Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (Citrullus lanatus)

Abstract

Fruit ripening is a highly complicated process that is accompanied by the formation of fruit quality. In recent years, a series of studies have demonstrated post-transcriptional control play important roles in fruit ripening and fruit quality formation. Till now, the post-transcriptional mechanisms for watermelon fruit ripening have not been comprehensively studied. In this study, we conducted PacBio single-molecule long-read sequencing to identify genome-wide alternative splicing (AS), alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) in watermelon fruit. In total, 6,921,295 error-corrected and mapped full-length non-chimeric (FLNC) reads were obtained. Notably, more than 42,285 distinct splicing isoforms were derived from 5,891,183 intron-containing full-length FLNC reads, including a large number of AS events associated with fruit ripening. In addition, we characterized 21,506 polyadenylation sites from 11,611 genes, 8703 of which have APA sites. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that fructose and mannose metabolism, starch and sucrose metabolism and carotenoid biosynthesis were both enriched in genes undergoing AS and APA. These results suggest that post-transcriptional regulation might potentially have a key role in regulation of fruit ripening in watermelon. Taken together, our comprehensive PacBio long-read sequencing results offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of watermelon fruit ripening.

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

“…These finding differ from the results of some fruit ripening studies. 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.…”

“…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.…”