title: Characterization and chromosomal organization of Ty1-copia retrotransposons in wax gourd.
abstract: Wax gourd (2n=2x=24) is an important vegetable species in Cucurbitaceae. Because it can be stored for a very long period of time, it plays an important role in ensuring the annual supply and regulating off-season supply of the vegetables. However, the availability of genetic information about wax gourd is limited. This study aimed to identify the useful genetic information for wax gourd. The conserved domains of reverse transcriptase (RT) genes of Ty1-copia retrotransposons were isolated from the genome of wax gourd using degenerate oligonucleotide primers. A total of twenty eight RT sequences were obtained, which showed high heterogeneity with the similarity ranging from 47.5% to 94.3%. Sixteen (57.1%) of them were found to be defective, being disrupted by stop codons and/or frameshift mutations. These 28 sequences were divided into five subfamilies. The comparative phylogenetic analysis with other Cucurbitaceae species from GenBank database showed that most retrotransposons derived from the same genus tended to cluster together, although there were a few exceptions. These results indicate that both vertical transmission and horizontal transmission are the sources of Ty1-copia retrotransposons in wax gourd. Fluorescent in situ hybridization (FISH) with Ty1-copia retrotransposon sequences as probes revealed that this kind of retrotransposons had a dispersed genomic organization, physically distributed among all the chromosomes of wax gourd, with clusters in the heterochromatin regions. This is the first report of Ty1-copia retrotransposons in wax gourd, which would be helpful for our understanding about the organization and evolutions of wax gourd genome and also provide valuable information for our utilization of wax gourd retrotransposons.
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China; Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou 510640, China.
authors.forename: Biao
authors.initials: B
authors.lastname: Jiang
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China; Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou 510640, China.
authors.forename: Wenrui
authors.initials: W
authors.lastname: Liu
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China.
authors.forename: Qingwu
authors.initials: Q
authors.lastname: Peng
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China; Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou 510640, China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: He
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China; Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou 510640, China. Electronic address: dasenxie@21cn.com.
authors.forename: Dasen
authors.initials: D
authors.lastname: Xie
mesh_terms: D000595:Amino Acid Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D019662:Cucurbitaceae / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D010802:Phylogeny; D012194:RNA-Directed DNA Polymerase / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
chemical_list: D018626:Retroelements; D012194:RNA-Directed DNA Polymerase
keywords: FISH; Heterogeneity; Reverse transcriptase; Ty1-copia retrotransposons; Wax gourd