|WANG, YUNSHENG - Clemson University|
|ZHOU, LIJUAN - University Of Florida|
|LI, DAZHI - Hunan Agricultural University|
|LAWTON-LAUH, AMY - Clemson University|
|SRIMANI, PRADIP - Clemson University|
|DAI, LIANGYING - Hunan Agricultural University|
|LUO, FENG - Clemson University|
Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2015
Publication Date: 3/26/2015
Citation: Wang, Y., Zhou, L., Li, D., Lawton-Lauh, A., Srimani, P.K., Dai, L., Duan, Y., Luo, F. 2015. Genome-Wide Comparative Analysis Reveals Similar Types of NBS Genes in Hybrid Citrus sinensis Genome and Original Citrus clementine Genome and Provides New Insights into Non-TIR NBS Genes. PLoS One. 10(3):e0121893. https://doi.org/10.1371/journal.pone.0121893.
Interpretive Summary: 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. Using the NCBI data and comparative genomics, we identified and re-annotated candidate disease resistance (R) genes with NBS domain from a Citrus clementina genome and two complete Citrus sinensis genome sequences (one from the USA and one from China). 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.
Technical Abstract: We identified and re-annotated candidate disease resistance (R) genes with nucleotide-binding sites (NBS) domain from a Citrus clementina genome and two complete Citrus sinensis genome sequences (one from the USA and one from China). We found similar numbers of NBS genes from three citrus genomes, ranging from 508 in C. sinensis USA to 650 NBS genes in C. sinensis China. The citrus NBS genes are highly clustered in chromosomes. Phylogenetic analysis of all citrus NBS genes across three genomes showed that there are three approximately evenly numbered NBS-LRR 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 also used NBS domain sequence distances amongst all NBS genes to partition NBS genes into clades. 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 Citrus maxima (pummelo) genomes and three Citrus reticulata (Mandarin orange) genomes onto the Citrus sinensis (sweet orange) genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pummelo and mandarin genome. The homologous NBS genes in C. maxima and C. reticulata may be the reason that NBS genes in their hybrid Citrus sinensis are similar to those in C. reticulata 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.