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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (8): 1195-1207.doi: 10.3724/SP.J.1006.2020.94163


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 Online:2020-08-12 Published:2020-04-26
  • Contact: Shi-Qiang LIN,Xuan-Yang CHEN E-mail:linshiqiang@fafu.edu.cn;cxy@fafu.edu.cn
  • Supported by:
    Fujian Provincial Department of Science & Technology(CN2017NZ0002-2)


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

Table 1

Number of genes encoding NBS-LRR protein in Ipomoea batatas"

Predicted domain
Me a
Os b
At c
Tu d
N类型N type NB N 118 14 45 1 270
NL类型NL type NB LRR NL 81 52 301 6 31
Predicted domain
Me a
Os b
At c
Tu d
CNL类型CNL type CC NB CN 22 11 7 5 55
CXN 29
CC NB LRR CNL 15 117 175 51 84
TNL类型TNL type TIR NB TN 9 5 3 23 0
TIR NB LRR TNL 7 29 88 0
PN类型PN type RPW8 NB PN 1
其他Other 99 1 33 15
总数Total 379 327 535 207 485
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

Fig. 1

Distribution of NBS-LRR family genes on Ipomoea batatas chromosomes"

Table 2

Statistics of NBS-LRR gene family clusters of Ipomoea batatas"

Gene cluster/gene number
Maximal gene cluster
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

Fig. 2

Distribution of conservative domains of CNL subfamily of Ipomoea batatas NBS-LRR gene family"

Fig. 3

Distribution of conservative domain of TNL subfamily of Ipomoea batatas NBS-LRR gene family"

Fig. 4

Conservation analysis of NB-ARC in Ipomoea batatas"

Fig. 5

Conservative domains and amino acids of NBS-LRR family genes in Ipomoea batatas"

Fig. 6

Phylogenetic tree of NBS-LRR family genes in Ipomoea batatas"

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