A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants.
BACKGROUND
Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.


RESULTS
To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR "gatekeeper" loci sharing syntenic orthologs across all analyzed genomes.


CONCLUSIONS
By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.
Johannes A
JA
Hofberger
Beifei
B
Zhou
Haibao
H
Tang
Jonathan D G
JD
Jones
Wageningen University & Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, Gelderland, The Netherlands. eric.schranz@wur.nl.
M Eric
ME
Schranz
D016000:Cluster Analysis; D019295:Computational Biology; D017124:Conserved Sequence; D060467:Disease Resistance; D019143:Evolution, Molecular; D020440:Gene Duplication; D056426:Genetic Loci; D018745:Genome, Plant; D023281:Genomics; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*; D010944:Plants / Q000145:classification / Q000235:genetics*; D054730:Protein Interaction Domains and Motifs / Q000235:genetics; D020080:Tandem Repeat Sequences
D010940:Plant Proteins