Characterization and chromosomal distribution of Ty3-gypsy-like retrotransposons in wax gourd (Benincasa hispida)

Abstract

Wax gourd (2n = 2x = 24) is an important vegetable species in the Cucurbitaceae family, yet little is known about its genome structure. As the largest component of most plant genomes, retrotransposons might play an important role in the genetic variation and genome evolution of wax gourd. In this study, the presence of Ty3-gypsy-like retrotransposons, their heterogeneity and chromosomal distribution in wax gourd have been investigated. The conserved domains of reverse transcriptase of Ty3-gypsy-like retrotransposons have been amplified, and this resulted in thirty-five unique sequences. Seventeen (49%) of the sequences were defective as they were disrupted by a premature stop codon and/or contained frameshift mutations. These 35 sequences were divided into four groups and showed low or even no homology with Ty3-gypsy-like sequences from other species, indicating lack of horizontal transfer. The Ty3-gypsy-like retrotransposons have a dispersed genomic organization, physically distributed on all chromosomes with clusters in the heterochromatin regions. These results suggest that retrotransposons of this kind are widely distributed in wax gourd with high copy numbers, and contributed to the formation of chromosomes with non-uniform insertion and amplification. This is the first report on the presence of reverse transcriptase sequences of Ty3-gypsy-like retrotransposons in wax gourd genome.