Abstract
Duplication, lateral gene transfer, domain fusion/fission and de novo domain creation play a key role in formation of initial common ancestral protein. Abundant protein diversities are produced by domain rearrangements, including fusions, fissions, duplications, and terminal domain losses. In this report, we explored the origin of the RPW8 domain and examined the domain rearrangements that have driven the evolution of RPW8-encoding genes in land plants. The RPW8 domain first emerged in the early land plant, Physcomitrella patens, and it likely originated de novo from a non-coding sequence or domain divergence after duplication. It was then incorporated into the NBS-LRR protein to create a main sub-class of RPW8-encoding genes, the RPW8-NBS-encoding genes. They evolved by a series of genetic events of domain fissions, fusions, and duplications. Many species-specific duplication events and tandemly duplicated clusters clearly demonstrated that species-specific and tandem duplications played important roles in expansion of RPW8-encoding genes, especially in gymnosperms and species of the Rosaceae. RPW8 domains with greater Ka/Ks values than those of the NBS domains indicated that they evolved faster than the NBS domains in RPW8-NBSs.
Highlights
New domains can be created and recruited with other domains to create new proteins, which frequently occur in genomes[1,2,3], and originate through multiple mechanisms, including duplication, lateral gene transfer, fusion/fission, and de novo origination[4]
resistance genes (R genes) are divided into the following five functionally different classes based on the presence of specific domains: (1) nucleotide-binding site leucine-rich repeat (NBS-LRR) genes, including coiled-coil NBS-LRR (CNL) and Toll/Interleukin[1] receptor-NBS-LRR (TNL)[26]; (2) receptor-like kinases (RLK); (3) receptor-like transmembrane proteins (RLP); (4) serine-theorine kinase (STK); and (5) the atypical R genes
Two other R genes encoding special CC-NBS-LRR proteins (CCR-NBS-LRR29) were Arabidopsis activated disease resistance gene 1 (ADR1), which participates in host-cell defense against Hyaloperonospora parasitica and Golovinomyces cichoracearum[30], and Nicotiana benthamiana N-required gene 1 (NRG1), which is active against tobacco mosaic virus[31]
Summary
New domains can be created and recruited with other domains to create new proteins, which frequently occur in genomes[1,2,3], and originate through multiple mechanisms, including duplication, lateral gene transfer, fusion/fission, and de novo origination[4]. R genes are divided into the following five functionally different classes based on the presence of specific domains: (1) nucleotide-binding site leucine-rich repeat (NBS-LRR) genes, including coiled-coil NBS-LRR (CNL) and Toll/Interleukin[1] receptor-NBS-LRR (TNL)[26]; (2) receptor-like kinases (RLK); (3) receptor-like transmembrane proteins (RLP); (4) serine-theorine kinase (STK); and (5) the atypical R genes. Two other R genes encoding special CC-NBS-LRR proteins (CCR-NBS-LRR29) were Arabidopsis activated disease resistance gene 1 (ADR1), which participates in host-cell defense against Hyaloperonospora parasitica and Golovinomyces cichoracearum[30], and Nicotiana benthamiana N-required gene 1 (NRG1), which is active against tobacco mosaic virus[31] These CC-NBS-LRR proteins, in which the amino-terminal CCR domain resembles the RPW8 domain[29], have an independent phylogenetic relationship to CNL and TNL proteins[23,32,33]. The evolutionary trajectory of these genes provides insight into the origin and diversification of novelties found in RPW8-encoding genes among land plants
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