXO70基因与纤维品质性状相关，陆地棉有更多的基因与产量性状相关且对环境逆境更为敏感。

关键词: 陆地棉, 海岛棉, EXO70基因家族, 表达模式, 性状关联分析, 逆境响应

Abstract:

【Objective】The two main types of allotetraploid cotton that are currently cultivated are upland cotton, known for its high yield and good adaptability, and island cotton, which boasts excellent fiber quality but lower yield. EXO70, a vital subunit of the exocyst complex, plays a significant role in plant growth, development, and stress response. By identifying and analyzing members of the EXO70 gene family in upland and island cotton at the whole-genome level, and studying their functions in fiber development and environmental adaptation, we can shed light on the molecular basis for the differences in traits between these two varieties. 【Method】The reference sequences of EXO70 protein in Arabidopsis were obtained from the TAIR database. HMMER, ExPASy, MEME, TBtools, and other analysis tools were used to identify and analyze the members of EXO70 gene family in the genomes of upland cotton TM-1 and island cotton Hai7124. The similarities and differences in gene expression patterns, correlations with crucial agronomic traits, and stress responses of this family were systematically compared. 【Result】Through genome-level analysis of upland cotton and sea-island cotton, 54 EXO70 family members were identified in both upland and sea-island cotton, which could be divided into eight subgroups based on phylogenetic analysis. Orthologous genes between upland cotton and sea-island cotton can be paired one-to-one and are distributed across the 20 chromosomes of both species. The majority of the members have single exons, while 12 pairs of homologous genes displayed significant differences in the reading frame sequences. Most orthologous genes in Gossypium hirsutum and Gossypium barbadense display similar expression patterns, but differences in expression levels are observed during the same fiber development stage, such as GH_A04G1208 and its orthologous gene GB_A04G1253 in subgroup A. Single gene association analysis revealed that more genes were associated with fiber quality traits in sea-island cotton, while more genes were associated with yield traits and environmental adversity sensitivity in upland cotton. Some trait association differences resulted from genetic structural differences between Gossypium hirsutum and Gossypium barbadense. Under different stresses, upland cotton showed a significantly higher number of induced genes compared to sea-island cotton. 【Conclusion】The sequence structure and gene expression patterns of the EXO70 family were found to be relatively conserved in both upland and island cotton during the formation, differentiation, and domestication of tetraploid cotton. However, in terms of EXO70 family members, island cotton had more genes related to fiber quality traits, while upland cotton had more genes related to yield traits and exhibited greater sensitivity to environmental stress.

Key words: Gossypium hirsutum, Gossypium barbadense, EXO70 gene family, expression pattern, trait association analysis, abiotic stress response

董琰钰, 徐碧玉, 董泽宇, 汪露瑶, 陈锦文, 方磊. 棉花EXO70基因家族全基因组的鉴定及种间比较[J]. 中国农业科学, 2023, 56(23): 4621-4634.

DONG YanYu, XU BiYu, DONG ZeYu, WANG LuYao, CHEN JinWen, FANG Lei. Genome-Wide Identification and Interspecific Comparative Analysis of the EXO70 Gene Family in Cotton[J]. Scientia Agricultura Sinica, 2023, 56(23): 4621-4634.

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参考文献 48

[1]	LI S P, VAN OS G M A, REN S C, YU D L, KETELAAR T, EMONS A M C, LIU C M. Expression and functional analyses of EXO70genes in Arabidopsis implicate their roles in regulating cell type-specific exocytosis. Plant Physiology, 2010, 154(4): 1819-1830. doi: 10.1104/pp.110.164178
[2]	WU L G, HAMID E, SHIN W, CHIANG H C. Exocytosis and endocytosis: Modes, functions, and coupling mechanisms. Annual Review of Physiology, 2014, 76: 301-331. doi: 10.1146/physiol.2014.76.issue-1
[3]	ZHANG L, XING J J, LIN J X. At the intersection of exocytosis and endocytosis in plants. The New Phytologist, 2019, 224(4): 1479-1489. doi: 10.1111/nph.v224.4
[4]	BONIFACINO J S, GLICK B S. The mechanisms of vesicle budding and fusion. Cell, 2004, 116(2): 153-166. doi: 10.1016/s0092-8674(03)01079-1 pmid: 14744428
[5]	PLESKOT R, CWIKLIK L, JUNGWIRTH P, ŽÁRSKÝ V, POTOCKÝ M. Membrane targeting of the yeast exocyst complex. Biochimica et Biophysica Acta, 2015, 1848(7): 1481-1489. doi: 10.1016/j.bbamem.2015.03.026 pmid: 25838123
[6]	YU I M, HUGHSON F M. Tethering factors as organizers of intracellular vesicular traffic. Annual Review of Cell and Developmental Biology, 2010, 26: 137-156. doi: 10.1146/annurev.cellbio.042308.113327 pmid: 19575650
[7]	TERBUSH D R, MAURICE T, ROTH D, NOVICK P. The Exocyst is a multiprotein complex required for exocytosis in Saccharomyces cerevisiae. The EMBO Journal, 1996, 15(23): 6483-6494. doi: 10.1002/embj.1996.15.issue-23
[8]	TERBUSH D R, NOVICK P. Sec6, Sec8, and Sec15 are components of a multisubunit complex which localizes to small bud tips in Saccharomyces cerevisiae. The Journal of Cell Biology, 1995, 130(2): 299-312. doi: 10.1083/jcb.130.2.299
[9]	HE B, GUO W. The exocyst complex in polarized exocytosis. Current Opinion in Cell Biology, 2009, 21(4): 537-542. doi: 10.1016/j.ceb.2009.04.007 pmid: 19473826
[10]	SYNEK L, SCHLAGER N, ELIÁS M, QUENTIN M, HAUSER M-T, ZÁRSKÝ V. AtEXO70A1, a member of a family of putative exocyst subunits specifically expanded in land plants, is important for polar growth and plant development. The Plant Journal, 2006, 48(1): 54-72. doi: 10.1111/tpj.2006.48.issue-1
[11]	FENDRYCH M, SYNEK L, PEČENKOVá T, TOUPALOVá H, COLE R, DRDOVá E, NEBESÁŘOVÁ J, ŠEDINOVÁ M, HÁLA M, FOWLER J E, ŽÁRSKÝ V. The Arabidopsis exocyst complex is involved in cytokinesis and cell plate maturation. The Plant Cell, 2010, 22(9): 3053-3065. doi: 10.1105/tpc.110.074351
[12]	WANG W, LIU N, GAO C Y, CAI H R, ROMEIS T, TANG D Z. The Arabidopsis exocyst subunits EXO70B1 and EXO70B2 regulate FLS2 homeostasis at the plasma membrane. The New Phytologist, 2020, 227(2): 529-544. doi: 10.1111/nph.v227.2
[13]	KULICH I, PEČENKOVÁ T, SEKEREŠ J, SMETANA O, FENDRYCH M, FOISSNER I, HÖFTBERGER M, ZÁRSKÝ V. Arabidopsis exocyst sub complex containing subunit EXO70B1 is involved in autophagy-related transport to the vacuole. Traffic (Copenhagen, Denmark), 2013, 14(11): 1155-1165. doi: 10.1111/tra.2013.14.issue-11
[14]	ZÁRSKÝ V, KULICH I, FENDRYCH M, PEČENKOVÁ T. Exocyst complexes multiple functions in plant cells secretory pathways. Current Opinion in Plant Biology, 2013, 16(6): 726-733. doi: 10.1016/j.pbi.2013.10.013 pmid: 24246229
[15]	LIU N, HAKE K, WANG W, ZHAO T, ROMEIS T, TANG D Z. Calcium-dependent protein kinase5 associates with the truncated NLR protein TIR-NBS2 to contribute to exo70B1-mediated immunity. The Plant Cell, 2017, 29(4): 746-759. doi: 10.1105/tpc.16.00822
[16]	LI S P, CHEN M, YU D L, REN S C, SUN S F, LIU L D, KETELAAR T, EMONS A M C, LIU C M. EXO70A1-mediated vesicle trafficking is critical for tracheary element development in Arabidopsis. The Plant Cell, 2013, 25(5): 1774-1786. doi: 10.1105/tpc.113.112144
[17]	KALMBACH L, HÉMATY K, DE BELLIS D, BARBERON M, FUJITA S, URSACHE R, DARASPE J, GELDNER N. Transient cell-specific EXO70A1 activity in the CASP domain and Casparian strip localization. Nature Plants, 2017, 3: 17058. doi: 10.1038/nplants.2017.58 pmid: 28436943
[18]	SYNEK L, VUKA¡INOVIĆ N, KULICH I, HÁLA M, ALDORFOVÁ K, FENDRYCH M, ŽÁRSKÝ V. EXO70C 2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology, 2017, 174(1): 223-240. doi: 10.1104/pp.16.01282
[19]	TU B, HU L, CHEN W L, LI T, HU B H, ZHENG L, LV Z, YOU S J, WANG Y P, MA B T, CHEN X W, QIN P, LI S G. Disruption of OsEXO70A1 causes irregular vascular bundles and perturbs mineral nutrient assimilation in rice. Scientific Reports, 2015, 5: 18609. doi: 10.1038/srep18609
[20]	FUJISAKI K, ABE Y, ITO A, SAITOH H, YOSHIDA K, KANZAKI H, KANZAKI E, UTSUSHI H, YAMASHITA T, KAMOUN S, TERAUCHI R. Rice Exo70 interacts with a fungal effector, AVR-Pii, and is required for AVR-Pii-triggered immunity. The Plant Journal, 2015, 83(5): 875-887. doi: 10.1111/tpj.12934 pmid: 26186703
[21]	DU Y, OVERDIJK E J R, BERG J A, GOVERS F, BOUWMEESTER K. Solanaceous exocyst subunits are involved in immunity to diverse plant pathogens. Journal of Experimental Botany, 2018, 69(3): 655-666. doi: 10.1093/jxb/erx442 pmid: 29329405
[22]	WANG H, MA Z H, MAO J, CHEN B H. Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L.). PeerJ, 2021, 9: e11176. doi: 10.7717/peerj.11176
[23]	丁颜朋, 葛晓阳, 王鹏, 吴洁, 王省芬, 李付广. 棉花盐胁迫应答基因GhEXO70B1功能分析. 棉花学报, 2018, 30(6): 423-434.
	DING Y P, GE X Y, WANG P, WU J, WANG X F, LI F G. Functional analysis of a salt stress response gene, GhEXO70B1, in upland cotton (Gossypium hirsutum L.). Cotton Science, 2018, 30(6): 423-434. (in Chinese)
[24]	ZHU Y Q, QIU L, LIU L L, LUO L, HAN X P, ZHAI Y H, WANG W J, REN M Z, XING Y D. Identification and comprehensive structural and functional analyses of the EXO70 gene family in cotton. Genes, 2021, 12(10): 1594. doi: 10.3390/genes12101594
[25]	DAI F, CHEN J D, ZHANG Z Q, LIU F J, LI J, ZHAO T, HU Y, ZHANG T Z, FANG L. COTTONOMICS: A comprehensive cotton multi-omics database. Database, 2022, 2022: baac080.
[26]	EL-GEBALI S, MISTRY J, BATEMAN A, EDDY S R, LUCIANI A, POTTER S C, QURESHI M, RICHARDSON L J, SALAZAR G A, SMART A, SONNHAMMER E L, HIRSH L, PALADIN L, PIOVESAN D, TOSATTO S C, FINN R D. The Pfam protein families database in 2019. Nucleic Acids Research, 2019, 47(D1): D427-D432.
[27]	CAMACHO C, COULOURIS G, AVAGYAN V, MA N, PAPADOPOULOS J, BEALER K, MADDEN T L. BLAST+: Architecture and applications. BMC Bioinformatics, 2009, 10: 421. doi: 10.1186/1471-2105-10-421 pmid: 20003500
[28]	BAILEY T L, BODEN M, BUSKE F A, FRITH M, GRANT C E, CLEMENTI L, REN J Y, LI W W, NOBLE W S. MEME Suite: Tools for motif discovery and searching. Nucleic Acids Research, 2009, 37(supp1_2): W202- W208. doi: 10.1093/nar/gkp335
[29]	CHEN C J, CHEN H, ZHANG Y, THOMAS H R, FRANK M H, HE Y H, XIA R. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 2020, 13(8): 1194-1202. doi: S1674-2052(20)30187-8 pmid: 32585190
[30]	WANG Y P, TANG H B, DEBARRY J D, TAN X, LI J P, WANG X Y, LEE T H, JIN H Z, MARLER B, GUO H, KISSINGER J C, PATERSON A H. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 2012, 40(7): e49. doi: 10.1093/nar/gkr1293
[31]	KRZYWINSKI M, SCHEIN J, BIROL I, CONNORS J, GASCOYNE R, HORSMAN D, JONES S J, MARRA M A. Circos: An information aesthetic for comparative genomics. Genome Research, 2009, 19(9): 1639-1645. doi: 10.1101/gr.092759.109 pmid: 19541911
[32]	CHEN S F, ZHOU Y Q, CHEN Y R, GU J. Fastp: An ultra-fast all-in- one FASTQ preprocessor. Bioinformatics, 2018, 34(17): i884-i890. doi: 10.1093/bioinformatics/bty560
[33]	KIM D, LANGMEAD B, SALZBERG S L. HISAT: A fast spliced aligner with low memory requirements. Nature Methods, 2015, 12(4): 357-360. doi: 10.1038/nmeth.3317 pmid: 25751142
[34]	LIAO Y, SMYTH G K, SHI W. FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 2014, 30(7): 923-930. doi: 10.1093/bioinformatics/btt656 pmid: 24227677
[35]	HU Y, CHEN J D, FANG L, ZHANG Z Y, MA W, NIU Y C, JU L Z, DENG J Q, ZHAO T, LIAN J M, BARUCH K, FANG D, LIU X, RUAN Y L, RAHMAN M U, HAN J L, WANG K, WANG Q, WU H T, MEI G F, ZANG Y H, HAN Z G, XU C Y, SHEN W J, YANG D F, SI Z F, DAI F, ZOU L F, HUANG F, BAI Y L, ZHANG Y G, BRODT A, BEN-HAMO H, ZHU X F, ZHOU B L, GUAN X Y, ZHU S J, CHEN X Y, ZHANG T Z. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nature Genetics, 2019, 51(4): 739-748. doi: 10.1038/s41588-019-0371-5
[36]	FANG L, GONG H, HU Y, LIU C X, ZHOU B L, HUANG T, WANG Y K, CHEN S Q, FANG D D, DU X M, CHEN H, CHEN J D, WANG S, WANG Q, WAN Q, LIU B L, PAN M Q, CHANG L J, WU H T, MEI G F, XIANG D, LI X H, CAI C P, ZHU X F, CHEN Z J, HAN B, CHEN X Y, GUO W Z, ZHANG T Z, HUANG X H. Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Genome Biology, 2017, 18(1): 33. doi: 10.1186/s13059-017-1167-5 pmid: 28219438
[37]	FANG L, ZHAO T, HU Y, SI Z F, ZHU X F, HAN Z G, LIU G Z, WANG S, JU L Z, GUO M L, MEI H, WANG L Y, QI B W, WANG H, GUAN X Y, ZHANG T Z. Divergent improvement of two cultivated allotetraploid cotton species. Plant Biotechnology Journal, 2021, 19(7): 1325-1336. doi: 10.1111/pbi.13547 pmid: 33448110
[38]	WANG K, LI M Y, HAKONARSON H. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 2010, 38(16): e164. doi: 10.1093/nar/gkq603
[39]	LI F G, FAN G Y, LU C R, XIAO G H, ZOU C S, KOHEL R J, MA Z Y, SHANG H H, MA X F, WU J Y, LIANG X M, HUANG G, PERCY R G, LIU K, YANG W H, CHEN W B, DU X M, SHI C C, YUAN Y L, YE W W, LIU X, ZHANG X Y, LIU W Q, WEI H L, WEI S J, HUANG G D, ZHANG X L, ZHU S J, ZHANG H, SUN F M, WANG X F, LIANG J, WANG J H, HE Q, HUANG L H, WANG J, CUI J J, SONG G L, WANG K B, XU X, YU J Z, ZHU Y X, YU S X. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nature Biotechnology, 2015, 33(5): 524-530. doi: 10.1038/nbt.3208
[40]	ZHU T, LIANG C Z, MENG Z G, SUN G Q, MENG Z, GUO S D, ZHANG R. CottonFGD: An integrated functional genomics database for cotton. BMC Plant Biology, 2017, 17(1): 101.
[41]	WANG M J, TU L L, YUAN D J, ZHU D, SHEN C, LI J Y, LIU F Y, PEI L L, WANG P C, ZHAO G N, YE Z X, HUANG H, YAN F L, MA Y Z, ZHANG L, LIU M, YOU J Q, YANG Y C, LIU Z P, HUANG F, LI B Q, QIU P, ZHANG Q H, ZHU L F, JIN S X, YANG X Y, MIN L, LI G L, CHEN L L, ZHENG H K, LINDSEY K, LIN Z X, UDALL J A, ZHANG X L. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature Genetics, 2019, 51(2): 224-229. doi: 10.1038/s41588-018-0282-x
[42]	KULICH I, VOJTÍKOVÁ Z, SABOL P, ORTMANNOVÁ J, NEDĚLA V, TIHLAŘÍKOVÁ E, ŽÁRSKÝ V. Exocyst subunit EXO70H4 has a specific role in callose synthase secretion and silica accumulation. Plant Physiology, 2018, 176(3): 2040-2051. doi: 10.1104/pp.17.01693 pmid: 29301954
[43]	YAMAZAKI T, KAWAMURA Y, MINAMI A, UEMURA M. Calcium-dependent freezing tolerance in Arabidopsis involves membrane resealing via synaptotagmin SYT1. The Plant Cell, 2009, 20(12): 3389-3404. doi: 10.1105/tpc.108.062679
[44]	SEKEREŠ J, PEJCHAR P, ŠANTRŮČEK J, VUKAŠINOVIĆ N, ŽÁRSKÝ V, POTOCKÝ M. Analysis of exocyst subunit EXO70 family reveals distinct membrane polar domains in tobacco pollen tubes. Plant Physiology, 2017, 173(3): 1659-1675. doi: 10.1104/pp.16.01709 pmid: 28082718
[45]	YU H H, LI M, SANDHU J, SUN G C, SCHNABLE J C, WALIA H, XIE W B, YU B, MOWER J P, ZHANG C. Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants. Nature Communications, 2022, 13: 820. doi: 10.1038/s41467-022-28449-8 pmid: 35145097
[46]	HURST L D. The Ka/Ks ratio: Diagnosing the form of sequence evolution. Trends in Genetics, 2002, 18(9): 486. doi: 10.1016/S0168-9525(02)02722-1
[47]	GUAN X Y, YU N, SHANGGUAN X X, WANG S, LU S, WANG L J, CHEN X Y. Arabidopsis trichome research sheds light on cotton fiber development mechanisms. Chinese Science Bulletin, 2007, 52(13): 1734-1741. doi: 10.1007/s11434-007-0273-2
[48]	KULICH I, VOJTÍKOVÁ Z, GLANC M, ORTMANNOVÁ J, RASMANN S, ŽÁRSKÝ V. Cell wall maturation of Arabidopsis trichomes is dependent on exocyst subunit EXO70H4 and involves callose deposition. Plant Physiology, 2015, 168(1): 120-131. doi: 10.1104/pp.15.00112