棉花学报 ›› 2019, Vol. 31 ›› Issue (3): 169-181.doi: 10.11963/1002-7807.zsywsf.20190412
• 研究与进展 • 下一篇
张松雨(),王敬敬,刘正文,张艳,杨君,马峙英,王省芬*(
)
收稿日期:
2018-02-28
发布日期:
2019-05-29
通讯作者:
王省芬
E-mail:303029052@qq.com;cotton@hebau.edu.cn
作者简介:
张松雨(1991―),女,硕士, 基金资助:
Zhang Songyu(),Wang Jingjing,Liu Zhengwen,Zhang Yan,Yang Jun,Ma Zhiying,Wang Xingfen*(
)
Received:
2018-02-28
Published:
2019-05-29
Contact:
Wang Xingfen
E-mail:303029052@qq.com;cotton@hebau.edu.cn
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。
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.
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2
四倍体棉花GAE基因家族保守基序"
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 |
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 |
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