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.

The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype

“…This situation, along with its large genome size 9 and 12 chromosomes, as in melon, makes it an excellent system for exploring the evolution of cucurbit genomes. Currently, only a high-density genetic map 10 , transcriptome sequences for several tissues 11 , and a small number of genomic fragments 12,13 have been developed for wax gourd. Hence, an assembled wax gourd genome is needed to facilitate a further investigation of cucurbit genome evolution and to explore the genetic basis of its diversity.…”

Heterogeneous evolution of Ty3-gypsy retroelements among bamboo species

“…Ty3-gypsy group retroelements in the bamboo genomes are highly heterogeneous, like those observed in other plant species (Jiang et al, 2013;Kolano et al, 2013). There are four possible explanations for this.…”

“…Second, according to Kumar and Bennetzen (1999), retroelement heterogeneity could gradually be maintained over generations, through vertical transmission. Third, repetitive DNA could be deleted from the genome through unequal crossing-over and illegitimate recombination (Devos et al, 2002;Pereira, 2004), a process that might occur in one species but perhaps not in another (Jiang et al, 2013;Kolano et al, 2013). Fourth, transposable elements undergo more stringent natural selection than other sequences, due to their potential impact on genic regions.…”

“…There are at least three deleterious effects of transposable elements in the host genome including mutations resulting from insertions into genes or regulatory sequences (Finnegan, 1992), chromosomal rearrangements caused by ectopic recombination between elements in non-homologous insertion sites (Devos et al, 2002;Pereira, 2004), and direct costs due to their transposition activity (Brookfield, 1991). Therefore, transposable elements undergo more stringent natural selection than other sequences, as the host could eliminate active transposable elements through stochastic loss or vertical extinction mechanisms to reduce the deleterious effects of transposition (Pritham, 2009;Jiang et al, 2013;Kolano et al, 2013). The positive value of Tajima's D obtained for the 165 bamboo Ty3-gypsy sequences (2.13) indicates that these retroelements indeed underwent strong natural selection.…”