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Comparative Study
. 2017 Apr 12;18(1):292.
doi: 10.1186/s12864-017-3682-x.

Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species

Liuxin Xiang  1   2 , Jinggao Liu  3 , Chaofeng Wu  2 , Yushan Deng  2 , Chaowei Cai  1 , Xiao Zhang  1 , Yingfan Cai  4
Affiliations
Comparative Study

Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species

Liuxin Xiang et al. BMC Genomics. .

Abstract

Background: Nucleotide binding site (NBS) genes encode a large family of disease resistance (R) proteins in plants. The availability of genomic data of the two diploid cotton species, Gossypium arboreum and Gossypium raimondii, and the two allotetraploid cotton species, Gossypium hirsutum (TM-1) and Gossypium barbadense allow for a more comprehensive and systematic comparative study of NBS-encoding genes to elucidate the mechanisms of cotton disease resistance.

Results: Based on the genome assembly data, 246, 365, 588 and 682 NBS-encoding genes were identified in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. The distribution of NBS-encoding genes among the chromosomes was nonrandom and uneven, and was tended to form clusters. Gene structure analysis showed that G. arboreum and G. hirsutum possessed a greater proportion of CN, CNL, and N genes and a lower proportion of NL, TN and TNL genes compared to that of G. raimondii and G. barbadense, while the percentages of RN and RNL genes remained relatively unchanged. The percentage changes among them were largest for TNL genes, about 7 times. Exon statistics showed that the average exon numbers per NBS gene in G. raimondii and G. barbadense were all greater than that in G. arboretum and G. hirsutum. Phylogenetic analysis revealed that the TIR-NBS genes of G. barbadense were closely related with that of G. raimondii. Sequence similarity analysis showed that diploid cotton G. arboreum possessed a larger proportion of NBS-encoding genes similar to that of allotetraploid cotton G. hirsutum, while diploid G. raimondii possessed a larger proportion of NBS-encoding genes similar to that of allotetraploid cotton G. barbadense. The synteny analysis showed that more NBS genes in G. raimondii and G. arboreum were syntenic with that in G. barbadense and G. hirsutum, respectively.

Conclusions: The structural architectures, amino acid sequence similarities and synteny of NBS-encoding genes between G. arboreum and G. hirsutum, and between G. raimondii and G. barbadense were the highest among comparisons between the diploid and allotetraploid genomes, indicating that G. hirsutum inherited more NBS-encoding genes from G. arboreum, while G. barbadense inherited more NBS-encoding genes from G. raimondii. This asymmetric evolution of NBS-encoding genes may help to explain why G. raimondii and G. barbadense are more resistant to Verticillium wilt, whereas G. arboreum and G. hirsutum are more susceptible to Verticillium wilt. The disease resistances of the allotetraploid cotton were related to their NBS-encoding genes especially in regard from which diploid progenitor they were derived, and the TNL genes may have a significant role in disease resistance to Verticillium wilt in G. raimondii and G. barbadense.

Keywords: Amino acid sequence similarity; Disease resistance; Gene structure; Gossypium species; NBS-encoding gene.

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Figures

Fig. 1
Fig. 1
Distribution of NBS-encoding genes in chromosomes. a Distribution in G. arboreum chromosomes. b Distribution in G. raimondii chromosomes
Fig. 2
Fig. 2
Synteny of NBS genes between the diploid and allotetraploid cotton. a Collinear gene pairs between G. raimondii and G. barbadense. b Collinear gene pairs of NBS genes between G. raimondii and G. hirsutum. c Collinear gene pairs of NBS genes between G. arboreum and G. hirsutum. d Collinear gene pairs of NBS genes between G. arboreum and G. barbadense
Fig. 3
Fig. 3
Phylogenetic tree derived from NBS-encoding genes containing TIR domain in G. arboreum, G. raimondii, G. hirsutum and G. barbadense. The neighbor-joining tree was constructed using the sequences of 131 TIR-NBS proteins in the four cotton species. Bootstrap values were indicated on the branches. Each NBS protein was labeled by its name (Additional file 1: Table S1). The filled circles, the hollow circles, the solid triangles and the hollow triangles represented the genes of G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively
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