title: Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  Manual 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.
  
  
  CONCLUSIONS
  Cucurbitaceae 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.
authors.affiliation: Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Lin
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.forename: Hanhui
authors.initials: H
authors.lastname: Kuang
authors.forename: Jiongjiong
authors.initials: J
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D019662:Cucurbitaceae / Q000235:genetics* / Q000276:immunology; D017931:DNA Primers / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics*; D020440:Gene Duplication; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D005838:Genotype; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics*; D011544:Pseudogenes / Q000235:genetics; D013045:Species Specificity
chemical_list: D017931:DNA Primers