Alternative splicing during fruit development among fleshy fruits

Abstract

Background Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known about alternative splicing during fruit development in fleshy fruits. Results We studied the alternative splicing at the immature and ripe stages during fruit development in cucumber, melon, papaya and peach. We found that 14.96–17.48% of multiexon genes exhibited alternative splicing. Intron retention was not always the most frequent event, indicating that the alternative splicing pattern during different developmental process differs. Alternative splicing was significantly more prevalent at the ripe stage than at the immature stage in cucumber and melon, while the opposite trend was shown in papaya and peach, implying that developmental stages adopt different alternative splicing strategies for their specific functions. Some genes involved in fruit ripening underwent stage-specific alternative splicing, indicating that alternative splicing regulates fruits ripening. Conserved alternative splicing events did not appear to be stage-specific. Clustering fruit developmental stages across the four species based on alternative splicing profiles resulted in species-specific clustering, suggesting that diversification of alternative splicing contributes to lineage-specific evolution in fleshy fruits. Conclusions We obtained high quality transcriptomes and alternative splicing events during fruit development across the four species. Dynamics and nonconserved alternative splicing were discovered. The candidate stage-specific AS genes involved in fruit ripening will provide valuable insight into the roles of alternative splicing during the developmental processes of fleshy fruits.

Integrated omics analysis identified genes and their splice variants involved in fruit development and metabolites production in Capsicum species

“…In tomato around 48-62% of MEGs were AltSpli during fruit development, while at nearly 15-18% of MEGs were AltSpli in eshy fruits at immature and ripe fruit stage (X. Yan et al, 2021). At EG, MG and Br fruit stage around 32-64% of MEGs underwent AltSpli across two Capsicum species which is similar to earlier ndings (Fig.…”

“…In addition to this, AA and IR AltSplievents were found to be the most conserved in monocots (Mei et al, 2017), between Populus and Eucalyptus , Brassica and Arabidopsis (Darracq & Adams, 2013), and between ashy fruits including papaya, melon, cucumber and peach (X. Yan et al, 2021).…”

“…For instance, during course of Capsicum fruit development, the differential expression of several genes such as Psy, PDS, CA1, Ccs, NCED3, SGR1, CaERF66, CaERF82, CaERF97, CaERF107, CaDIV1, CaMYB3R-1, CabHLH09, CabHLH032, CabHLH095, and CabHLH100 are directly or indirectly involved in regulation of carotenoid biosynthesis (Berry et In plants, expression of genes is regulated through various post-transcriptional mechanisms (PTM), which in turn regulate/affect the diverse developmental or physiological processes (Floris et al, 2009; X. Yan et al, 2021). Alternative splicing (AltSpli) is one of the indispensable PTM in the regulation of key biological processes such as fruit development and ripening (Y.…”

“…For instance, in tomato around ~34% of auxin response factor (ARF) genes underwent splicing during the early fruit development (Zouine et al, 2014), and in Arabidopsis, the retention of intronic region in one of transcripts of Phytochrome interacting factor 6 (PIF6) was shown to be associated with seed dormancy while other transcript with spliced out of intronic region reduced seed dormancy (Pen eld et al, 2010). Yan et al, (2021) reported splicing of cell-wall softening genes such as polygalacturonases (PGs) and galactanase (TBG4) is more ripe fruit stage than immature stage in four different plant species (X. Yan et al, 2021), indicating the tissue speci c and conservation of AltSpli events during the fruit development.…”

“…Yan et al, (2021) reported splicing of cell-wall softening genes such as polygalacturonases (PGs) and galactanase (TBG4) is more ripe fruit stage than immature stage in four different plant species (X. Yan et al, 2021), indicating the tissue speci c and conservation of AltSpli events during the fruit development. Multiple spliced transcripts of a gene can be generated through the uni cation of multiple exons in many ways; generally known as AltSpli events (AltSpli-events) which can be categorised into ve categories: i) intron-retention (IR): retention of intronic region in mature messenger RNA, ii) skipped-exon (SE): skipping one or more alternative exons, iii) mutually exclusive exons (MX): between two exons exclusion or splicing out either of exon, iv) alternative acceptor (AA), and v) alternative donor (AD): includes enigmatic use of 3' splice junction (SJ) or 3' acceptor and 5' SJ or donor site.…”