Genome-wide Identification and Expression Analysis GATA Family of Populus trichocarpa

doi:10.7525/j.issn.1673-5102.2021.01.014

Abstract

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

CLC Number:

S792.11

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.

Figures/Tables 8

Table 1

Primers for quantitative real-time PCR of P.trichocarpa GATA family

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

Table 1

Table 2

Summary of GATA genes in P.trichocarpa

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

Table 2

Fig.1

Fig.2

Fig.3

Fig.4

Fig.5

Fig.6

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