Yunsheng Wang, Lijuan Zhou, Dazhi Li, Amy Lawton-Rauh, Pradip K. Srimani, Liangying Dai, Yongping Duan, Feng Luo
Background Recently available whole genome sequences of three citrus species: one Citrus clementina and two Citrus sinensis genomes have made it possible to understand the features of candidate disease resistance genes with nucleotide-binding sites (NBS) domain in Citrus and how NBS genes differ between hybrid and original Citrus species. Result We identified and re-annotated NBS genes from three citrus genomes and found similar numbers of NBS genes in those citrus genomes. Phylogenetic analysis of all citrus NBS genes across three genomes showed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR) domain and two different groups that contain the Coiled Coil (CC) domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three citrus genomes. This suggests that NBS genes in three citrus genomes may come from shared ancestral origins. We also mapped the re-sequenced reads of three pomelo and three Mandarin orange genomes onto the Citrus sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genome. The homologous NBS genes in pomelo and mandarin may explain why the NBS genes in their hybrid Citrus sinensis are similar to those in Citrus clementina in this study. Furthermore, sequence variation amongst citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different citrus genomes. Conclusion Our comparative analyses yield valuable insight into the understanding of the structure, evolution and organization of NBS genes in Citrus genomes. There are significantly more NBS genes in Citrus genomes compared to other plant species. NBS genes in hybrid C. sinensis genomes are very similar to those in progenitor C. clementina genome and they may be derived from possible common ancestral gene copies. Furthermore, our comprehensive analysis showed that there are three groups of plant NBS genes while CC-containing NBS genes can be divided into two groups.