棉花β-tubulin基因家族的鉴定及其在纤维发育中的表达

doi:10.3864/j.issn.0578-1752.2023.23.003

Abstract

Abstract:

【Objective】β-tubulin is the basic structural unit of cotton fiber, regulates fiber cell morphogenesis, and plays a vital role in fiber development. But there is less understood how β-tubulin gene influenced the distinct characteristic of fiber quality traits in cotton. In this study, members of the β-tubulin gene family were identified in cotton, their expression profiles were analyzed, and role of β-tubulin genes were explored for fiber quality. 【Method】BLAST method was used to identify members of the β-tubulin gene family in the genomes of four cotton species. ProtParam tool was utilized to analyze physicochemical properties, MEGA7.0 to construct phylogenetic tree, Mapchart2.2 to draw chromosomal localization map, MEME to analyze conserved motif, and PlantCARE to analyze promoter cis-acting elements. Expression levels of β-tubulin genes were characterized by using transcriptome data from 39 studies on fiber development. Spearman correlation analysis was used to identify candidate genes for fiber quality traits. 【Result】Importantly, 36, 37, 19 and 18 β-tubulin genes were identified in the genomes of Gossypium hirsutum (AD₁), Gossypium barbadense (AD₂), Gossypium arboretum (A₂) and Gossypium raimondii (D₅), respectively. The number of β-tubulin genes in tetraploid cotton species is almost double than that of diploid cotton species. Phylogenetic analysis classified these genes into 5 main clusters. Phylogenetic and collinearity analysis revealed that β-tubulin genes in Gossypium barbadense is closely related to Gossypium arboretum and Gossypium raimondii as compared to Gossypium hirsutum. Furthermore, all genes have typical conservative domains with Tubulin and Tubulin-C. The genes physicochemical properties showed amino acids range from 421 to 508 with isoelectric point of 4.68 to 5.09. The analysis of promoter cis-acting elements identified growth responsive, hormone responsive, and stress responsive elements which showed β-tubulin mediates various mechanisms of cell growth regulation. Interestingly, cluster analysis on 36 β-tubulin gene expression profiles showed 42% genes in cluster П had dominant expression in fiber. In particular, 1, 6, and 11 β-tubulin genes exhibited significant correlation with fiber micronaire value, fiber strength, and fiber length, respectively. Four genes were found to influence fiber length and fiber strength traits simultaneously. 【Conclusion】A total of 110 β-tubulin gene family members were identified in the four cotton species. Their physicochemical properties and sequences of amino acids were highly conserved and the promoter sequence had diverse regulatory elements. This study characterized the expression profiles as well as molecular function of β-tubulin gene family in cotton fiber. Further discovered the potential candidate genes that probably regulate fiber quality traits in cotton. Our results may have great potential for cotton fiber quality improvement by genetic engineering.

Key words: cotton, β-tubulin gene family, bioinformatics, expression analysis, fiber development

DANG YuanYue, MA JianJiang, YANG ShuXian, SONG JiKun, JIA Bing, FENG Pan, CHEN QuanJia, YU JiWen. Genome-Wide Identification and Expression Analysis of β-tubulin Family in Cotton Fiber Development[J].Scientia Agricultura Sinica, 2023, 56(23): 4585-4601.

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https://www.chinaagrisci.com/EN/Y2023/V56/I23/4585

Figures/Tables 8

Fig. 1

Table 1

Basic physicochemical properties of β-tubulin gene family in cotton"

物种 Species	基因ID Gene ID	等电点 pI	分子量 Molecular weight (kDa)	蛋白长度 <BOLD>P</BOLD>rotein length (aa)	亚细胞定位 Subcellular localization
陆地棉 Gossypium hirsutum	GH_A01G1087	4.74	50.65	452	细胞质Cytoplasm
	GH_A03G0257	4.76	50.13	445	细胞核Nucleus
	GH_A03G0258	4.76	50.07	445	细胞核Nucleus
	GH_A03G0260	5.09	55.66	495	叶绿体Chloroplast
	GH_A03G0596	4.75	50.00	444	细胞核Nucleus
	GH_A03G0911	4.73	50.21	447	细胞质Cytoplasm
	GH_A05G0919	4.74	50.30	446	细胞核Nucleus
	GH_A05G1119	4.76	50.01	445	细胞质Cytoplasm
	GH_A05G1860	4.70	50.50	450	细胞核Nucleus
	GH_A05G2570	4.80	50.66	449	细胞核Nucleus
	GH_A06G0029	4.79	50.39	449	细胞核Nucleus
	GH_A08G2076	4.76	50.00	445	细胞核Nucleus
	GH_A08G2085	4.79	49.85	444	细胞核Nucleus
	GH_A09G0513	4.68	50.59	448	细胞质Cytoplasm
	GH_A09G1787	4.86	53.27	472	内质网Endoplasmic reticulum
	GH_A09G1903	4.76	49.73	445	细胞核Nucleus
	GH_A11G3495	4.75	50.30	447	细胞核Nucleus
	GH_A13G2534	4.75	49.97	444	细胞核Nucleus
	GH_D01G1129	4.68	50.71	452	细胞核Nucleus
	GH_D02G1082	4.72	50.21	447	细胞质Cytoplasm
	GH_D03G1367	4.75	50.00	444	细胞核Nucleus
	GH_D03G1707	4.86	49.98	444	细胞核Nucleus
	GH_D03G1709	4.76	50.10	445	细胞核Nucleus
	GH_D03G1710	4.76	50.13	445	细胞核Nucleus
	GH_D05G0911	4.70	50.21	446	细胞核Nucleus
	GH_D05G1114	4.74	50.14	446	细胞质Cytoplasm
	GH_D05G1898	4.70	50.52	450	细胞核Nucleus
	GH_D06G0016	4.73	50.67	452	细胞核Nucleus
	GH_D07G1281	4.77	50.26	447	细胞核Nucleus
	GH_D08G2085	4.76	50.00	445	细胞核Nucleus
	GH_D08G2099	4.79	49.83	444	细胞核Nucleus
	GH_D09G0508	4.71	50.36	447	细胞核Nucleus
	GH_D09G1737	4.89	53.36	472	细胞质Cytoplasm
	GH_D09G1854	4.80	49.82	445	细胞核Nucleus
	GH_D11G3501	4.75	50.30	447	细胞核Nucleus
	GH_D13G2529	4.75	49.95	444	细胞核Nucleus
海岛棉 Gossypium barbadense	GB_A01G1091	4.72	50.65	452	细胞质Cytoplasm
	GB_A03G0251	4.76	50.13	445	细胞核Nucleus
	GB_A03G0252	4.76	50.07	445	细胞核Nucleus
	GB_A03G0254	4.85	49.88	444	细胞核Nucleus
	GB_A03G0586	4.75	50.01	444	细胞核Nucleus
	GB_A03G0919	4.75	50.18	447	叶绿体Chloroplast
	GB_A05G0927	4.70	50.24	446	细胞核Nucleus
	GB_A05G1127	4.76	50.01	445	细胞质Cytoplasm
	GB_A05G1887	4.70	50.50	450	细胞核Nucleus
	GB_A05G2602	4.77	50.66	449	细胞核Nucleus
	GB_A06G0033	4.77	50.78	452	细胞核Nucleus
	GB_A08G2182	4.76	50.00	445	细胞核Nucleus
	GB_A08G2191	4.79	49.85	444	细胞核Nucleus
	GB_A09G0575	4.68	50.59	448	细胞质Cytoplasm
	GB_A09G1907	4.86	53.27	472	内质网Endoplasmic reticulum
	GB_A09G2018	4.76	49.72	445	细胞核Nucleus
	GB_A11G3569	4.75	50.30	447	细胞核Nucleus
	GB_A13G2683	4.75	49.97	444	细胞核Nucleus
	GB_D01G1171	4.68	50.71	452	细胞核Nucleus
	GB_D02G1129	4.75	50.80	452	细胞质Cytoplasm
	GB_D03G1389	4.75	50.00	444	细胞核Nucleus
	GB_D03G1742	4.86	49.98	444	细胞核Nucleus
	GB_D03G1744	4.76	50.10	445	细胞核Nucleus
	GB_D03G1745	4.76	50.13	445	细胞核Nucleus
	GB_D05G0908	4.70	50.21	446	细胞核Nucleus
	GB_D05G1112	4.74	50.14	446	细胞质Cytoplasm
	GB_D05G1913	4.70	50.52	450	细胞核Nucleus
	GB_D05G2606	4.76	47.37	421	细胞核Nucleus
	GB_D06G0034	4.73	50.67	452	细胞核Nucleus
	GB_D07G1286	4.81	50.33	447	细胞核Nucleus
	GB_D08G2163	4.76	50.00	445	细胞核Nucleus
	GB_D08G2175	4.79	49.83	444	细胞核Nucleus
	GB_D09G0514	4.70	50.44	447	细胞核Nucleus
	GB_D09G1750	4.86	53.38	472	细胞质Cytoplasm
	GB_D09G1866	4.80	49.82	445	细胞核Nucleus
	GB_D11G3544	5.08	57.42	508	叶绿体Chloroplast
	GB_D13G2621	4.75	49.97	444	细胞核Nucleus
亚洲棉 Gossypium arboretum	Ga01G1198	4.72	48.89	436	细胞核Nucleus
	Ga01G2180	4.75	50.00	444	细胞核Nucleus
	Ga01G2554	4.76	50.13	445	细胞核Nucleus
	Ga01G2555	4.76	50.08	445	细胞核Nucleus
	Ga01G2557	4.85	49.86	444	细胞核Nucleus
	Ga03G1117	4.73	50.21	447	细胞质Cytoplasm
	Ga05G0964	4.70	48.91	433	细胞质Cytoplasm
	Ga05G1174	4.76	50.01	445	细胞质Cytoplasm
	Ga05G1974	4.70	50.52	450	细胞核Nucleus
	Ga05G2720	4.79	50.70	449	细胞核Nucleus
	Ga06G0039	4.77	50.78	452	细胞核Nucleus
	Ga07G1306	4.81	50.32	447	细胞核Nucleus
	Ga08G2131	4.76	50.00	445	细胞核Nucleus
	Ga08G2143	4.79	49.85	444	细胞核Nucleus
	Ga09G0571	4.68	50.58	448	细胞核Nucleus
	Ga09G1894	4.76	49.71	445	细胞核Nucleus
	Ga09G1948	4.76	50.19	445	细胞核Nucleus
	Ga11G0323	4.75	50.30	447	细胞核Nucleus
	Ga13G2741	4.75	49.97	444	细胞核Nucleus
雷蒙德氏棉 Gossypium raimondii	Gorai.001G132500	4.81	50.32	447	细胞核Nucleus
	Gorai.002G123400	4.68	50.71	452	细胞核Nucleus
	Gorai.003G126300	4.75	50.00	444	细胞核Nucleus
	Gorai.003G159100	4.86	49.98	444	细胞核Nucleus
	Gorai.003G159300	4.76	50.07	445	细胞核Nucleus
	Gorai.003G159400	4.76	50.12	445	细胞核Nucleus
	Gorai.004G210600	4.76	50.00	445	细胞核Nucleus
	Gorai.004G211800	4.79	49.83	444	细胞核Nucleus
	Gorai.005G118100	4.72	50.20	447	细胞质Cytoplasm
	Gorai.006G049000	4.70	50.51	448	细胞核Nucleus
	Gorai.006G179900	4.86	53.38	472	细胞质Cytoplasm
	Gorai.006G191900	4.80	49.74	445	细胞核Nucleus
	Gorai.007G351900	4.75	50.30	447	细胞核Nucleus
	Gorai.009G094600	4.70	50.21	446	细胞核Nucleus
	Gorai.009G115600	4.74	50.14	446	细胞质Cytoplasm
	Gorai.009G194500	4.70	50.52	450	细胞核Nucleus
	Gorai.010G003800	4.73	50.67	452	细胞核Nucleus
	Gorai.013G261300	4.75	49.95	444	细胞核Nucleus

Table 1

Fig. 2

Fig. 3

Fig. 4

Fig. 5

Fig.6

Fig. 7

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Genome-Wide Identification and Expression Analysis of β-tubulin Family in Cotton Fiber Development

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