毛果杨GATA基因家族全基因组水平鉴定及表达分析

doi:10.7525/j.issn.1673-5102.2021.01.014

摘要/Abstract

摘要：

GATA转录因子基因家族在植物生长发育、细胞分化以及响应环境变化中具有重要作用。然而，目前在木本植物中尚无该基因家族全基因组水平的分析报导。本项研究从基因组水平对毛果杨GATA家族成员的数量、基因结构、染色体定位、系统进化、编码蛋白的理化特征和保守基序等信息进行了系统分析，结果表明，毛果杨GATA家族包含39个基因，共分布于15条染色体上，其中5号染色体上含有6个基因，9号、13号和19号染色体含有基因数量为1，其余染色上无基因分布。该家族各基因的结构与编码蛋白的基本特性均存在一定异性，可分成4个亚族。qRT-PCR研究表明，GATA家族各基因在不同发育阶段的茎部表达量存在明显差异，且盐胁迫对各基因的表达特性影响显著。以上结果表明，毛果杨GATA家族基因在复制后，基因的结构与功能产生了明显分化，其中部分基因在毛果杨次生生长与盐胁迫响应中可能具有重要作用。本项研究为全面解析毛果杨GATA家族各成员在其生长发育与盐胁迫响应中的生物学功能奠定了基础。

关键词: 毛果杨, GATA基因, 盐胁迫, 表达模式

Abstract:

The GATA transcription factor gene family played an important role in plant growth and development， cell differentiation， and response to environmental changes. However， no genome-wide analysis of this gene family has been reported in woody plants so far. We systematically analyzed the number， gene structure， chromosome positioning， phylogenetic evolution， physicochemical characteristics and conserved motifs of the GATA family members from the genome level respectively. The results showed that the GATA family contains 39 genes distributed on 15 chromosomes， and 6 genes distributed on chromosome 5， and only 1 gene distributed on chromosomes 9， 13 or 19 respectively. The rest chromosomes had no gene distributed on. The genes structure in this family and the basic characteristics encoded protein were somewhat heterogeneous， and could be divided into 4 subfamilies. By the qRT-PCR， there were significant differences in the expression levels of the genes of the GATA family at different developmental stages， and salt stress significantly affected the expression characteristics of the genes. The above results indicated that the structure and function of the genes were significantly differentiated after the replication of GATA family genes， and some of these genes might play an important role in the secondary growth of Populus trichocarpa and the response to salt stress. This study laid the foundation for a comprehensive analysis of the biological functions of the members of the GATA family of P.trichocarpa in their growth and development and response to salt stress.

Key words: Populus trichocarpa, GATA gene, salt stress, expression pattern

中图分类号:

S792.11

任梦轩, 张洋, 王爽, 王瑞琪, 刘聪, 魏志刚. 毛果杨GATA基因家族全基因组水平鉴定及表达分析[J]. 植物研究, 2021, 41(1): 107-118.

Meng-Xuan REN, Yang ZHANG, Shuang WANG, Rui-Qi WANG, Cong LIU, Zhi-Gang WEI. Genome-wide Identification and Expression Analysis GATA Family of Populus trichocarpa[J]. Bulletin of Botanical Research, 2021, 41(1): 107-118.

图/表 8

表1

毛果杨GATA家族基因qRT-PCR的引物

基因名字

Gene name

登录号

Accession number

引物名称

Primer name

引物序列

Primer sequence(5′-3′)

PtrGATA1.1

Potri.001G053500.1

DL-Ptr001G053500-F

DL-Ptr001G053500-R

AGACACGGCTGCTTGTTTCA

GCCCTTCTGGATTTTTTGCT

PtrGATA1.2

Potri.001G151700.1

DL-Ptr001G151700-F

DL-Ptr001G151700-R

TTGCTCTGGATTACAACGAAGG

TCCGAGTTGGATATGGCTGAC

PtrGATA1.3

Potri.001G188500.1

DL-Ptr001G188500-F

DL-Ptr001G188500-R

CCAAACCAACATCCACATCCT

CATTTTAGTGGTGGATGGGACA

PtrGATA2.1

Potri.002G110800.1

DL-Ptr002G110800-F

DL-Ptr002G110800-R

CGTTTTCCCTGCTGTTACCC

AACTGCCCATTCTTGCGG

PtrGATA2.2

Potri.002G110900.1

DL-Ptr002G110900-F

DL-Ptr002G110900-R

AACCTCAACGAGCAGCTTCA

TGACGGACACCATATCTAACTTTC

PtrGATA2.3

Potri.002G142800.1

DL-Ptr002G142800-F

DL-Ptr002G142800-R

AGTGATGACGTGGCAGAGCTA

TGCTACAAGATTTGATGCGAGA

PtrGATA2.4

Potri.002G199800.1

DL-Ptr002G199800-F

DL-Ptr002G199800-R

ATCAGACAGAGGAAGAGGAGGAG

CCACAAGATAAAGCCATCAAGAG

PtrGATA3.1

Potri.003G082800.1

DL-Ptr003G082800-F

DL-Ptr003G082800-R

TATGACAATAGGGTTGCTCTGGA

ACAACTGATTGGGCTGGACC

PtrGATA3.2

Potri.003G174800.1

DL-Ptr003G174800-F

DL-Ptr003G174800-R

GCCCAGTCTCCGTTCTTGA

TCTCCCCATTTTTGCTACTGAC

PtrGATA3.3

Potri.003G213300.1

DL-Ptr003G213300-F

DL-Ptr003G213300-R

TGCTTACCCCAAGTCCTACAGT

GCTACTGTGTTGAGGAGTGTTCG

PtrGATA4.1

Potri.004G161500.1

DL-Ptr004G161500-F

DL-Ptr004G161500-R

GCTTGAATGGGTATCTCACTTTG

AACCAGGAGTTTTTGCGAGAG

PtrGATA4.2

Potri.004G211800.1

DL-Ptr004G211800-F

DL-Ptr004G211800-R

CAAGCAGAAGCAAACCCATC

TTGTCGCATTTTCGGTGG

PtrGATA5.1

Potri.005G020500.1

DL-Ptr005G020500-F

DL-Ptr005G020500-R

ATCACTACAGCCACAACAACAAAC

TCCTTTGGCACCTTTGTTTCT

PtrGATA5.2

Potri.005G066100.1

DL-Ptr005G066100-F

DL-Ptr005G066100-R

TGGATAGGCAGTGAACTTAGCG

TCCCAAAAAATCCCCAAAAT

PtrGATA5.3

Potri.005G117600.1

DL-Ptr005G117600-F

DL-Ptr005G117600-R

TGAACTTTGTGTGCCGACG

ACAAGGCTCTGTTAGGACCGA

PtrGATA5.4

Potri.005G122700.1

DL-Ptr005G122700-F

DL-Ptr005G122700-R

ATCCCCCTCAAGCCCATAA

TTGCCCTTCTCTCTTCCTTCTT

PtrGATA5.5

Potri.005G152500.1

DL-Ptr005G152500-F

DL-Ptr005G152500-R

TTTCCCTGCTGTTACCCCA

CACGGAATCTAACAAGTGAGGC

PtrGATA5.6

Potri.005G152800.1

DL-Ptr005G152800-F

DL-Ptr005G152800-R

TGGAAATGACGCCTCAAAAC

AACCTCCTGACGGACACCATA

PtrGATA6.1

Potri.006G229200.1

DL-Ptr006G229200-F

DL-Ptr006G229200-R

AACCAAACCTGGAGAGTCGC

GAACTTTCACCACTTTCTTCAGCT

PtrGATA6.2

Potri.006G237700.1

DL-Ptr006G237700-F

DL-Ptr006G237700-R

CCACTGTGACTTTCGTTGATAGC

TCATCATACGGCACGCAAA

PtrGATA7.1

Potri.007G016600.1

DL-Ptr007G016600-F

DL-Ptr007G016600-R

AGGAGGAGGGGGGAGATAAA

CGTCGGCACACAAAGTTCAC

PtrGATA7.2

Potri.007G024500.1

DL-Ptr007G024500-F

DL-Ptr007G024500-R

CCACCTCAAGCCCATAAAACT

TCTCTCTTCCTTTTTGAACCGA

PtrGATA7.3

Potri.007G116600.1

DL-Ptr007G116600-F

DL-Ptr007G116600-R

TGGTCCAAGTGGTCCAAGAA

GCCGCAGTTATGGTATCAGAAT

PtrGATA7.4

Potri.007G116700.1

DL-Ptr007G116700-F

DL-Ptr007G116700-R

TGGGAATGATGGCGTGTTT

GCATTCCTGGCATTCTGTTG

PtrGATA8.1

Potri.008G038900.1

DL-Ptr008G038900-F

DL-Ptr008G038900-R

GAAGCCTGACGATGAAGAAAGA

CTCAAGGACAGAAACTGGGCT

PtrGATA8.2

Potri.008G213900.1

DL-Ptr008G213900-F

DL-Ptr008G213900-R

AAAGGGGCAGCAAATGACA

AGACCCATAAGACAACGCCAT

PtrGATA9.1

Potri.009G123400.1

DL-Ptr009G123400-F

DL-Ptr009G123400-R

TTCGTGGATGATTCCGTGTC

CAAGAAGTTTTTGCGAAAGTAGG

PtrGATA10.1

Potri.010G001300.1

DL-Ptr010G001300-F

DL-Ptr010G001300-R

ATTAGGGTTGAATAAGGGAGGG

TTGAACCAAGACTTCTCTACCCA

PtrGATA10.2

Potri.010G223300.1

DL-Ptr010G223300-F

DL-Ptr010G223300-R

CATGGACGAGATAGATTGTGGAA

TGAGACGACCAAATACCAGGAA

PtrGATA10.3

Potri.010G251600.1

DL-Ptr010G251600-F

DL-Ptr010G251600-R

TTTTTGACTCTGTTTCACCTGGA

CCTGACAGCCCCCTATTATTACT

PtrGATA13.1

Potri.013G059600.1

DL-Ptr013G059600-F

DL-Ptr013G059600-R

TACAGAAGAAAACCCCCCAAA

CTGAAGCAAAGGAGGGTCTGA

PtrGATA14.1

Potri.014G058600.1

DL-Ptr014G058600-F

DL-Ptr014G058600-R

CCACTGACTTCACTGACCATCTC

TGAGCGTTTGCTGCGAGA

PtrGATA14.2

Potri.014G124400.1

DL-Ptr014G124400-F

DL-Ptr014G124400-R

GAGCGGAGAGGAGTAAAAATAAGA

CGGACCAAGCCACAAGATAA

PtrGATA17.1

Potri.017G042200.1

DL-Ptr017G042200-F

DL-Ptr017G042200-R

GAGAGCCTGAGACATCCACAAT

ACCTTTCCAGGGAGGCAAT

PtrGATA17.2

Potri.017G042300.1

DL-Ptr017G042300-F

DL-Ptr017G042300-R

AATCGGTTCAAAGTCCACTCC

CCTCTACCTGCAGTAAGTTCACAA

PtrGATA18.1

Potri.018G044900.1

DL-Ptr018G044900-F

DL-Ptr018G044900-R

GCTTTGCGTGCCCTATGAT

TCTTGGATGATTCGTCTGGC

PtrGATA18.2

Potri.018G053600.1

DL-Ptr018G053600-F

DL-Ptr018G053600-R

TCATCGAAAACGGAGGACG

GTTTCTGAGCGATTTGAGTTGG

PtrGATA19.1

Potri.019G033000.1

DL-Ptr019G033000-F

DL-Ptr019G033000-R

AAAACCCCCCAAAACCCT

GGAGCAAAGGAGGGTCTGAG

PtrGATAT.1

Potri.T158300.1

DL-PtrT158300-F

DL-PtrT158300-R

CTCTCATCATGACGTTCACTTAGG

TCTTGGATGATTCGTCTGGC

表1

表2

毛果杨GATA家族各基因概况

基因号 Gene ID	基因名字 Gene name	基因的位置 Genomic position	长度 Length(aa)	分子量 MW(Da)	等电点 pl	CDs长度 Length of CDs(bp)
Potri.001G053500.1	PtrGATA1.1	Chr01:4086401..4088825 reverse	336	38 285.85	9.68	1 011
Potri.001G151700.1	PtrGATA1.2	Chr01:12502479..12509399 reverse	552	61 305.85	6.96	1 659
Potri.001G188500.1	PtrGATA1.3	Chr01:16658546..16659881 reverse	250	28 010.26	5.41	753
Potri.002G110800.1	PtrGATA2.1	Chr02:8198186..8203728 reverse	360	39 278.43	4.87	1 083
Potri.002G110900.1	PtrGATA2.2	Chr02:8206492..8211812 reverse	290	31 465.78	5.93	873
Potri.002G142800.1	PtrGATA2.3	Chr02:10597460..10598816 forward	246	27 390.13	6.03	741
Potri.002G199800.1	PtrGATA2.4	Chr02:16060278..16061389 forward	147	16 627.16	9.40	444
Potri.003G082800.1	PtrGATA3.1	Chr03:11053999..11060297 forward	540	60 284.54	6.58	1 623
Potri.003G174800.1	PtrGATA3.2	Chr03:18351164..18353616 forward	259	29 021.80	9.17	780
Potri.003G213300.1	PtrGATA3.3	Chr03:21117706..21119661 reverse	226	25 422.98	8.74	681
Potri.004G161500.1	PtrGATA4.1	Chr04:18221923..18223879 forward	327	36 306.48	8.53	984
Potri.004G211800.1	PtrGATA4.2	Chr04:21951641..21956060 reverse	301	33 973.34	8.57	906
Potri.005G020500.1	PtrGATA5.1	Chr05:1593397..1595249 forward	161	17 587.24	9.78	486
Potri.005G066100.1	PtrGATA5.2	Chr05:4766766..4769587 reverse	356	29 329.51	8.75	771
Potri.005G117600.1	PtrGATA5.3	Chr05:9096540..9098179 reverse	333	36 840.45	7.10	1 002
Potri.005G122700.1	PtrGATA5.4	Chr05:9549440..9551215 reverse	254	28 599.41	7.55	765
Potri.005G152500.1	PtrGATA5.5	Chr05:14348124..14353280 reverse	365	39 708.23	5.13	1 098
Potri.005G152800.1	PtrGATA5.6	Chr05:14386485..14398559 reverse	288	31 463.70	5.67	867
Potri.006G229200.1	PtrGATA6.1	Chr06:24012190..24015009 forward	355	39 445.47	9.04	1 068
Potri.006G237700.1	PtrGATA6.2	Chr06:24697287..24699200 forward	373	41 397.57	6.04	1 122
Potri.007G016600.1	PtrGATA7.1	Chr07:1263957..1265632 reverse	376	41 808.29	6.95	1 131
Potri.007G024500.1	PtrGATA7.2	Chr07:1849537..1850974 reverse	254	28 668.60	8.46	765
Potri.007G116600.1	PtrGATA7.3	Chr07:13732111..13734218 forward	142	14 882.95	8.47	429
Potri.007G116700.1	PtrGATA7.4	Chr07:13736385..13742259 forward	384	43 220.87	4.90	1 155
Potri.008G038900.1	PtrGATA8.1	Chr08:2194430..2198138 forward	354	38 941.87	6.52	1 065
Potri.008G213900.1	PtrGATA8.2	Chr08:16937468..16938757 reverse	138	14 783.70	9.69	417
Potri.009G123400.1	PtrGATA9.1	Chr09:10283234..10285131 forward	329	36 593.74	6.61	990
Potri.010G001300.1	PtrGATA10.1	Chr10:149903..150769 reverse	153	16 419.65	9.85	462
Potri.010G223300.1	PtrGATA10.2	Chr10:20747463..20750870 reverse	446	49 067.91	5.93	1 341
Potri.010G251600.1	PtrGATA10.3	Chr10:22342132..22345674 forward	307	33 369.72	7.80	924
Potri.013G059600.1	PtrGATA13.1	Chr13:4460579..4462220 forward	295	32 672.55	6.53	888
Potri.014G058600.1	PtrGATA14.1	Chr14:4540248..4541744 forward	251	27 963.80	6.42	756
Potri.014G124400.1	PtrGATA14.2	Chr14:9595039..9596182 forward	133	14 704.83	9.77	402
Potri.017G042200.1	PtrGATA17.1	Chr17:3570422..3576737 reverse	406	46 027.48	5.36	1 221
Potri.017G042300.1	PtrGATA17.2	Chr17:3583593..3583948 reverse	115	12 867.23	9.94	348
Potri.018G044900.1	PtrGATA18.1	Chr18:4078772..4080396 reverse	380	42 109.26	6.22	1 143
Potri.018G053600.1	PtrGATA18.2	Chr18:5587016..5588879 forward	303	33 666.66	8.78	912
Potri.018G033000.1	PtrGATA19.1	Chr19:3788859..3790666 reverse	294	32 198.69	6.18	885
Potri.T158300.1	PtrGATAT.1	scaffold_694:4641..6156 forward	354	39 505.39	6.19	1 065

表2

图1

图2

图3

图4

图5

图6

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