四倍体棉花GAE基因家族的鉴定及其在棉纤维发育中的表达分析

doi:10.11963/1002-7807.zsywsf.20190412

摘要/Abstract

摘要：

【目的】通过对陆地棉及海岛棉GAE基因家族进行全基因组分析,为深入研究GAE基因家族在棉纤维发育中的功能提供理论依据。【方法】利用生物信息学分析软件,对GAE基因家族进行全基因组鉴定,根据转录组数据分析在纤维发育过程中的表达规律。【结果】陆地棉GhGAE家族包含21个成员,海岛棉GbGAE家族有22个成员,分为3个亚组,多数GhGAEs和GbGAEs基因没有内含子,共分布在12条染色体上。GAE氨基酸序列保守基序有4个,保守性较强,且GAE蛋白均定位于高尔基体膜。根据GAEs在陆地棉、海岛棉纤维发育不同时期的表达变化,将其分为纤维起始期高表达、纤维伸长期高表达、次生壁增厚期高表达、全时期低表达4类模式。其中GhGAE01、GhGAE02、GhGAE11、GhGAE12在陆地棉中高水平表达,GbGAE01、GbGAE02、GbGAE11、GbGAE12在海岛棉中高水平表达,推测这些基因可能在纤维发育过程中发挥着重要作用。【结论】上述结果为研究GAE基因家族在棉纤维发育中的功能提供了参考依据。

关键词: 陆地棉; 海岛棉; 葡糖醛酸异构酶; 生物信息学; 纤维发育; 基因表达

Abstract:

[Objective] The UDP-D-glucuronate 4-epimerase (GAE) families of Gossypium hirsutum L. and G. barbadense were investigated from whole genomes to provide a theoretical basis for further studies regarding the GAE family’s function in cotton fiber development. [Methods] The GAE family was identified using bioinformatics analysis software, and the expression pattern during fiber development was analyzed using transcriptional data. [Results] In total, 21 and 22 GAE genes were systematically identified from G. hirsutum and G. barbadense, respectively. They were classified into three subfamilies. Most of the GhGAEs and GbGAEs had no introns. They co-distributed over 12 chromosomes and contained four conserved motifs. All of the GAE proteins were predicted to localize to the Golgi membrane. On the basis of changes in the GAEs’ expression levels at different stages of fiber development, GAE proteins were divided into four categories, high expression at the initial stage, high expression at the fiber elongation stage, high expression at the secondary wall thickening period and low expression during the whole period. GhGAE01, -02, -11 and -12 and GbGAE01, -02, -11 and -21 were highly expressed in G. hirsutum and G. barbadense, respectively. These genes might play important roles in fiber development. [Conclusion] These results provide useful references for studying the GAE gene family’s function in cotton fiber development.

Key words: Gossypium hirsutum; Gossypium barbadense; UDP-D-glucuronate 4-epimerase; bioinformatics; fiber development; gene expression

张松雨,王敬敬,刘正文,张艳,杨君,马峙英,王省芬. 四倍体棉花GAE基因家族的鉴定及其在棉纤维发育中的表达分析[J]. 棉花学报, 2019, 31(3): 169-181.

Zhang Songyu,Wang Jingjing,Liu Zhengwen,Zhang Yan,Yang Jun,Ma Zhiying,Wang Xingfen. Genome-wide Identification and Expression Analysis of GAE Gene Family in Fiber Developmental Stages of Tetraploid Cotton[J]. Cotton Science, 2019, 31(3): 169-181.

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链接本文: https://journal.cricaas.com.cn/Jweb_mhxb/CN/10.11963/1002-7807.zsywsf.20190412

https://journal.cricaas.com.cn/Jweb_mhxb/CN/Y2019/V31/I3/169

图/表 9

表1

四倍体棉花GAE基因家族信息"

基因名称 Gene name		基因ID Gene ID	染色体 Chromosome		起始 Start		结束 End		正负链 Strand		基因长度 Gene length/bp
GhGAE01		Gh_A02G0188	A02		2 087 283		2 088 644		+		1 362
GhGAE02		Gh_A05G3665	scaffold1168_A05		808 089		809 384		-		1 296
GhGAE03		Gh_A07G1357	A07		34 026 293		34 027 606		-		1 314
GhGAE04		Gh_A08G0266	A08		3 146 256		3 147 563		+		1 308
GhGAE05		Gh_A08G1215	A08		82 487 321		82 488 622		-		1 302
GhGAE06		Gh_A08G1563	A08		93 761 589		93 762 890		+		1 302
基因名称 Gene name	基因 ID Gene ID			染色体 Chromosome		起始 Start		结束 End		正负链 Strand	基因长度 Gene length/bp
GhGAE07	Gh_A08G2086			A08		102 118 419		102 119 711		+	1 293
GhGAE08	Gh_A10G1134			A10		57 669 306		57 670 670		+	1 365
GhGAE09	Gh_A11G0732			A11		7 083 415		7 084 728		+	1 314
GhGAE10	Gh_A11G1930			A11		52 535 439		52 536 113		-	675
GhGAE11	Gh_D02G0251			D02		2 891 062		2 892 423		+	1 362
GhGAE12	Gh_D04G0825			D04		20 679 620		20 680 645		+	1 026
GhGAE13	Gh_D07G1467			D07		25 168 767		25 170 080		-	1 314
GhGAE14	Gh_D08G2643			scaffold4246_D08		34 442		35 734		-	1 293
GhGAE15	Gh_D08G0358			D08		3 677 295		3 678 602		+	1 308
GhGAE16	Gh_D08G0951			D08		22 608 909		22 610 210		+	1 302
GhGAE17	Gh_D08G1498			D08		48 297 925		48 299 226		-	1 302
GhGAE18	Gh_D08G1869			D08		56 351 467		56 352 768		+	1 302
GhGAE19	Gh_D10G1364			D10		26 732 408		26 733 772		-	1 365
GhGAE20	Gh_D11G0850			D11		7 329 977		7 331 290		+	1 314
GhGAE21	Gh_D11G2045			D11		27 910 635		27 912 195		+	1 561
GbGAE01	GOBAR_AA14816			A02		1 452 713		1 454 074		+	1 362
GbGAE02	GOBAR_AA14388			A05		79 544 094		79 545 389		-	1 296
GbGAE03	GOBAR_AA20553			A07		34 785 514		34 786 827		+	1 314
GbGAE04	GOBAR_AA30469			A08		3 847 003		3 848 310		+	1 308
GbGAE05	GOBAR_AA07847			A08		94 867 417		94 868 679		-	1 263
GbGAE06	GOBAR_AA11853			A08		106 694 793		106 697 068		+	2 276
GbGAE07	GOBAR_AA16747			A08		114 650 493		114 651 527		+	1 035
GbGAE08	GOBAR_AA18409			A10		66 170 970		66 172 334		+	1 365
GbGAE09	GOBAR_AA15397			A11		7 544 121		7 547 075		-	2 955
GbGAE10	GOBAR_AA01034			A11		58 750 135		58 751 432		-	1 298
GbGAE11	GOBAR_DD03925			scaffold_1714.D02		142 014		143 375		-	1 362
GbGAE12	GOBAR_DD07164			D04		18 368 064		18 369 359		-	1 296
GbGAE13	GOBAR_DD16379			D07		26 645 567		26 646 880		+	1 314
GbGAE14	GOBAR_DD35403			D08		3 636 334		3 637 641		-	1 308
GbGAE15	GOBAR_DD35402			D08		3 639 960		3 641 267		-	1 308
GbGAE16	GOBAR_DD04906			D08		20 166 196		20 167 497		-	1 302
GbGAE17	GOBAR_DD15982			D08		46 615 876		46 617 138		+	1 263
GbGAE18	GOBAR_DD03498			D08		54 225 052		54 227 332		+	2 281
GbGAE19	GOBAR_DD21430			D08		62 145 468		62 146 082		+	615
GbGAE20	GOBAR_DD00120			scaffold_1910.D10		221 244		222 608		-	1 365
GbGAE21	GOBAR_DD17456			D11		7 063 278		7 067 530		-	4 253
GbGAE22	GOBAR_DD18142			D11		26 455 969		26 457 524		+	1 556

表1

图1

图2

图3

表2

图4

表3

四倍体棉花GAE基因家族理化性质及亚细胞定位"

基因名称 Gene name	氨基酸数量 Number of amino acids	分子量Molecular weight/kDa	理论等电点 Theoretical pI	蛋白不稳定指数 Instability index	脂溶指数 Aliphatic index	总平均疏水性 GRAVY	亚细胞定位Subcellular location	跨膜区数量 Numbers of transmembrane domain
GhGAE01	453	50.263	9.61	29.92	84.59	-0.257	Golgi membrane	3
GhGAE02	431	47.757	9.62	33.90	80.77	-0.248	Golgi membrane	2
GhGAE03	437	48.519	9.96	49.90	82.38	-0.242	Golgi membrane	1
GhGAE04	435	48.612	9.93	47.15	81.38	-0.234	Golgi membrane	1
GhGAE05	433	48.289	9.94	47.22	80.65	-0.251	Golgi membrane	2
GhGAE06	433	47.615	9.91	42.92	86.49	-0.208	Golgi membrane	2
基因名称 Gene name	氨基酸数量 Number of amino acids	分子量Molecular weight/kDa	理论等电点 Theoretical pI	蛋白不稳定指数 Instability index	脂溶指数 Aliphatic index	总平均疏水性 GRAVY	亚细胞定位Subcellular location	跨膜区数量 Numbers of transmembrane domain
GhGAE07	430	47.884	9.69	37.54	80.30	-0.272	Golgi membrane	2
GhGAE08	454	50.082	9.70	30.01	85.51	-0.248	Golgi membrane	1
GhGAE09	437	48.481	9.83	46.73	83.71	-0.228	Golgi membrane	1
GhGAE10	224	24.865	10.34	42.42	94.46	-0.140	Golgi membrane	2
GhGAE11	453	50.322	9.61	28.63	83.93	-0.275	Golgi membrane	3
GhGAE12	275	30.004	9.70	28.75	91.42	-0.217	Golgi membrane	0
GhGAE13	437	48.533	9.98	49.07	82.38	-0.243	Golgi membrane	1
GhGAE14	430	47.916	9.69	37.74	79.63	-0.277	Golgi membrane	2
GhGAE15	435	48.606	9.86	44.06	81.15	-0.225	Golgi membrane	1
GhGAE16	355	39.586	9.02	49.04	72.03	-0.334	Golgi membrane	1
GhGAE17	433	48.161	9.91	47.34	80.65	-0.253	Golgi membrane	2
GhGAE18	433	47.609	9.90	39.32	88.52	-0.185	Golgi membrane	2
GhGAE19	454	50.167	9.72	29.51	85.51	-0.256	Golgi membrane	1
GhGAE20	437	48.397	9.76	47.37	83.71	-0.211	Golgi membrane	1
GhGAE21	389	42.762	10.00	45.10	94.47	-0.133	Golgi membrane	1
GbGAE01	453	50.277	9.61	29.92	84.59	-0.257	Golgi membrane	3
GbGAE02	431	47.772	9.62	34.10	81.00	-0.248	Golgi membrane	2
GbGAE03	437	48.535	9.96	49.90	81.92	-0.249	Golgi membrane	1
GbGAE04	435	48.711	9.93	47.15	81.38	-0.235	Golgi membrane	1
GbGAE05	402	44.774	9.84	44.61	81.04	-0.276	Golgi membrane	0
GbGAE06	438	48.609	9.41	39.22	86.80	-0.151	Golgi membrane	0
GbGAE07	344	37.801	9.40	34.69	80.84	-0.164	Golgi membrane	2
GbGAE08	454	50.116	9.72	29.32	84.65	-0.253	Golgi membrane	1
GbGAE09	491	54.175	9.71	41.44	88.19	-0.095	Golgi membrane	2
GbGAE10	407	44.842	9.97	37.73	92.26	-0.148	Golgi membrane	2
GbGAE11	453	50.301	9.57	28.23	84.37	-0.266	Golgi membrane	3
GbGAE12	431	47.757	9.62	34.54	81.00	-0.248	Golgi membrane	2
GbGAE13	437	48.549	9.98	49.07	81.92	-0.249	Golgi membrane	2
GbGAE14	435	48.621	9.86	44.81	81.38	-0.226	Golgi membrane	1
GbGAE15	435	48.606	9.88	44.03	82.05	-0.218	Golgi membrane	1
GbGAE16	388	43.167	9.33	43.75	74.18	-0.313	Golgi membrane	2
GbGAE17	402	44.778	9.82	45.41	80.07	-0.280	Golgi membrane	0
GbGAE18	536	60.253	9.47	41.77	83.47	-0.298	Golgi membrane	0
GbGAE19	204	22.55	9.01	43.29	86.57	-0.069	Golgi membrane	1
GbGAE20	454	50.096	9.72	29.41	85.51	-0.249	Golgi membrane	1
GbGAE21	569	62.529	9.64	42.12	86.91	-0.191	Golgi membrane	1
GbGAE22	340	37.455	9.51	36.68	84.32	-0.225	Golgi membrane	0

表3

图5

图6

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序号	保守基序 Conservative motif	整体序列 Whole representation
1	TDQPASLYAATKKAGEEIAHTYNHIYGLSLTGLRFFTVYGPWGRPDMAYF	TDQPASLYAATKKAGEEI[AT]HTYNHIYGLS[LI]TGLRFFTVYGPWGRPDMAYF
2	FTHVMHLAAQAGVRYAMZNPGSYVHSNIAGFVNLLEVCKSANPQPAIVWA	FTHV[ML]HLAAQAGVRYAM[EQ]NP[GQ]SYVHSNIAG[FL]V[NST]LLEV[CA]K[SA]ANPQPAIVWA
3	MKLPRNGDVPFTHANISLAQRELGYKPTTDLQTGLKKFVRW	[MV]K[LM]P[RG]NGDV[PQ]FTHAN[IV][ST]LAQ[RK][ED][LF]GYKP[TS]TDLQ[TA]GL[KR]KFV[RK]W
4	KGCLGALDTAEKSTGSGGKKKGPAQLRVYNLG	KGCL[GA][AS]LDT[AS][EKG]KSTGSGGKK[KR]GPA[QP][LY]R[VI][YF]NLG