Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod, 671316, Kerala, India.
Funct Integr Genomics. 2022 Dec;22(6):1189-1209. doi: 10.1007/s10142-022-00902-3. Epub 2022 Sep 29.
To date, several transcriptomic studies during fruit development have been reported; however, no comprehensive integrated study on expression diversity, alternative splicing, and metabolomic profiling was reported in Capsicum. This study analyzed RNA-seq data and untargeted metabolomic profiling 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 117,416 and 96,802 alternatively spliced events (AltSpli-events) were identified 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 stage of Cann and Cfrut were AltSpli. The study identified spliced variants of genes including transcription factors (TFs) potentially involved in fruit development/ripening (Aux/IAA 16-like, ETR, SGR1, ARF, CaGLK2, ETR, CaAGL1, MADS-RIN, FUL1, SEPALLATA1), carotenoid (PDS, CA1, CCD4, NCED3, xanthoxin dehydrogenase, CaERF82, CabHLH100, CaMYB3R-1, SGR1, CaWRKY28, CaWRKY48, CaWRKY54), and capsaicinoids or flavonoid biosynthesis (CaMYB48, CaWRKY51), which were significantly differentially spliced (DS) between consecutive Capsicum fruit stages. Also, this study observed that differentially expressed isoforms (DEiso) from 38 genes with differentially spliced events (DSE) were significantly enriched in various metabolic pathways such as starch and sucrose metabolism, amino acid metabolism, cysteine cutin suberin and wax biosynthesis, and carotenoid biosynthesis. Furthermore, the metabolomic profiling revealed that metabolites from aforementioned pathways such as carbohydrates (mainly sugars such as D-fructose, D-galactose, maltose, and sucrose), organic acids (carboxylic acids), and peptide groups significantly altered during fruit development. Taken together, our findings could help in alternative splicing-based targeted studies of candidate genes involved in fruit development and ripening in Capsicum crop.
迄今为止，已有多项关于果实发育过程中转录组学的研究报告；然而，在辣椒中，尚未有关于表达多样性、选择性剪接和代谢组学分析的综合研究报告。本研究分析了来自印度东北部两个辣椒物种，即 C. annuum（Cann）和 C. frutescens（Cfrut）的早期绿熟（EG）、成熟绿熟（MG）和裂果（Br）阶段的 RNA-seq 数据和非靶向代谢组学分析。从 Cann 和 Cfrut 中分别鉴定出 117416 个和 96802 个选择性剪接事件（AltSpli-events）。在 AltSpli-events 中，内含子保留（IR；32.2% Cann 和 25.75% Cfrut）紧随其后的是选择性受体（AA；15.4% Cann 和 18.9% Cfrut）是辣椒中最丰富的。在 Cann 和 Cfrut 的至少一个果实发育阶段表达的约 7600 个基因是 AltSpli。该研究鉴定了潜在参与果实发育/成熟的基因的剪接变体（转录因子（TFs）Aux/IAA 16-like、ETR、SGR1、ARF、CaGLK2、ETR、CaAGL1、MADS-RIN、FUL1、SEPALLATA1）、类胡萝卜素（PDS、CA1、CCD4、NCED3、黄质氧化酶、CaERF82、CabHLH100、CaMYB3R-1、SGR1、CaWRKY28、CaWRKY48、CaWRKY54）和辣椒素或类黄酮生物合成（CaMYB48、CaWRKY51），它们在连续的辣椒果实阶段之间存在显著的差异剪接（DS）。此外，本研究观察到，具有差异剪接事件（DSE）的 38 个基因的差异表达同工型（DEiso）在各种代谢途径中显著富集，如淀粉和蔗糖代谢、氨基酸代谢、半胱氨酸角质素亚油酸和蜡生物合成以及类胡萝卜素生物合成。此外，代谢组学分析表明，来自上述途径的代谢物，如碳水化合物（主要是糖，如 D-果糖、D-半乳糖、麦芽糖和蔗糖）、有机酸（羧酸）和肽组，在果实发育过程中显著改变。综上所述，我们的研究结果可以帮助辣椒作物中涉及果实发育和成熟的候选基因的基于选择性剪接的靶向研究。
