title: 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.
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Thangasamy
authors.initials: T
authors.lastname: Saminathan
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Padma
authors.initials: P
authors.lastname: Nimmakayala
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Sumanth
authors.initials: S
authors.lastname: Manohar
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Malkaram
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Aldo
authors.initials: A
authors.lastname: Almeida
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Cantrell
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Tomason
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Lavanya
authors.initials: L
authors.lastname: Abburi
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Mohammad A
authors.initials: MA
authors.lastname: Rahman
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Venkata G
authors.initials: VG
authors.lastname: Vajja
authors.affiliation: Genome International Corporation, 8000 Excelsior Drive, Suite 202, Madison, WI 53717, USA.
authors.forename: Amit
authors.initials: A
authors.lastname: Khachane
authors.affiliation: Genome International Corporation, 8000 Excelsior Drive, Suite 202, Madison, WI 53717, USA.
authors.forename: Brajendra
authors.initials: B
authors.lastname: Kumar
authors.affiliation: Genome International Corporation, 8000 Excelsior Drive, Suite 202, Madison, WI 53717, USA.
authors.forename: Harsha K
authors.initials: HK
authors.lastname: Rajasimha
authors.affiliation: US Vegetable Laboratory, USDA-ARS, 2875 Savannah Highway, Charleston, SC 29414, USA.
authors.forename: Amnon
authors.initials: A
authors.lastname: Levi
authors.affiliation: Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609, USA.
authors.forename: Todd
authors.initials: T
authors.lastname: Wehner
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA ureddy@wvstateu.edu.
authors.forename: Umesh K
authors.initials: UK
authors.lastname: Reddy
mesh_terms: D017398:Alternative Splicing; D029773:Citrullus / Q000235:genetics* / Q000378:metabolism; D004171:Diploidy; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D057891:Tetraploidy
chemical_list: D010940:Plant Proteins
keywords: RACE-PCR; RNA-seq; alternative splicing; gene expression; genome duplication; tetraploid; watermelon (Citrullus lanatus).