title: 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.
abstract: In this study, we identified and compared nucleotide-binding site (NBS) domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China). Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR) domain and two different Non-TIR groups in which most of proteins 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 three Citrus genomes have similar numbers and types of NBS genes. We also mapped the re-sequenced reads of three pomelo and three mandarin genomes onto the C. sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genomes. The homologous NBS genes in pomelo and mandarin suggest that the parental species of C. sinensis may contain similar types of NBS genes. This explains why the hybrid C. sinensis and original C. clementina have similar types of NBS genes in this study. Furthermore, we found that 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. Our comparative analyses yield valuable insight into the structure, organization and evolution of NBS genes in Citrus genomes. Furthermore, our comprehensive analysis showed that the non-TIR NBS genes can be divided into two groups that come from different evolutionary origins. This provides new insights into non-TIR genes, which have not received much attention.
authors: College of Plant Protection, Hunan Agricultural University, Changsha, China; School of Computing, Clemson University, Clemson, South Carolina, United States of America.
authors: Yunsheng
authors: Y
authors: Wang
authors: Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, Florida, United States of America.
authors: Lijuan
authors: L
authors: Zhou
authors: National Center for Citrus Improvement, Hunan Agricultural University, Changsha, China.
authors: Dazhi
authors: D
authors: Li
authors: College of Plant Protection, Hunan Agricultural University, Changsha, China.
authors: Liangying
authors: L
authors: Dai
authors: Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America.
authors: Amy
authors: A
authors: Lawton-Rauh
authors: School of Computing, Clemson University, Clemson, South Carolina, United States of America.
authors: Pradip K
authors: PK
authors: Srimani
authors: Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, Florida, United States of America.
authors: Yongping
authors: Y
authors: Duan
authors: School of Computing, Clemson University, Clemson, South Carolina, United States of America.
authors: Feng
authors: F
authors: Luo
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D002957:Citrus / Q000235:genetics*; D032084:Citrus sinensis / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D005785:Gene Conversion; D020440:Gene Duplication; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D006824:Hybridization, Genetic; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D005810:Multigene Family; D009154:Mutation / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D017434:Protein Structure, Tertiary; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid
chemical_list: D004251:DNA Transposable Elements; D010940:Plant Proteins