Abstract
Papaya is a productive and nutritious tropical fruit. Papaya Ringspot Virus (PRSV) is the most devastating pathogen threatening papaya production worldwide. Development of transgenic resistant varieties is the most effective strategy to control this disease. However, little is known about the genome-wide functional changes induced by particle bombardment transformation. We conducted transcriptome sequencing of PRSV resistant transgenic papaya SunUp and its PRSV susceptible progenitor Sunset to compare the transcriptional changes in young healthy leaves prior to infection with PRSV. In total, 20,700 transcripts were identified, and 842 differentially expressed genes (DEGs) randomly distributed among papaya chromosomes. Gene ontology (GO) category analysis revealed that microtubule-related categories were highly enriched among these DEGs. Numerous DEGs related to various transcription factors, transporters and hormone biosynthesis showed clear differences between the two cultivars, and most were up-regulated in transgenic papaya. Many known and novel stress-induced and disease-resistance genes were most highly expressed in SunUp, including MYB, WRKY, ERF, NAC, nitrate and zinc transporters, and genes involved in the abscisic acid, salicylic acid, and ethylene signaling pathways. We also identified 67,686 alternative splicing (AS) events in Sunset and 68,455 AS events in SunUp, mapping to 10,994 and 10,995 papaya annotated genes, respectively. GO enrichment for the genes displaying AS events exclusively in Sunset was significantly different from those in SunUp. Transcriptomes in Sunset and transgenic SunUp are very similar with noteworthy differences, which increased PRSV-resistance in transgenic papaya. No detrimental pathways and allergenic or toxic proteins were induced on a genome-wide scale in transgenic SunUp. Our results provide a foundation for unraveling the mechanism of PRSV resistance in transgenic papaya.
Highlights
Papaya (Carica papaya L.) is a major tropical fruit crop with outstanding nutritional and medicinal values
We found that genes annotated as ABC-2 type transporter, tonoplast intrinsic protein, laccase 11, and plant L-ascorbate oxidase in Arabidopsis thaliana were down-regulated in SunUp, while genes such as nitrate transporter, zinc transporter, mechanosensitive channel of small conductance-like were significantly up-regulated in SunUp (Table 4)
A greater number of alternative splicing (AS) events were found in SunUp compared to Sunset (68,455 vs. 67,686), while the number of genes undergoing AS in both cultivars was similar. These findings suggest that ∼39% of papaya genes potentially undergo the AS process, but AS events occurring in papaya increased upon Papaya Ringspot Virus (PRSV) CP transgene insertion
Summary
Papaya (Carica papaya L.) is a major tropical fruit crop with outstanding nutritional and medicinal values. Papaya is in the order Brassicales with the model plant Arabidopsis thaliana that diverged about 72 million years ago, facilitating comparative structural and evolutional genomic research in both species (Wikström et al, 2001) These characteristics make papaya an excellent model for tree fruit species. PRSV is a single-stranded positive sense RNA virus that belongs to the genus Potyvirus of family Potyviridae (Tripathi et al, 2008) It can be transmitted in a non-persistent manner by aphids and mechanical means, but difficult to control due to the lack of naturally resistant germplasm from Carica papaya (Gonsalves, 1998; Ming and Moore, 2014). Transgenic papaya acreage is about 85% of the total in the state of Hawaii
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