Full-length transcriptome sequencing of pepper fruit during development and construction of a transcript variation database

Liu Zhoubin, Yang Bozhi, Zhang Tianyuan, Sun Hao, Mao Lianzhen, Yang Sha, Dai Xiongze, Suo Huan, Zhang Zhuqing, Chen Wenchao, Chen Hu, Xu Wangjie, Dossa Komivi, Zou Xuexiao, Ou Lijun. 2024. Full-length transcriptome sequencing of pepper fruit during development and construction of a transcript variation database. Horticulture Research, 11 (9):uhae198, 13 p.

https://doi.org/10.1093/hr/uhae198

Article de revue ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total

Prévisualisation

Version publiée - Anglais
Sous licence

.
uhae198.pdf
Télécharger (19MB) | Prévisualisation

Url - jeu de données - Entrepôt autre : http://pepper-database.cn/ / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1046572

Résumé : Chili pepper is an important spice and a model plant for fruit development studies. Large-scale omics information on chili pepper plant development continues to be gathered for understanding development as well as capsaicin biosynthesis. In this study, a full-spectrum transcriptome data of eight chili pepper tissues at five growth stages using the Oxford Nanopore long-read sequencing approach was generated. Of the 485 351 transcripts, 35 336 were recorded as reference transcripts (genes), while 450 015 were novel including coding, lnc, and other non-coding RNAs. These novel transcripts belonged to unknown/intergenic (347703), those retained introns (26336), and had multi-exons with at least one junction match (20333). In terms of alternative splicing, retained intron had the highest proportion (14795). The number of tissue-specific expressed transcripts ranged from 22 925 (stem) to 40 289 (flower). The expression changes during fruit and placenta development are discussed in detail. Integration of gene expression and capsaicin content quantification throughout the placental development clarifies that capsaicin biosynthesis in pepper is mainly derived from valine, leucin, and isoleucine degradation as well as citrate cycle and/or pyrimidine metabolism pathways. Most importantly, a user-friendly Pepper Full-Length Transcriptome Variation Database (PFTVD 1.0) (http://pepper-database.cn/) has been developed. PFTVD 1.0 provides transcriptomics and genomics information and allows users to analyse the data using various tools implemented. This work highlights the potential of long-read sequencing to discover novel genes and transcripts and their diversity in plant developmental biology.

Mots-clés Agrovoc : expression des gènes, Transcription génique, biosynthèse, capsaïcine, transcription, Capsicum annuum, séquence nucléotidique, génie génétique

Mots-clés géographiques Agrovoc : Chine

Agences de financement hors UE : National Natural Science Foundation of China, Ministry of Finance, Ministry of Agriculture and Rural Affairs

Auteurs et affiliations