Transcriptomic analysis of alternative splicing events for different stages of growth and development in Sistan Yaghooti grape clusters

Montazerinezhad, Somayeh; Solouki, Mahmood; Emamjomeh, Abbasali; Kavousi, Kaveh; Taheri, Ali; Shiri, Yasoub

doi:10.1016/j.gene.2023.148030

Cited by 1 publication

(1 citation statement)

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“…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].…”

Section: Discussionmentioning

confidence: 99%

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

Yu,

Bi,

et al. 2024

Genes

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To date, genomic and transcriptomic data on Coffea arabica L. in public databases are very limited, and there has been no comprehensive integrated investigation conducted on alternative splicing (AS). Previously, we have constructed and sequenced eighteen RNA-seq libraries of C. arabica at different ripening stages of fruit development. From this dataset, a total of 3824, 2445, 2564, 2990, and 3162 DSGs were identified in a comparison of different fruit ripening stages. The largest proportion of DSGs, approximately 65%, were of the skipped exon (SE) type. Biologically, 9 and 29 differentially expressed DSGs in the spliceosome pathway and carbon metabolism pathway, respectively, were identified. These DSGs exhibited significant variations, primarily in S1 vs. S2 and S5 vs. S6, and they involve many aspects of organ development, hormone transduction, and the synthesis of flavor components. Through the examination of research findings regarding the biological functions and biochemical pathways associated with DSGs and DEGs, it was observed that six DSGs significantly enriched in ABC transporters, namely, LOC113712394, LOC113726618, LOC113739972, LOC113725240, LOC113730214, and LOC113707447, were continually down-regulated at the fruit ripening stage. In contrast, a total of four genes, which were LOC113732777, LOC113727880, LOC113690566, and LOC113711936, including those enriched in the cysteine and methionine metabolism, were continually up-regulated. Collectively, our findings may contribute to the exploration of alternative splicing mechanisms for focused investigations of potential genes associated with the ripening of fruits in C. arabica.

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