桃GRAS家族全基因组鉴定与响应UV-B的表达模式分析

doi:10.3864/j.issn.0578-1752.2019.24.011

摘要/Abstract

摘要：

【目的】GRAS基因家族成员在调节植物生长发育中发挥着关键作用。通过生物信息学分析GRAS在桃基因组中的分布、结构及进化,研究家族成员在不同组织中的表达特异性及其对UV-B的响应,解析GRAS基因家族的生物学功能。【方法】对设施油桃‘中油5号’（Prunus persica var. nectarina cv. Zhongyou5）补充适量UV-B（Ultraviolet-B）剂量,利用Plant TFDB数据库鉴定桃GRAS基因家族成员。采用Clustal W、MEGA6.0、ProtParam tool、MCScanX、Circos、SMART、NCBI-CDD、ExPASy、GSDS和MEME等软件构建系统进化树,绘制染色体定位图,预测蛋白的相对分子质量与等电点等理化性质等,分析GRAS基因家族成员在不同组织中的表达模式,利用qRT-PCR技术检测桃GRAS在UV-B处理下的表达情况。【结果】从桃全基因组中鉴定出48个GRAS转录因子家族基因,构建系统进化树将这48个成员分为9个亚家族,PpGRAS在桃的8条染色体上呈不均匀分布。对GRAS基因家族进行理化性质分析发现,其蛋白平均长度为590.52 aa,等电点在4.36—7.56。GRAS家族基因结构分析表明,有40个基因不含内含子,8个基因含有1个内含子。保守元件分析显示,GRAS家族包含20个保守元件,其中Motif 2和4在GRAS的家族中高度保守,同一个亚家族成员含有相同的保守元件,其可能具备相似的功能。然而,有些亚家族成员的表达模式不同,这可能与其保守基序之外的序列有关。PpGRAS在不同组织中具有不同的表达模式。叶片中PpGRAS5经UV-B处理后上调表达最显著,而有多达15个基因表达量呈现下调。果实中PpGRAS13经UV-B处理后上调表达,但有9个基因表达下调。韧皮部中,UV-B处理后有14个基因上调表达,而PpGRAS16经处理后在韧皮部中表达下调最明显。【结论】从桃基因组中共鉴定出48个GRAS基因家族成员,分布于8条染色体上;多数PpGRAS能响应UV-B处理,但在不同组织中的表达不尽相同。

关键词: 桃, GRAS基因家族, 生物信息学分析, UV-B

Abstract:

【Objective】 GRAS transcription factor family genes play a key role in the regulation of plant growth and development. The objectives of this study were to analyze the distribution, structure and evolution of GRAS in the peach genome by bioinformatics, to study the expression specificity of family members in different tissues and their responses to UV-B optical signal, and to investigate the biological function of GRAS transcription factor family genes in peach. 【Method】 The facility nectarine ‘Prunus persica var. nectarina cv. Zhongyou5 was supplemented with an appropriate dose of UV-B (Ultraviolet-B). The peach GRAS gene in the peach genome was identified by using the Plant TFDB database. Phylogenetic tree, chromosome localization, relative mass and isoelectric point and other physical and chemical properties of GRAS member were analyzed with Clustal W, MEGA6.0, ProtParam tool, MCScanX, Circos, SMART, NCBI-CDD, ExPASy, GSDS2.0, and MEME, respectively. The expression pattern of GRAS gene family in different tissues was analyzed, and the expression of some members of GRAS gene family in peach treated with UV-B was detected by real-time fluorescence quantitative PCR (qRT-PCR).【Result】48 members of GRAS transcription factor family were identified from the whole genome of the peach, and they could be divided into 9 categories by constructing a phylogenetic tree. The PpGRAS gene showed uneven distribution on 8 chromosomes of peach. The theoretical isoelectric point of the family protein was ranged from 4.36 to 7.56, and the average number of amino acids encoded was 590.52. Gene’s structure analysis showed that 40 genes contained no introns, and 8 genes contained 1 intron. Conservative elemental analysis revealed that the GRAS family contains 20 conserved elements, of which Motif 2 and Motif 4 were highly conserved in the GRAS family. Members of the same subfamily contained the same conserved elements, suggesting that members of the same subfamily might have similar functions. However, some subfamily members had different expression patterns, which might be related to sequences other than the conserved motif. The PpGRAS genes had different expression patterns in different tissues; and most of PpGRAS genes could respond to UV-B treatment, but the expression changes were different in different tissues. In leaves, PpGRAS5 was up-regulated after UV-B treatment, while up to 15 genes were down-regulated. In the fruit, PpGRAS13 was up-regulated by UV-B treatment, but 9 genes were down-regulated. In the phloem, 14 genes were up-regulated after UV-B treatment, while PpGRAS16 was most down-regulated in the phloem after treatment. 【Conclusion】A total of 48 GRAS gene family members were identified from the peach genome and distributed on 8 chromosomes; most PpGRAS genes responded to UV-B treatment, but the expression changes were different in different tissues. This study laid the foundation for further analysis of the PpGRAS family of genes in response to UV-B light signals and other potential functions.

Key words: peach, GRAS gene family, bioinformatic analysis, UV-B

李晨,赵雪惠,王庆杰,王旭旭,肖伟,陈修德,付喜玲,李玲,李冬梅. 桃GRAS家族全基因组鉴定与响应UV-B的表达模式分析[J]. 中国农业科学, 2019, 52(24): 4567-4581.

Chen LI,XueHui ZHAO,QingJie WANG,XuXu WANG,Wei XIAO,XiuDe CHEN,XiLing Fu,Ling LI,DongMei LI. Genome Identification of PpGRAS Family and Expression Pattern Analysis of Responding to UV-B in Peach[J]. Scientia Agricultura Sinica, 2019, 52(24): 4567-4581.

图/表 8

表1

48个PpGRAS的qRT-PCR引物序列"

引物名称 Locus name	上游序列（5'-3'） Forward primer (5'-3')	下游序列（5'-3'） Reverse primer (5'-3')
Prupe.1G119100	CACCCTTCTTTGTCACACGG	CCCAGCCCTCACATTCCTAA
Prupe.1G119200	AACAATTGTGGGGACTTCGC	ACCTGCCCTACAAACCCTAC
Prupe.1G199300	TCCTCTCCGAGTTCAACCAC	CGAGCCTTATCCCGGAATCT
Prupe.1G237500	ACTGGAGGAGCTCTGAGAGA	ATGACGTTCCTGATTTCGCG
Prupe.1G329600	CTGAGTTCGCAATGAGGAGC	GGGCCTCAATAAAACGGGTC
Prupe.1G501500	GCATGCGTTCGATCTGGATT	CAATGAGCTCGTGGAAGTCG
Prupe.2G028700	CCATCCTCATCGGCTCAGAT	CTTTCTCGGCGAGCTCTTTC
Prupe.2G138400	CACCACCTGACCAGTACCAT	TCCGTTTCTGGCAGGGTATT
Prupe.2G237300	GAGGGAAAGGAAAGGGTGGA	TCCTTCCATCCCAACAGCAT
Prupe.2G299400	TTAGCTTTGAAGTCCCGGGT	ATTCGTCGCTGATTTGTCCG
Prupe.3G040400	GCGGATTAGTGCAGAGATGC	GACTCCTGATAGCCTCCGTC
Prupe.3G162500	TCAAGGCAGCCAGTGGATTA	AATTGCCTCTCCTGGTCGAA
Prupe.3G187000	TGGTGGACGAAGATGCAGAT	GAACCCCTCGTACGCTATCA
Prupe.3G201900	GCATGCGAAGGAGAGGAAAG	TCCAAAATGAAGTGCACCGG
Prupe.3G222800	CACCCTTCTTTGTCACACGG	CCCAGCCCTCACATTCCTAA
Prupe.3G249700	ACGACTCTGAGCCACAAGAA	TTCTGCTTCTTTGAACCCGC
Prupe.3G309800	GCAGCATTCTTCCCCGTATG	GCCAAGAAATGTGACACCGT
Prupe.4G007500	AGGGGTAGGGGAAGCTAGAA	TGCTTCTCCCTTCTTCTGCA
Prupe.4G132100	AGTGGTGGCTATTTCGGTGA	GCCTCCTCAACTCCCTTCTT
Prupe.4G200200	TCTTCCACTTCCAAGCGCTA	CCCAGCCCTCACATACCTAG
Prupe.4G233000	TGGCAGGCTAGGTATGTGAG	CTTTCCATCCCTGCAGCATC
Prupe.4G258200	TCTTCCACTTCTCTGCCCTG	GCAAACCAGCCCTTGTACAA
Prupe.5G072300	AGAGTTGTGAGGCCTGAGAC	CTTCCATCCTTGCAGCATCC
Prupe.5G091700	TCTGAGCACAAAGAGGGGAG	GCCTTATCTGCCTGAGTTGC
Prupe.5G156100	GCTGGCGATTGTTAACGGAT	ATCCTTTCTGAACCCTCGCA
Prupe.6G037000	CCCTCTCTTCTTCAACCGGT	CAAAACCTGCCCTCCTCAAC
Prupe.6G073300	TTGGTCAATCTTTGGAGCGC	GAACCCCTTCTCCCATGTCA
Prupe.6G073400	GGCCACAAGTTCCTCCTTTG	CTACCGCCAAGTTGCTCATC
Prupe.6G073500	GTTGACGGGCTTGACTTTGT	ACTAAACGTCACGGGGCTAA
Prupe.6G073600	TTTTGCAAGGCCACAGACTC	ACCGTTTGAAGCCACATGAC
Prupe.6G073700	GACATCGATGAGGAGGAGCT	TGTGGATCAAATGGAGGCCT
Prupe.6G073800	TGGTCATGTCCGAGGTGTAC	CCATTGTTCTCCTCCACCCT
Prupe.6G073900	CGATGAACCAAGGGATGCAG	TCGCCACAAACCCTCTGTAT
Prupe.6G074000	TCGAAATCTCCGAGCTCTCC	ATTGGCGGTGAAGTGAGAGA
Prupe.6G220800	GATTTGGCGACGCTGAGATT	GCTCCACCATATGCCTCTCT
Prupe.6G223200	AGGAAGGAGGAAGGGGAGAT	TTGACTTGGTTATGGGGCCT
Prupe.6G257000	AAAGATGGAGGACACTGGCA	GGTTGTCTCATTGTGCTGCA
Prupe.6G282800	CTGGCTATCTCCTGGGATGG	TCAGGAGAGGCTAGCTGAGA
Prupe.6G300900	GGAGGGTGTGGAGAGAGAAG	AGAGAGGCCTTTCGTTCCAA
Prupe.7G150900	CGCTTTCTCTCTCACTCCCT	CAGAAAACCGGAACCCAGTG
Prupe.7G153700	ACGAAGGGTCATCATCTGCA	TGGGAAATTTGCTCAAGGGC
Prupe.7G236100	ACTCACTCGATGCTAGCCTC	CCAAAGTGTACCCATCGCAG
Prupe.8G016200	CCCCTTCATCAAGTTTGCCC	ATGTTCCCACTCCGGTCATT
Prupe.8G054000	TGAGGGAAATGGAGCAGAGG	GCCACACGCTGAAAAGAAGA
Prupe.8G220900	TTGCATGCCACCAAGAAGTC	TCTTCTGCTTGCCTGCTACT
Prupe.8G266100	TCTCATGCACCTCCGATCTC	ATATGGAATGGTCGGGCGAT
Prupe.I004400	AAGACCAGTCACTTCTCCGG	CGAAACGCTGCTTCCGATTA
Prupe.I004500	CAAGAGCTATTGGTTCGGGC	CCTGTTTCGATCAGCTCTGC
Actin	GTTATTCTTCATCGGCGTCTTCG	CTTCACCATTCCAGTTCCATTGTC

表1

表2

桃GRAS及其相关信息"

基因编号 Gene name	基因登录号 Locus name	染色体 Chromosome	类别 Group	定位 Locus	开放阅读框长度 ORF length (bp)	蛋白长度 Protein length (aa)	分子量 Molecular weight (Da)	等电点 Isoelectric point
PpGRAS1	Prupe.1G119100	1	Ⅵ	9323354 9325141	1788	596	66738.9	4.93
PpGRAS2	Prupe.1G119200	1	Ⅴ	9326642 9327967	1326	442	49126.9	6.94
PpGRAS3	Prupe.1G199300	1	Ⅲ	19270496 19271845	1350	450	50539.2	5.08
PpGRAS4	Prupe.1G237500	1	Ⅴ	25203094 25204641	1548	516	57213.2	6.51
PpGRAS5	Prupe.1G329600	1	Ⅳ	31282447 31283783	1311	437	48095.8	6.83
PpGRAS6	Prupe.1G501500	1	Ⅶ	41498576 41500096	1521	507	55337.3	5.20
PpGRAS7	Prupe.2G028700	2	Ⅴ	2987997 2990761	1386	462	52324.3	6.28
PpGRAS8	Prupe.2G138400	2	Ⅷ	19548826 19551964	2145	715	78010.1	5.40
PpGRAS9	Prupe.2G237300	2	Ⅱ	25838372 25841556	2007	669	75561.2	5.62
PpGRAS10	Prupe.2G299400	2	Ⅰ	28850212 28852416	1938	646	70121.6	7.19
PpGRAS11	Prupe.3G040400	3	Ⅲ	2895471 2897333	1647	549	61096.3	6.41
PpGRAS12	Prupe.3G162500	3	Ⅳ	18144529 18147307	1782	594	64551.4	4.91
PpGRAS13	Prupe.3G187000	3	Ⅴ	20103771 20105111	1341	447	48568	5.80
PpGRAS14	Prupe.3G201900	3	Ⅰ	21021917 21025350	1668	556	62383.7	6.96
PpGRAS15	Prupe.3G222800	3	Ⅲ	22307572 22309814	1590	530	58784.2	6.51
PpGRAS16	Prupe.3G249700	3	Ⅵ	23979126 23980343	1218	406	45828.1	7.56
PpGRAS17	Prupe.3G309800	3	Ⅶ	26939961 26942210	2127	709	78477.6	6.15
PpGRAS18	Prupe.4G007500	4	Ⅰ	396663 398565	1623	541	60455.4	6.24
PpGRAS19	Prupe.4G132100	4	Ⅵ	7314327 7315982	1599	533	59633.6	4.61
PpGRAS20	Prupe.4G200200	4	Ⅰ	12432037 12435877	1758	586	65220.3	5.84
PpGRAS21	Prupe.4G233000	4	Ⅰ	14976407 14979370	1713	571	63145.4	5.17
PpGRAS22	Prupe.4G258200	4	Ⅵ	18325403 18326818	1416	472	52583.6	6.00
PpGRAS23	Prupe.5G072300	5	Ⅷ	8700201 8703734	2268	756	82196.4	6.55
PpGRAS24	Prupe.5G091700	5	Ⅴ	10228192 10230468	2094	698	76771.2	5.37
PpGRAS25	Prupe.5G156100	5	Ⅵ	13931708 13933297	1590	530	58679	6.31
PpGRAS26	Prupe.6G037000	6	Ⅰ	2793373 2794605	1233	411	46253.6	6.94
PpGRAS27	Prupe.6G073300	6	Ⅱ	4999593 5001653	2061	687	77912	4.95
PpGRAS28	Prupe.6G073400	6	Ⅱ	5005442 5008392	2154	718	81656.6	6.58
PpGRAS29	Prupe.6G073500	6	Ⅱ	5010337 5012421	2085	695	78198.1	6.34
PpGRAS30	Prupe.6G073600	6	Ⅱ	5020790 5022844	2055	685	77016.8	6.09
PpGRAS31	Prupe.6G073700	6	Ⅱ	5025889 5029019	2076	692	78813.9	6.22
PpGRAS32	Prupe.6G073800	6	Ⅱ	5037609 5040687	2121	707	79850.6	5.92
PpGRAS33	Prupe.6G073900	6	Ⅱ	5044672 5047324	2355	785	88209.9	5.58
PpGRAS34	Prupe.6G074000	6	Ⅱ	5052682 5054723	1998	666	74774.8	6.41
PpGRAS35	Prupe.6G220800	6	Ⅲ	22642849 22644378	1530	510	57075.9	5.46
PpGRAS36	Prupe.6G223200	6	Ⅰ	22836944 22839388	1437	479	53107.6	5.58
PpGRAS37	Prupe.6G257000	6	Ⅱ	24964599 24968826	2253	751	84278.9	6.66
PpGRAS38	Prupe.6G282800	6	Ⅲ	26358992 26360827	1611	537	60502	4.36
PpGRAS39	Prupe.6G300900	6	Ⅴ	27305816 27309379	2550	850	91964.8	6.81
PpGRAS40	Prupe.7G150900	7	Ⅷ	16214663 16216336	1674	558	62194.2	6.20
PpGRAS41	Prupe.7G153700	7	Ⅵ	16381917 16385916	1806	602	65807.8	5.08
PpGRAS42	Prupe.7G236100	7	Ⅳ	20509687 20511389	1614	538	59160.2	5.81
PpGRAS43	Prupe.8G016200	8	Ⅰ	1519578 1522426	1641	547	60817.4	4.83
PpGRAS44	Prupe.8G054000	8	Ⅳ	6129612 6131018	1407	469	53325	7.17
PpGRAS45	Prupe.8G220900	8	Ⅵ	20048389 20050058	1539	513	57646.5	6.55
PpGRAS46	Prupe.8G266100	8	Ⅶ	22267137 22269341	1923	641	72100.3	5.58
PpGRAS47	Prupe.I004400	U	Ⅱ	740 3677	2121	707	79888.5	5.82
PpGRAS48	Prupe.I004500	U	Ⅱ	13496 16456	2037	679	76744.6	6.60

表2

图1

图2

图3

图4

图5

图6

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