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

Abstract

To date, several transcriptomic studies during fruit development have been reported, however no comprehensive integrated study on expression diversity, alternative splicing and metabolomic pro ling was reported in Capsicum. This study analyzed RNA-seq data and untargeted metabolomic pro ling from early green (EG), mature green (MG) and breaker (Br) fruit stages from two Capsicum species i.e. C. annuum (Cann) and C. frutescens (Cfrut) from Northeast India. A total of 117416 and 96802 alternatively spliced events (AltSpli-events) were identi ed from Cann and Cfrut, respectively. Among AltSpli-events, intron retention (IR; 32.2% Cann and 25.75% Cfrut) followed by alternative acceptor (AA; 15.4% Cann and 18.9% Cfrut) were the most abundant in Capsicum. Around, 7600 genes expressed in at least one fruit stages of Cann and Cfrut, were AltSpli. The study identi ed spliced variants of genes including transcription factors (TFs) involved in fruit development/ripening (Aux/IAA 16-

Transcriptomic Analysis of Alternative Splicing Events during Different Fruit Ripening Stages of Coffea arabica L.

“…For instance, IR was the most common AS type in cucumber, melon, and papaya, while A3SS was the most common AS type in peach [35]. For grape berries, the predominant AS type varies across studies [31,40,41], which may be caused by the different varieties, ripening stages, or genomes used. Indeed, comprehensive information on AS transcripts in Arabidopsis indicates that many low-abundance and incompletely spliced RI transcripts constitute noise in the splicing process, suggesting that the number of RIs may be overestimated in the genome [42].…”

“…In fact, AS is involved in all stages of plant growth and development, and it plays an important role in fruit development, flowering transition, and abiotic stress [25]. Previous studies have analyzed alternative splicing in fruit ripening and development, including tomato [26], blueberry [27], longan [28], banana [29], grape [30], Capsicum [31], kiwifruit [32], peach [33], sweet cherry [34], and watermelon [35]. However, different results have emerged.…”

Integrating proteomics and metabolomics to elucidate the molecular network regulating of inosine monophosphate-specific deposition in Jingyuan chicken

“…It is a relatively new discipline developed after the modern omics technology inherited from genomics, transcriptomics, and proteomics ( Nicholson and Lindon, 2008 ). Metabonomics is an important part of systems biology that studies the type, quantity, and modification rules of metabolites ( Rawoof et al, 2022 ). In the last decade, metabonomics has been continuously developed and has proven to be a powerful technical tool for predicting and interpreting complex phenotypes in a variety of biological systems ( Putri et al, 2013 ; Di Minno et al, 2022 ).…”