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作物学报 ›› 2021, Vol. 47 ›› Issue (12): 2348-2361.doi: 10.3724/SP.J.1006.2021.04268

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

马铃薯GAUT基因家族的全基因组鉴定及表达分析

牛娜1,2(), 刘震2, 黄鹏翔2,3, 朱金勇1,2, 李志涛1,2, 马文婧1,2, 张俊莲2,3, 白江平1,2,*(), 刘玉汇1,2,*()   

  1. 1甘肃农业大学农学院,甘肃兰州 730070
    2甘肃省干旱生境作物学重点实验室 / 甘肃省作物遗传改良与种质创新重点实验室,甘肃兰州 730070
    3甘肃农业大学园艺学院,甘肃兰州 730070
  • 收稿日期:2020-12-09 接受日期:2021-04-14 出版日期:2021-12-12 网络出版日期:2021-06-03
  • 通讯作者: 白江平,刘玉汇
  • 作者简介:E-mail: 2413748774@qq.com
  • 基金资助:
    国家自然科学基金项目(31860398);甘肃省高等学校创新基金项目(2020A-056);甘肃省杰出青年基金项目(17JR5RA138);甘肃省陇原青年创新团队项目(LRYCT-2020-1)

Genome-wide identification and expression analysis of potato GAUT gene family

NIU Na1,2(), LIU Zhen2, HUANG Peng-Xiang2,3, ZHU Jin-Yong1,2, LI Zhi-Tao1,2, MA Wen-Jing1,2, ZHANG Jun-Lian2,3, BAI Jiang-Ping1,2,*(), LIU Yu-Hui1,2,*()   

  1. 1College of Agronomy, Gansu Agricultural University, Lanzhou 730070, Gansu, China
    2Gansu Provincial Key Laboratory of Arid Land Crop Science / Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, Gansu, China
    3College of Horticulture, Gansu Agricultural University, Lanzhou 730070, Gansu, China
  • Received:2020-12-09 Accepted:2021-04-14 Published:2021-12-12 Published online:2021-06-03
  • Contact: BAI Jiang-Ping,LIU Yu-Hui
  • Supported by:
    National Natural Science Foundation of China(31860398);Program for Innovation Foundation of the Higher Education Institutions of Gansu Province(2020A-056);Gansu Science Foundation for Distinguished Young Scholars(17JR5RA138);Program for Longyuan Youth Innovation Team of Gansu Province(LRYCT-2020-1)

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摘要：

半乳糖醛酸转移酶(GAUT)是一种参与催化糖基化反应的酶类,在植物生长发育过程中发挥着重要作用。本研究鉴定了马铃薯GAUT家族成员,并对其理化性质、染色体定位、基因结构、保守蛋白结构域、基因重复事件和表达模式进行了分析。结果表明,鉴定到的41个GAUT家族成员(StGAUT),不均匀的分布在10条染色体上。根据基因的结构和系统发育蛋白特征,将41个StGAUT分为4个亚组。共线性分析表明,StGAUT基因家族存在12对片段重复基因,均在纯化选择下进化。通过对马铃薯双单倍体(DM)的不同组织部位和非生物胁迫下的RNA-seq数据进行分析,筛选出了组织特异性表达及响应非生物胁迫的StGAUT基因。此外,进一步对不同四倍体栽培种彩色马铃薯的薯皮和薯肉进行RNA-seq测序和分析,获得了可能参与花色素苷生物合成的StGAUT基因。本研究结果为进一步阐明StGAUT基因在马铃薯中的功能提供了有价值的信息。

关键词: 马铃薯, 半乳糖醛酸转移酶, 表达分析, 花色素苷生物合成

Abstract:

Galacturonyltransferases (GAUTs) are enzymes responsible for catalyzing glycosylation reactions and play an important role in the growth and development of plant. In this study, GAUT genes family members in potato (StGAUT) were identified, and their physical and chemical characteristics, distribution on chromosomes, gene structure, conserved motifs, gene duplication events, and expression patterns were analyzed. The results showed that a total of 41 StGAUTs were identified and distributed extensively and unevenly on 10 chromosomes. According to their structural and phylogenetic protein features, these 41 StGAUT genes were divided into four subclasses. Collinearity analysis indicated that 12 pairs of StGAUTs were segmental duplication genes, and these gene pairs evolved under purifying selection. RNA-seq data of different tissues and abiotic stresses were used to analyze tissue-specific and abiotic stress-responses of the StGAUT genes in doubled monoploid potato (DM). Results revealed that StGAUT genes might be involved in anthocyanin biosynthesis in three different-colored potato cultivars based on RNA-seq data. The results provide valuable information regarding further functional elucidation of StGAUT genes in potato.

Key words: potato (Solanum tuberosum L.), galacturonyltransferase, the relative expression level, anthocyanin biosynthesis

表1

qPCR引物序列"

基因名称
Gene name		 正向引物
Forward sequence (5°-3°)		 反向引物
Reverse sequence (5°-3°)
StEF-1α GGTCGTGTTGAGACTGGTGTGATC GCTTCGTGGTGCATCTCTACAGAC
PG0024800 ACAGAGTATTCGCTTGGCAGGTTC CTTCCATCCGGCAGCCTCTAAAC
PG0024782 CATTGGAGTGGAGGTGGCAAACC TGCAAATCATATCGAGCCCAGAGC
PG0020103
PG0000827		 CTGATCTCGGCGTCGGAATTACAC
AAGCTCCAGCATTCCGCAACG		 AGCCAGAACCAATGAACGGTGATC
CGGAGGTAAGGGGAGGAGTAATCG
PG0003522 GCCGTTGATGGTGAAGTTGAAGC GCCGCCGATGGAGCAGTTATG
PG0001444 CAGACAGTTGCCTTCACCAGAGC GGCAGCCAGGATGTTGTCAGTG
PG0001396 GGGAAACCTTGGGTCAGGCTTG CATCGCTCTTCGCTCTTGATCGTC
PG0001388 ACTTGCATCGGTCATTGGTGTCAC TAAGCGGCGTAGGCATTCACAAG

图1

StGAUT基因在马铃薯12条染色体上的分布"

图2

拟南芥和马铃薯GAUT基因家族进化分析 不同颜色的半圆代表不同的亚组。蓝色圆表示StGAUT基因,红色五角星表示AtGAUT基因。"

表2

StGAUT基因家族理化性质及亚细胞定位"

基因名称
Gene name		 染色体定位Chromosome
localization		 亚组
分类Subgroup		 氨基酸长度Amino acid
length		 等电点
Point isoelectric (pI)		 相对分子量
Molecular
weight (kD)		 亚细胞定位
Subcellular localization
PG0025139 ch02 C III 533 9.30 60,619.92 线粒体 Mitochondrial
PG0003522 ch02 C II 337 5.48 38,646.39 细胞外 Extracellular
PG0015490 ch02 C II 327 5.52 37,560.90 细胞外 Extracellular
PG0001183 ch02 C I 285 5.77 31,985.75 细胞膜 Plasma membrane
PG0001388 ch02 C IV 547 8.47 63,223.59 线粒体 Mitochondrial
PG0001396 ch02 C I 365 8.84 42,038.75 细胞膜 Plasma membrane
PG0010088 ch02 C I 345 6.24 38,390.78 细胞膜 Plasma membrane
PG0001444 ch02 C III 534 9.09 60,404.61 线粒体 Mitochondrial
PG0004427 ch00 C III 423 9.04 48,777.15 线粒体 Mitochondrial
PG2003179 ch07 C IV 597 9.33 68,386.80 线粒体 Mitochondrial
PG0017341 ch07 C III 545 7.36 61,040.35 细胞膜 Plasma membrane
PG0019228 ch07 C III 533 9.10 60,862.53 线粒体 Mitochondrial
PG0018996 ch01 C II 555 8.84 65,196.17 细胞核 Nuclear
基因名称
Gene name		 染色体定位Chromosome
localization		 亚组
分类Subgroup		 氨基酸长度Amino acid
length		 等电点
Point isoelectric (pI)		 相对分子量
Molecular
weight (kD)		 亚细胞定位
Subcellular localization
PG0046135 ch01 C II 321 6.02 36,737.36 细胞质 Cytoplasmic
PG0018997 ch01 C II 504 8.56 58,979.96 细胞质 Cytoplasmic
PG0000010 ch01 C IV 688 9.46 78,276.85 线粒体 Mitochondrial
PG0005216 ch01 C II 336 6.02 38,507.42 细胞质 Cytoplasmic
PG0012098 ch01 C III 90 10.39 10,714.47 线粒体 Mitochondrial
PG0024782 ch01 C I 353 9.26 40,529.85 细胞膜 Plasma membrane
PG0014677 ch01 C IV 680 8.34 78,728.64 细胞核 Nuclear
PG0023500 ch05 C II 533 8.96 60,350.47 细胞膜 Plasma membrane
PG0000827 ch05 C I 351 8.64 40,823.85 细胞膜 Plasma membrane
PG0022608 ch05 C I 385 8.32 44,667.17 细胞膜 Plasma membrane
PG0019367 ch12 C I 116 9.45 13,445.85 细胞膜 Plasma membrane
PG0007896 ch12 C IV 579 9.00 66,706.29 线粒体 Mitochondrial
PG0014637 ch06 C I 350 8.68 40,382.78 细胞膜 Plasma membrane
PG0011872 ch06 C II 465 8.68 52,580.83 细胞膜 Plasma membrane
PG0020103 ch06 C IV 557 9.23 63,946.48 线粒体 Mitochondrial
PG0003843 ch09 C I 356 8.63 40,860.88 细胞外 Extracellular
PG0027950 ch09 C IV 288 7.21 32,817.57 细胞膜 Plasma membrane
PG0031840 ch09 C I 353 9.02 40,214.14 细胞膜 Plasma membrane
PG0024623 ch09 C IV 536 6.95 62,348.31 细胞膜 Plasma membrane
PG0027227 ch04 C IV 678 9.26 77,430.93 细胞核 Nuclear
PG0016880 ch04 C I 351 5.99 39,345.05 细胞膜 Plasma membrane
PG0008016 ch04 C II 579 8.70 67,676.72 细胞质 Cytoplasmic
PG0024824 ch04 C IV 534 9.18 61,816.85 细胞膜 Plasma membrane
PG0008015 ch04 C II 564 9.02 66,085.84 细胞核 Nuclear
PG0011479 ch04 C II 533 9.05 60,263.41 细胞膜 Plasma membrane
PG0024800 ch04 C II 648 6.24 75,006.44 细胞质 Cytoplasmic
PG0014401 ch10 C III 533 6.58 60,586.97 细胞质 Cytoplasmic
PG0010264 ch10 C IV 635 9.24 72,635.34 线粒体 Mitochondrial

图3

StGAUT的进化关系、基因结构和保守基序分析 A：StGAUT进化树。B：StGAUT基因的外显子/内含子结构;蓝色框表示外显子,相同长度的黑线表示内含子,红色方框表示上游/下游区域,数字0、1和2表示内含子的剪接阶段。C：StGAUT中保守基序的分布;10个不同颜色的框代表了10个不同的基序。"

图4

StGAUT基因的片段重复事件 灰色线表示马铃薯基因组中的所有同线性区块,红色线表示StGAUT基因的片段重复。"

表3

StGAUT片段重复基因的Ka/Ks比值"

序号
No.		 基因1
Gene 1		 基因2
Gene 2		 非同义替换率
Ka		 同义替换率
Ks		 非同义替换率/同义替换率
Ka/Ks		 P值
P-value		 类型
Type
1 PG0001396 PG0022608 0.946754 1.20121 0.788168 4.76E-08 片段重复Segmental repeat
2 PG0024782 PG0031840 0.291121 3.40619 0.0854681 0 片段重复Segmental repeat
3 PG0003843 PG0014637 0.121239 1.39384 0.0869818 1.54E-98 片段重复Segmental repeat
4 PG0010088 PG0016880 0.179392 4.47249 0.0401102 0 片段重复Segmental repeat
5 PG0001183 PG0010088 0.0740382 2.24318 0.0330059 2.71E-125 片段重复Segmental repeat
6 PG0011479 PG0023500 0.103092 0.542081 0.190177 1.53E-47 片段重复Segmental repeat
7 PG0005216 PG0046135 0.264587 3.85123 0.0687019 0 片段重复Segmental repeat
8 PG0003522 PG0015490 0.103439 1.30535 0.0792418 1.55E-87 片段重复Segmental repeat
9 PG0014401 PG0019228 0.077988 0.755095 0.103282 3.94E-89 片段重复Segmental repeat
10 PG0001444 PG0025139 0.0574037 0.557829 0.102906 6.74E-66 片段重复Segmental repeat
11 PG0020103 PG0027950 0.957665 1.1718 0.817262 1.33E-05 片段重复Segmental repeat
12 PG0007896 PG2003179 0.172114 0.703844 0.244535 2.81E-54 片段重复Segmental repeat

图5

StGAUT基因在不同组织中的表达 对41个StGAUT基因表达量取以2为底的对数进行标准化处理,不同颜色的色块表示基因在不同组织中的表达水平。"

图6

StGAUT基因在盐、干旱、热胁迫下的表达量 盐胁迫、甘露醇胁迫和高温胁迫下StGAUT基因在DM马铃薯中的表达量。标尺表示与对照相比各基因的表达倍数(log2 FC)。"

图7

StGAUT基因在不同薯皮薯肉颜色中的表达 对41个StGAUT基因表达量取以2为底的对数进行标准化处理,不同颜色的色块表示基因在不同颜色薯皮薯肉中的表达水平。XDS、HMS和LTS分别代表‘新大坪’、‘黑美人’和‘铃田红美’的薯皮。XDF、HMF和LTF分别代表‘新大坪’、‘黑美人’和‘铃田红美’的薯肉。"

图8

8个StGAUT基因在白色和彩色薯皮和薯肉中的定量表达分析 XDS、HMS和LTS分别代表‘新大坪’、‘黑美人’和‘铃田红美’的薯皮。XDF、HMF和LTF分别代表‘新大坪’、‘黑美人’和‘铃田红美’的薯肉。"

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