中国农业科学 ›› 2019, Vol. 52 ›› Issue (24): 4567-4581.doi: 10.3864/j.issn.0578-1752.2019.24.011
李晨,赵雪惠,王庆杰,王旭旭,肖伟,陈修德,付喜玲,李玲,李冬梅()
收稿日期:
2019-06-11
接受日期:
2019-08-03
出版日期:
2019-12-16
发布日期:
2020-01-15
通讯作者:
李冬梅
作者简介:
李晨,Tel:15650453756;E-mail:15650453756@163.com。
基金资助:
Chen LI,XueHui ZHAO,QingJie WANG,XuXu WANG,Wei XIAO,XiuDe CHEN,XiLing Fu,Ling LI,DongMei LI()
Received:
2019-06-11
Accepted:
2019-08-03
Online:
2019-12-16
Published:
2020-01-15
Contact:
DongMei LI
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。
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.
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 |
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