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作物学报 ›› 2020, Vol. 46 ›› Issue (8): 1195-1207.doi: 10.3724/SP.J.1006.2020.94163

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

甘薯基因组NBS-LRR类抗病家族基因挖掘与分析

黄小芳1,2,毕楚韵1,2,石媛媛2,胡韵卓3,周丽香4,梁才晓4,黄碧芳4,许明1,2,林世强1,4,*(),陈选阳1,2,5,*()   

  1. 1福建农林大学作物生物技术福建省高校重点实验室, 福建福州 350002
    2福建农林大学农学院, 福建福州 350002
    3福建农林大学植物保护学院, 福建福州 350002
    4福建农林大学生命科学学院, 福建福州 350002
    5福建农林大学教育部作物遗传育种与综合利用重点实验室, 福建福州 350002
  • 收稿日期:2019-11-01 接受日期:2020-04-15 出版日期:2020-08-12 网络出版日期:2020-04-26
  • 通讯作者: 林世强,陈选阳
  • 作者简介:黄小芳, E-mail: 1102718600@qq.com, Tel: 059183789483|毕楚韵, E-mail: 494028227@qq.com, Tel: 059183789483.
  • 基金资助:
    福建省科技重大专项子专题(CN2017NZ0002-2)

Discovery and analysis of NBS-LRR gene family in sweet potato genome

HUANG Xiao-Fang1,2,BI Chu-Yun1,2,SHI Yuan-Yuan2,HU Yun-Zhuo3,ZHOU Li-Xiang4,LIANG Cai-Xiao4,HUANG Bi-Fang4,XU Ming1,2,LIN Shi-Qiang1,4,*(),CHEN Xuan-Yang1,2,5,*()   

  1. 1Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou 350002, Fujian, China
    2College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
    3College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
    4College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
    5Key Laboratory of Genetics, Breeding and Multiple Application of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
  • Received:2019-11-01 Accepted:2020-04-15 Published:2020-08-12 Published online:2020-04-26
  • Contact: Shi-Qiang LIN,Xuan-Yang CHEN
  • Supported by:
    Fujian Provincial Department of Science & Technology(CN2017NZ0002-2)

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摘要：

NBS-LRR类基因家族是植物抗病R基因(Resistance gene)数量最多的一类, 具有NBS (Nucleotide-binding site)和LRR (Leucine-leucine-repeat)结构域。甘薯(Ipomoea batatas)栽培种基因组已完成测序, 但尚未注释, 本研究对甘薯基因组序列进行外显子预测, 得到甘薯染色体组全基因组蛋白序列, 在此基础上进一步对NBS-LRR家族基因鉴定和分析表明, 甘薯基因组中含有379个NBS-LRR家族基因, 占全基因组基因总数的0.212%, 其中N型亚家族120个, NL型103个, CNL型133个, TNL型22个, PN型1个。所有染色体上均有NBS-LRR家族基因分布, 但数量明显不同, 其中有60.9%的NBS-LRR基因序列呈簇状分布。NBS-LRR基因序列有15个保守结构域, 在N端较为保守。研究结果为甘薯进一步开展NBS-LRR家族基因的功能研究和抗性育种提供了参考。

关键词: 甘薯, NBS-LRR, R基因, 基因家族, 生物信息学

Abstract:

The NBS-LRR gene families possess the most abundant resistance genes in plants. Members of the NBS-LRR gene families contain nucleotide-binding site (NBS) and leucine-leucine repeat (LRR) domains. The genome of sweet potato (Ipomoea batatas) cultivar has been sequenced but the genes have not been annotated yet. In this study, we predicted the exons of sweet potato genome and obtained the proteins sequences, which were then used to identify and analyze genes of NBS-LRR family. There were 379 genes within NBS-LRR family, amounting to 0.212% of the total genes of sweet potato. The number of the N type, NL type, CNL type, TNL type and PN type was 120, 103, 133, 22, and 1, respectively. All of the chromosomes had NBS-LRR family genes but varied in number and 60.9% of them were clustered. NBS-LRR genes included 15 conservative domains and the genes were conservative within N terminal domain. The results provide references for further studies on the function of NBS-LRR family genes and resistance breeding of sweet potato.

Key words: Ipomoea batatas, NBS-LRR, R gene, gene family, bioinformatics

表1

甘薯编码NBS-LRR蛋白的基因数量及其分类"

项目
Item		 预测结构域
Predicted domain		 代码
Code		 甘薯
Ib		 木薯a
Me a		 水稻b
Os b		 拟南芥c
At c		 乌拉尔图小麦d
Tu d
N类型N type NB N 118 14 45 1 270
NCCC 1 — — — —
NB NB NN 1 — — — —
NL类型NL type NB LRR NL 81 52 301 6 31
NLN 1 — — — —
项目
Item		 预测结构域
Predicted domain		 代码
Code		 甘薯
Ib		 木薯a
Me a		 水稻b
Os b		 拟南芥c
At c		 乌拉尔图小麦d
Tu d
NLC 1 — — — —
NB LRR LRR NLL 16 — — — 19
NLLC 1 — — — —
NB LRR LRR LRR NLLL 1 — — — 1
NB NB LRR NNL 2 — 3 — 1
CNL类型CNL type CC NB CN 22 11 7 5 55
CXN 29 — — — —
CC NB LRR CNL 15 117 175 51 84
CXNL 37 — — — —
CNCL 1 — — — —
CNLC 1 — — — —
CXNLC 1 — — — —
LCXNL 1 — — — —
CC NB LRR LRR CNLL 4 — — — 8
CXNLL 5 — — — —
CC NB LRR LRR LRR CXNLLL 1 — — — 1
CC NB NB LRR LRR CNNLL 1 — — — —
CC CC NB CXCN 4 — — — —
CXCXN 1 — — — —
CC CC NB LRR CCNL 2 — — — —
CXCNL 6 — — — —
CC CC NB LRR LRR CXCNLL 1 — — — —
CC CC CC CC NB LRR LRR CCCCNLL 1 — — — —
TNL类型TNL type TIR NB TN 9 5 3 23 0
TIR NB NB TNN 1 — — — —
TIR NB LRR TNL 7 29 — 88 0
TIR NB LRR LRR TNLL 3 — — — —
TIR NB LRR LRR LRR TNLLL 2 — — — —
PN类型PN type RPW8 NB PN 1 — — — —
其他Other — 99 1 33 15
总数Total 379 327 535 207 485
基因组中基因总数
Total number of genes in the genome		 178458 30666 37544 25498 32265
基因组大小Genome size (Mb) 633.42 ~760 389 125 3747.05

图1

甘薯NBS-LRR家族基因在染色体上的分布"

表2

甘薯NBS-LRR基因家族基因簇统计表"

染色体
Chromosome		 基因
Gene		 基因簇/基因数目
Gene cluster/gene number		 最大基因簇
Maximal gene cluster		 百分比
Percentage (%)
1 26 4/14 4 53.8
2 28 4/13 4 46.4
3 11 2/7 4 63.6
4 22 5/15 5 68.2
5 18 4/13 6 72.2
6 18 2/4 2 22.2
7 53 16/41 4 77.4
8 29 4/9 3 31.0
9 35 8/30 9 85.7
10 40 12/30 4 75.0
11 3 1/2 2 66.7
12 26 5/14 4 53.8
13 54 11/33 9 61.1
14 9 0/0 0 0
15 7 3/6 2 85.7
总数Total 379 81/231 60.9

图2

甘薯NBS-LRR家族中CNL亚家族保守结构域分布"

图3

甘薯NBS-LRR家族中TNL亚家族保守结构域分布"

图4

甘薯NB-ARC保守性分析"

图5

甘薯NBS-LRR家族基因保守结构域及其氨基酸保守性分析"

图6

甘薯NBS-LRR家族基因系统进化树"

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