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作物杂志,2018, 第6期: 58–67 doi: 10.16035/j.issn.1001-7283.2018.06.010

• 遗传育种·种质资源·生物技术 • 上一篇    下一篇

小麦GASA基因家族生物信息学分析

吕亮杰,陈希勇,张业伦,刘茜,王莉梅,马乐,李辉   

  1. 河北省农林科学院粮油作物研究所/河北省作物遗传育种实验室,050035,河北石家庄
  • 收稿日期:2018-06-18 修回日期:2018-09-06 出版日期:2018-12-15 发布日期:2018-12-06
  • 作者简介:吕亮杰,助理研究员,主要从事小麦遗传育种研究
  • 基金资助:
    河北省现代农业科技创新工程项目(F18R01;494-0402-YBN-RDC4);河北省农林科学院财政专项(F17R0013;2018060303);河北省农林科学院粮油作物研究所开放课题(LYS2016004)

Bioinformatics Identification of GASA Gene Family Expression Profiles in Wheat

Lü Liangjie,Chen Xiyong,Zhang Yelun,Liu Qian,Wang Limei,Ma Le,Li Hui   

  1. Hebei Academy of Agriculture and Forestry Sciences, Institute of Cereal and Oil Crops/Crop Genetics and Breeding Laboratory of Hebei, Shijiazhuang 050035, Hebei, China
  • Received:2018-06-18 Revised:2018-09-06 Online:2018-12-15 Published:2018-12-06

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摘要：

赤霉素调节的GASA（Gibberellic Acid-Stimulated in Arabidopsis）基因家族是植物特有的转录因子家族,在调控植物生长发育过程中起重要作用。关于小麦GASA基因家族全基因组分析的研究尚未见报道。为进一步探讨小麦GASA基因的功能,通过对小麦最新基因组数据进行分析,获得了35个TaGASA基因,命名为TaGASAs,根据染色体编号排列为TaGASA1~TaGASA35。结合公布的小麦品种Chinese Spring的基因组数据,采用生物信息学方法对其基因结构、染色体分布、蛋白结构、系统进化及表达谱进行了分析。结果表明,35个小麦TaGASA基因分布于除3A、4A、3B、3D染色体外的其余17条染色体上,基因编码长度为78~264个氨基酸的蛋白质,基因外显子数量从2个到7个不等;串联重复片段分析结果表明,片段复制和串联重复是小麦TaGASA家族基因扩张的主要模式;小麦TaGASA蛋白进化树和7种作物GASA基因的系统进化树表明,GASA基因分为4个类别,同一类之间的结构较为相似;小麦35个TaGASA基因家族成员含有10个motif,推测小麦TaGASA基因家族应都含有motif1、motif2和motif3。在13个组织器官中都检测到了35个TaGASA基因的转录本,不同组织器官中TaGASA基因的表达存在明显差异。

关键词: 小麦, GASA, 生物信息学, 进化树, 表达谱

Abstract:

The Gibberellic Acid-Stimulated in Arabidopsis (GASA) gene family is a specific transcription factor in the plant that plays an important role in the regulation of plant growth and development. However,genome-wide analysis of the GASA gene family has not been reported in wheat. To further explore the function of the wheat GASA gene, 35 TaGASA genes, named TaGASAs, were obtained by analyzing the latest genomic data of wheat and were ranked according to the chromosome number as TaGASA1-TaGASA35. Combined with the published genome data of cultivar Chinese Spring, genes structure, chromosome distribution, the conserved domain of proteins, phylogenetic trees and gene expression profiles of the wheat cultivars were analyzed using bioinformatics methods. The results showed that 35 wheat TaGASA genes were distributed on the remaining 17 chromosomes except for 3A, 4A, 3B and 3D chromosomes. The genes encoded 78-264 amino acids in length and the number of gene exons was from 2 to 7. The results of tandem repeat analysis showed that fragment replication and tandem repeats were the main patterns of gene expansion in the wheat TaGASA family. The phylogenetic tree of wheat TaGASA proteins and the seven crops GASA proteins showed that GASA genes were divided into four categories, and the structure of the same class was similar. The 35 TaGASA genes family in wheat contain 10 motifs, and it is speculated that the wheat TaGASA gene family should contain motif1, motif2 and motif3. 35 TaGASA genes were all detected in 13 tissues and organs, and the expression of TaGASA genes in different tissues were significantly different.

Key words: Wheat, GASA, Bioinformatics, Phylogenetic tree, Expression profiling

表1

35个小麦TaGASA基因的基本信息"

基因名
Gene name		 基因号
Gene ID		 染色体
Chromosome		 基因位置
Gene position		 编码区长度(bp)
Coding sequence length		 蛋白质预测Protein prediction
氨基酸
Amino acid		 分子量（kDa）
Molecular mass		 等电点
Isoelectric point
TaGASA1 TRIAE_CS42_1AL_TGACv1_000841_AA0020140 1AL 11 587-12 505 234 78 8 614.10 8.86
TaGASA2 TRIAE_CS42_1AL_TGACv1_001082_AA0024620 1AL 45 226-52 080 276 92 9 682.22 8.63
TaGASA3 TRIAE_CS42_1AL_TGACv1_001087_AA0024740 1AL 80 457-81 335 309 103 11 179.17 8.81
TaGASA4 TRIAE_CS42_2AS_TGACv1_113018_AA0349790 2AS 10 196-10 865 276 92 10 008.82 8.63
TaGASA5 TRIAE_CS42_5AL_TGACv1_374351_AA1197750 5AL 109 217-110 185 336 112 12 493.61 8.72
TaGASA6 TRIAE_CS42_5AL_TGACv1_375002_AA1213750 5AL 39 823-40 585 282 94 9 785.41 8.90
TaGASA7 TRIAE_CS42_5AL_TGACv1_377138_AA1244440 5AL 8 818-10 778 294 98 10 405.23 9.01
TaGASA8 TRIAE_CS42_6AL_TGACv1_470886_AA1497600 6AL 203 827-205 475 348 116 11 953.76 8.27
TaGASA9 TRIAE_CS42_7AS_TGACv1_569647_AA1821120 7AS 74 216-74 910 303 101 10 250.03 8.97
TaGASA10 TRIAE_CS42_1BL_TGACv1_030884_AA0102980 1BL 104 154-105 075 309 103 11 352.46 8.80
TaGASA11 TRIAE_CS42_1BL_TGACv1_031264_AA0110580 1BL 17 666-18 665 276 92 9 775.39 8.62
TaGASA12 TRIAE_CS42_1BL_TGACv1_031280_AA0110820 1BL 12 426-13 100 288 96 10 283.13 9.34
TaGASA13 TRIAE_CS42_1BL_TGACv1_031520_AA0115510 1BL 89 188-90 015 276 92 9 748.32 8.46
TaGASA14 TRIAE_CS42_2BS_TGACv1_146134_AA0456280 2BS 148 955-149 945 315 105 10 795.84 8.47
TaGASA15 TRIAE_CS42_2BS_TGACv1_146482_AA0466170 2BS 94 799-95 305 276 92 9 946.66 8.44
TaGASA16 TRIAE_CS42_2BS_TGACv1_146482_AA0466210 2BS 106 417-115 675 792 264 28 627.28 8.64
TaGASA17 TRIAE_CS42_2BL_TGACv1_130684_AA0416060 2BL 40 977-41 825 321 107 10 985.85 8.90
TaGASA18 TRIAE_CS42_4BS_TGACv1_328307_AA1086010 4BS 137 696-138 720 294 98 10 390.35 9.30
TaGASA19 TRIAE_CS42_5BL_TGACv1_404222_AA1291170 5BL 136 136-149 510 501 167 17 405.47 9.34
基因名
Gene name		 基因号
Gene ID		 染色体
Chromosome		 基因位置
Gene position		 编码区长度(bp)
Coding sequence length		 蛋白质预测Protein prediction
氨基酸
Amino acid		 分子量（kDa）
Molecular mass		 等电点
Isoelectric point
TaGASA20 TRIAE_CS42_5BL_TGACv1_405876_AA1336880 5BL 8 923-10 104 336 112 12 488.54 8.44
TaGASA21 TRIAE_CS42_6BL_TGACv1_499717_AA1589900 6BL 81 146-82 979 321 107 10 970.83 8.77
TaGASA22 TRIAE_CS42_7BS_TGACv1_593258_AA1949920 7BS 57 596-58 508 297 99 10 235.10 9.06
TaGASA23 TRIAE_CS42_7BL_TGACv1_578066_AA1888740 7BL 32 717-33 645 366 122 13 359.77 9.30
TaGASA24 TRIAE_CS42_1DL_TGACv1_061126_AA0186270 1DL 98 006-98 923 276 92 9 792.37 8.46
TaGASA25 TRIAE_CS42_1DL_TGACv1_061126_AA0186290 1DL 149 160-150 029 276 92 9 720.31 8.62
TaGASA26 TRIAE_CS42_1DL_TGACv1_061906_AA0205490 1DL 58 046-58 960 309 103 11 217.24 8.86
TaGASA27 TRIAE_CS42_2DS_TGACv1_177275_AA0571860 2DS 135 526-136 135 276 92 9 919.81 8.99
TaGASA28 TRIAE_CS42_2DS_TGACv1_179436_AA0607130 2DS 19 436-20 154 312 104 10 670.67 8.47
TaGASA29 TRIAE_CS42_4DS_TGACv1_362006_AA1175620 4DS 35 367-36 295 294 98 10 387.39 9.41
TaGASA30 TRIAE_CS42_5DL_TGACv1_433605_AA1417320 5DL 17 722-18 845 333 111 12 308.25 8.44
TaGASA31 TRIAE_CS42_5DL_TGACv1_433682_AA1419290 5DL 8 699-10 005 294 98 10 386.18 8.90
TaGASA32 TRIAE_CS42_5DL_TGACv1_435968_AA1456750 5DL 11 236-15 210 744 248 26 889.90 9.14
TaGASA33 TRIAE_CS42_6DL_TGACv1_527263_AA1701530 6DL 12 943-14 520 354 118 12 265.15 8.47
TaGASA34 TRIAE_CS42_7DS_TGACv1_622044_AA2031550 7DS 2 526-3 744 282 94 9 921.88 9.24
TaGASA35 TRIAE_CS42_7DL_TGACv1_602652_AA1963930 7DL 31 497-33 925 387 129 14 160.53 9.18

图1

小麦TaGASA基因同源进化分析"

图2

小麦TaGASA基因家族的蛋白系统进化树和基因结构"

图3

小麦与其他物种GASA基因的系统进化树"

图4

小麦TaGASA基因家族的motif分析"

图5

小麦TaGASA基因家族的蛋白三级结构"

图6

小麦TaGASA基因在不同组织器官中的表达谱分析 1：胚芽鞘;2：胚根;3：胚乳;4：根;5：花冠;6：叶;7：幼穗;8：花苞;9：雌蕊;10：花药;11：3~5 DAP颖果;12：22 DAP胚;13：22 DAP胚乳"

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