Abstract
BackgroundThe sequenced genomes of cucumber, melon and watermelon have relatively few R-genes, with 70, 75 and 55 copies only, respectively. The mechanism for low copy number of R-genes in Cucurbitaceae genomes remains unknown.ResultsManual annotation of R-genes in the sequenced genomes of Cucurbitaceae species showed that approximately half of them are pseudogenes. Comparative analysis of R-genes showed frequent loss of R-gene loci in different Cucurbitaceae species. Phylogenetic analysis, data mining and PCR cloning using degenerate primers indicated that Cucurbitaceae has limited number of R-gene lineages (subfamilies). Comparison between R-genes from Cucurbitaceae and those from poplar and soybean suggested frequent loss of R-gene lineages in Cucurbitaceae. Furthermore, the average number of R-genes per lineage in Cucurbitaceae species is approximately 1/3 that in soybean or poplar. Therefore, both loss of lineages and deficient duplications in extant lineages accounted for the low copy number of R-genes in Cucurbitaceae. No extensive chimeras of R-genes were found in any of the sequenced Cucurbitaceae genomes. Nevertheless, one lineage of R-genes from Trichosanthes kirilowii, a wild Cucurbitaceae species, exhibits chimeric structures caused by gene conversions, and may contain a large number of distinct R-genes in natural populations.ConclusionsCucurbitaceae species have limited number of R-gene lineages and each genome harbors relatively few R-genes. The scarcity of R-genes in Cucurbitaceae species was due to frequent loss of R-gene lineages and infrequent duplications in extant lineages. The evolutionary mechanisms for large variation of copy number of R-genes in different plant species were discussed.
Highlights
The sequenced genomes of cucumber, melon and watermelon have relatively few R-genes, with 70, 75 and 55 copies only, respectively
Low copy number of R-genes in Cucurbitaceae Using HMMER, BLASTN search, and R protein database search, 70, 71, 48, 75 and 55 Rgenes were identified from the sequenced genomes of three cucumber cultivars (9930, Gy14 and B10), melon and watermelon, respectively
Eighteen gene models for all R-genes in Cucurbitaceae The amino acid sequences between the P-loop and GLPL motifs encoded by all identified R-genes from Cucurbitaceae were used to construct a Neighbor Joining (NJ) tree (Figure 1)
Summary
The sequenced genomes of cucumber, melon and watermelon have relatively few R-genes, with 70, 75 and 55 copies only, respectively. Many R-genes within a cluster belong to the same subfamily and may have had frequent sequence exchanges (either by gene conversion or recombination) resulting in chimeric structures [4,5,6,7,8,9,10,11,12,13,14,15,16] Those chimeras, termed Type I R-genes, are highly diverse in different genotypes of a species, and a large number of R-genes with distinct sequences are predicted in a population/species [12,13,17].
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
