Abstract
BackgroundNucleotide 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.ResultsBased 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.ConclusionsThe 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.
Highlights
Nucleotide binding site (NBS) genes encode a large family of disease resistance (R) proteins in plants
Searches with HMMER 3.1b2 in the G. arboreum, G. raimondii, G. hirsutum and G. barbadense genomes resulted in the identification of 246, 365, 588 and 682 NBS genes containing NB-ARC domain, respectively (Table 1 and Additional file 1: Table S1)
The two allotetraploid cotton plants possessed almost twice the number of NBS genes compared to the two diploid cotton plants, probably because of hybridization between G. arboreum and G. raimondii without gene losses, or hybridization with rapid gene losses followed by gene replication after their divergence from the initial hybrid
Summary
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. The most widely cultivated cotton species today are allotetraploid Gossypium hirsutum followed by Gossypium barbadense, both of which are originated from interspecific hybridization between the A-genome species Gossypium arboreum (A2) and the D-genome species Gossypium raimondii (D5) [1]. Verticillium wilt is caused by the soilborne fungal pathogen Verticillium dahliae. Fusarium wilt is caused by another soilborne fungal pathogen Fusarium oxysporum f. G. barbadense is often more susceptible to F. oxysporum compared to G. arboreum and G. hirsutum [9, 10]
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