Genome-wide Identification and Expression Analysis of nsLTP Gene Family in Populus trichocarpa

doi:10.7525/j.issn.1673-5102.2022.03.011

Abstract

Abstract:

Non-specific lipid transfer proteins（nsLTP）， a polygene family of basic lipid transfer proteins， are responsible for the transfer of phospholipids between fatty acids and membrane in vitro， and play an important role in plant growth and development and the response to stress. There have been no reports on the nsLTP family of Populus trichocarpa. In this study， the number of genes， genetic relationship， gene structure and conserved motif of coding proteins of PtrnSLTP family members were analyzed at the genome-wide level. The results showed that the PtrnsLTP family was composed of 39 genes and evolved into five subfamilies， among which six genes in subfamily A， two genes in subfamily B， 13 genes in subfamily C， three genes in subfamily D， and 15 genes in subfamily E. PtrnsLTP family contained seven pairs of paragenetic homologous genes， among which one pair was greater than one， and the six pairs of Ka/Ks were all far less than one. Moreover， these six pairs of genes were all on the same large evolutionary branch， and different evolutionary pressures led to functional differentiation among genes. Both encoded proteins contained conserved motifs in Motif 1 and Motif 2. Using qRT-PCR technology combined with P. trichocarpa data to study the tissue expression of PtrnsLTP and the response characteristics of salt stress， it was found that all family members expressed in the roots， stems and leaves of P. trichocarpa. The results were basically consistent with the prediction results by the bioinformatics analysis of the website. There were 11， 15 and 13 members respectively having higher expression in roots， stems and leaves， indicated that this gene family was involved in the growth and development of different tissues of P. trichocarpa. Under NaCl stress， among the 39 genes in the family， 26 genes expressed in the root and 14 genes expressed in the leaves increased with the increase of stress time， while 32 genes expressed in the stem first increased and then decreased. The results have a positive role in promoting the identification of the biological function of PtrnsLTP family genes and the work of salt stress response gene resources.

Key words: Populus trichocarpa, nsLTP, bioinformatics analysis, salt stress

CLC Number:

S792.11

He CHENG, Shuanghui TIAN, Yang ZHANG, Cong LIU, De’an XIA, Zhigang WEI. Genome-wide Identification and Expression Analysis of nsLTP Gene Family in Populus trichocarpa[J]. Bulletin of Botanical Research, 2022, 42(3): 412-423.

Figures/Tables 9

Table 1

PtrnsLTP quantitative primer sequence

定量引物名称 qRT-PCR primer name	F端引物序列（5′—3′） F-terminal primer sequence（5′—3′）	R端引物序列（5′—3′） R-terminal primer sequence（5′—3′）
PtrnsLTP1.1	ATCTCTCCAAGTGTAGTAGCGGC	GGTTTCCCAGTGCCATTCAT
PtrnsLTP1.2	TCACACTCAAACAACAACCAAGA	AATCAGAATTCCGATCACTGCA
PtrnsLTP1.3	AGTGTAGTAGCGGCAGCAATG	GGCCTCAGGTCCTTGATTACAT
PtrnsLTP1.4	CAAGTGTAGTAGCGGCAGCAAT	CAGCAGGTGGTTTCCCAGTA
PtrnsLTP1.5	GCACATCCTTGTGGTAGCACTT	AAGAGTACACAAGCAAGGCTGG
PtrnsLTP1.6	AGCACTGTTGATGAAAAGGCA	GTTGACGCTTGTAGAGACGGG
PtrnsLTP2.1	GAGTCTAGTGCTTGCCCTCATG	CACCTTTGGTCCCTTTTTGG
PtrnsLTP2.2	AGATGGCGAAGAGGCAGC	GCCCCAGAAACAGCCTTG
PtrnsLTP4.1	TGCTTATAGCGATGGTTGTTAGTG	AGGATTTCAAACAGTTGCAGACC
PtrnsLTP4.2	GCTTGTAGCGATGGTTGTTAGTG	CTTACCAGCCAAGGATTTCAAAC
PtrnsLTP4.3	TGCCTACCAGCAATCTCGTC	CAAAGACAAGGCTTCTGCTCC
PtrnsLTP6.1	TGCCTCACCTACCTGAAGAAAG	ACTTTGGAGGCGGTTTGTTT
PtrnsLTP7.1	CTCGCATTGTTGGGTTTCTG	GGTCCACGTCGAACTTAGCC
PtrnsLTP7.2	CCCCATCTTCAGAGGCACC	CAGTATGAACCTGCGAGAAAATC
PtrnsLTP8.1	GGCGACTCCAATGAAGTACATT	AGCACTGGCTCGAAACTGAAG
PtrnsLTP9.1	CAAGTGTAGTGGTGGCAGCAAT	GTTCACACAAGGCCTCAGGTC
PtrnsLTP9.2	CAAATCCAGATGCTCCCGAT	ACAGCCTTCTCCATGCTAATCA
PtrnsLTP9.3	ACGCACAAAGAATTTTGTCGTT	CCTGTCTGCACTGATGGCTTAC
PtrnsLTP10.1	CTTGGGTTGTGACTGTGTTGGT	AGGCAGTAACTTTGGAGCAGC
PtrnsLTP10.2	TCAATCAAGTTGACGGGGC	AACAGCGCATAGGCAGGC
PtrnsLTP11.1	AATAGTGGTGGCTGTGATTGCT	GTAGTAGTCAAGAATGGGAGGCAG
PtrnsLTP11.2	GTATTCTGTTTTTTGGGCAGTGA	TCCCTTTTGTCTTTCCTGTTGA
PtrnsLTP11.3	CTGTTTTCTGGGCAGTGATTTT	GAGACACTACCCAGCAAGAACG
PtrnsLTP12.1	CAATCACATCTTCTACTCCACCAA	GCTTCTGTTCCTTGATCTTGCT
PtrnsLTP12.2	TCACTCAAGTCTCTTAGCTCCCC	GTACTAGGGTTGGTGTTCGGTG
PtrnsLTP12.3	CTCCTGTTGCTGTTGCTCTCAT	CCACAGAAGCCAGGCAGAGTA
PtrnsLTP14.1	ACTTGTCTGCTTGCGTTTCCTA	GATGCAGCCTCATCCTTCATATC
PtrnsLTP14.2	AGCAGCAATGAGCACTCATCTAT	ACAGCAAGTCTTTGACGGATCT
PtrnsLTP14.3	TCCTTTGTGTGGCTCTATTGCT	GCGGTAGGGTTAGGAGGAGTTA
PtrnsLTP15.1	ATTGGTGCTTCTTCTGGCTCA	GCAGGGCTTCTGTTCCTTGAT
PtrnsLTP15.2	CAGTGCAGACTCAACTGGCTC	TACAACACTCAGCATTCGGGT
PtrnsLTP16.1	TTCATCGGTCTTCTGGGATTG	TCACCTGAAGGCAGCAACTG
PtrnsLTP16.2	AACAACCGCCGCTCAACT	GTGGATGTGCTGATCTTGTACG
PtrnsLTP16.3	TGATCTGTGCTCTCTTGCTATGC	TTGTTGACATTCTGAACTCCTTTG
PtrnsLTP16.4	TGATCTGTGCTCTCTTGCTATGC	CGTTGTTGACATTCTGAACTCCTC
PtrnsLTP16.5	TCCACCACTAAAGCAGCGATT	AGTCCAGCAGCAAGAGCAACA
PtrnsLTP16.6	GAGAGCCCTTCATTTAGTTTGC	TGAAATCGCTGCTTTAGTGGT
PtrnsLTP17.1	TTCGGAGAGTAAATGCGAGC	CAGTCCACGCTTCGCTAATC
PtrnsLTP17.2	TAACCCAGGGCAGTTGAGC	AAGTGGTGGAGGGTGGTGTAG
PtrActin	AGGCAGGTTTCGCAGGAGATGA	TCCATCACCAGAATCCAGCACA

Table 1

Fig.1

Table 2

Overview of the PtrnsLTP gene family

基因名称 Gene name	登录号 Gene ID	基因的位置 Genomic location	蛋白长度 Protein length /aa	分子量 Molecular weight /kDa	等电点 pI	亚细胞定位 Subcellular localization
PtrnsLTP1.1	Potri.001G023200.1	1768060-1768956	113	12.009 12	6.78	CM
PtrnsLTP1.2	Potri.001G023300.1	1770676-1771673	134	14.607 19	7.56	CM
PtrnsLTP1.3	Potri.001G232700.1	24461327-24462000	118	11.975 05	8.14	CW
PtrnsLTP1.4	Potri.001G232900.1	24483523-24484495	118	12.014 09	8.46	CW
PtrnsLTP1.5	Potri.001G271000.1	27859786-27860575	88	9.291 93	6.71	CM
PtrnsLTP1.6	Potri.001G460900.1	49454026-49454302	84	8.582 16	8.74	CW
PtrnsLTP2.1	Potri.002G012300.1	714913-715376	124	14.124 77	8.8	CW
PtrnsLTP2.2	Potri.002G251000.1	24097409-24098806	102	10.740 64	4.85	CM
PtrnsLTP4.1	Potri.004G086500.1	7250939-7252044	118	11.809 93	9.22	CW
PtrnsLTP4.2	Potri.004G086600.1	7257055-7257885	118	11.668 74	9.06	CW
PtrnsLTP4.3	Potri.004G096000.1	8252603-8253488	93	9.645 56	9.14	CM
PtrnsLTP6.1	Potri.006G108100.1	8428753-8429723	116	11.881 21	9.32	CW
PtrnsLTP7.1	Potri.007G138400.1	14998848-14999195	115	13.108 28	5.45	CW
PtrnsLTP7.2	Potri.007G138500.1	15002557-15003632	153	16.955 85	6.39	CW
PtrnsLTP8.1	Potri.008G061800.1	3715997-3716768	119	12.545 76	8.6	CM
PtrnsLTP9.1	Potri.009G025200.1	3644075-3645235	118	11.870 75	8.13	CW
PtrnsLTP9.2	Potri.009G048800.1	5396543-5396830	95	10.243 31	9.07	CW，CM
PtrnsLTP9.3	Potri.009G112500.1	9594032-9594787	109	11.662 80	8.83	CM
PtrnsLTP10.1	Potri.010G100600.1	12200539-12202205	120	12.268 74	9.91	CM
PtrnsLTP10.2	Potri.010G196300.1	18966272-18967159	119	12.541 65	8.07	CM
PtrnsLTP11.1	Potri.011G021900.1	1852821-1853530	118	12.831 99	8.13	CW，CM
PtrnsLTP11.2	Potri.011G022100.1	1860483-1860995	119	12.987 31	8.64	CW
PtrnsLTP11.3	Potri.011G022200.1	1869485-1870289	119	13.027 37	8.43	CW
PtrnsLTP12.1	Potri.012G054300.1	5504366-5505126	93	10.033 02	9.24	CW
PtrnsLTP12.2	Potri.012G137400.1	15263548-15264499	94	96.432 60	6.66	CM
PtrnsLTP12.3	Potri.012G139700.1	15398444-15399190	118	12.415 55	4.27	CW
PtrnsLTP14.1	Potri.014G046500.1	3643120-3644008	117	12.105 16	6.53	CW
PtrnsLTP14.2	Potri.014G098000.1	7655899-7656796	127	13.578 99	9.06	CW
PtrnsLTP14.3	Potri.014G149900.1	11496745-11497691	103	10.687 80	8.62	CM
PtrnsLTP15.1	Potri.015G044500.1	4411154-4411923	93	10.083 00	9.36	CW，CM
PtrnsLTP15.2	Potri.015G139100.1	14741017-14741301	94	9.760 28	5.97	CM
PtrnsLTP16.1	Potri.016G104300.1	10353074-10353978	116	11.902 98	8.11	CM
PtrnsLTP16.2	Potri.016G135400.1	13871619-13872561	116	11.879 93	8.89	CW
PtrnsLTP16.3	Potri.016G135500.1	13890545-13891464	129	14.051 54	9.36	CW
PtrnsLTP16.4	Potri.016G135700.1	13908471-13909450	117	12.825 26	9.23	CW
PtrnsLTP16.5	Potri.016G135800.1	13915635-13916479	120	12.498 66	9.26	CW
PtrnsLTP16.6	Potri.016G136000.1	13922459-13923572	120	12.662 74	9.01	CW
PtrnsLTP17.1	Potri.017G013200.1	1105887-1106566	116	13.385 69	8.03	CW
PtrnsLTP17.2	Potri.017G118700.1	13300324-13300829	94	9.926 79	8.68	CM

Table 2

Fig.2

Fig.3

Table 3

Fig.4

Fig.5

Fig.6

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同源基因Paralogues		Ka（JC）	Ks（JC）	Ka/Ks	同源片段长度 Homologous fragment length /bp	同源性 Homology /%
Gene1	Gene2	Ka（JC）	Ks（JC）	Ka/Ks	同源片段长度 Homologous fragment length /bp	同源性 Homology /%
PtrnsLTP4.1	PtrnsLTP4.2	0.050 751	0.058 338	0.869 942	339	95
PtrnsLTP8.1	PtrnsLTP10.2	0.060 735	0.274 117	0.221 566	325	90
PtrnsLTP9.1	PtrnsLTP1.3	0.117 490	0.210 058	0.559 323	312	87
	PtrnsLTP1.4	0.108 696	0.241 534	0.450 025	312	87
PtrnsLTP11.2	PtrnsLTP11.3	0.025 754	0.064 835	0.397 217	348	97
PtrnsLTP16.3	PtrnsLTP16.4	0.112 034	0.068 727	1.630 148	317	91
PtrnsLTP16.5	PtrnsLTP16.6	0.028 199	0.064 493	0.437 239	346	98

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