Differential gene expression and alternative splicing between diploid and tetraploid watermelon

Abstract

The exploitation of synthetic polyploids for producing seedless fruits is well known in watermelon. Tetraploid progenitors of triploid watermelon plants, compared with their diploid counterparts, exhibit wide phenotypic differences. Although many factors modulate alternative splicing (AS) in plants, the effects of autopolyploidization on AS are still unknown. In this study, we used tissues of leaf, stem, and fruit of diploid and tetraploid sweet watermelon to understand changes in gene expression and the occurrence of AS. RNA-sequencing analysis was performed along with reverse transcription quantitative PCR and rapid amplification of cDNA ends (RACE)-PCR to demonstrate changes in expression and splicing. All vegetative tissues except fruit showed an increased level of AS in the tetraploid watermelon throughout the growth period. The ploidy levels of diploids and the tetraploid were confirmed using a ploidy analyser. We identified 5362 and 1288 genes that were up- and downregulated, respectively, in tetraploid as compared with diploid plants. We further confirmed that 22 genes underwent AS events across tissues, indicating possibilities of generating different protein isoforms with altered functions of important transcription factors and transporters. Arginine biosynthesis, chlorophyllide synthesis, GDP mannose biosynthesis, trehalose biosynthesis, and starch and sucrose degradation pathways were upregulated in autotetraploids. Phloem protein 2, chloroplastic PGR5-like protein, zinc-finger protein, fructokinase-like 2, MYB transcription factor, and nodulin MtN21 showed AS in fruit tissues. These results should help in developing high-quality seedless watermelon and provide additional transcriptomic information related to other cucurbits.

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

“…Moreover, polyploids have been reported to affect the gene expression at the transcription level compared with diploids. For example, studies in watermelon have shown that 5,362 and 1,288 genes were up- and down-regulated, respectively, in autotetraploid compared with diploid watermelon46. So further studies are required to reveal the reason for tetraploid formation and the effect on gene expression after genome duplication event in S. psammophila .…”

RNA-seq-based transcriptome profiling reveals differential gene expression in the lungs of Sprague–Dawley rats during early-phase acute hypobaric hypoxia

“…RNA-seq technology has been applied to different model as well as non-model organisms for a variety of studies covering allele specific gene expression, new splice variants (Saminathan et al 2015), fusion transcript variants (Norton et al 2013;Ma et al 2014), quantitative trait loci regions (Lionikas et al 2012) and tissue specific putative biomarkers (Metsalu et al 2014). We believe that there may be enhanced expression of those early-phase response genes, which may trigger signaling events that would prepare the lung tissue of tolerant animals to undergo changes that help fight or protect against or else repair the injury caused due to hypobaric hypoxia exposure, while gene expression pattern in lungs of susceptible rats might indicate an opposite pattern.…”

The Impact of CdS Nanoparticles on Ploidy and DNA Damage of Rucola (Eruca sativa Mill.) Plants

“…This study acknowledged the tendency to increase for the amounts of polyploid cells in plant if it is treated with NPs. There are lots of researches proclaiming that increase in ploidy leads to improvements in economically valued plants attributes, for example, biomass increase and stress tolerance escalation [28][29][30][31]. The mitotic indexes obtained from rucola cells of untreated plants and from plants treated with nanoparticles are presented in Table 3.…”