Browse Articles

Article|29 Apr 2022|OPEN
Large-scale discovery of non-conventional peptides in grape (Vitis vinifera L.) through peptidogenomics
Mao-Song Pei1,2 , Hai-Nan Liu1,2 and Tong-Lu Wei1,2 , Yi-He Yu1,2 , Da-Long Guo,1,2 ,
1College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
2Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
*Corresponding author. E-mail: guodalong@haust.edu.cn

Horticulture Research 9,
Article number: uhac023 (2022)
doi: https://doi.org/10.1093/hr/uhac023
Views: 361

Received: 22 Nov 2021
Revised: 16 Jun 2022
Accepted: 24 Jan 2022
Published online: 29 Apr 2022

Abstract

Non-conventional peptides (NCPs), which are peptides derived from previously unannotated coding sequences, play important biological roles in plants. In this study, we used peptidogenomic methods that integrated mass spectrometry (MS) peptidomics and a six-frame translation database to extensively identify NCPs in grape. In total, 188 and 2021 non-redundant peptides from the Arabidopsis thaliana and Vitis vinifera L. protein database at Ensembl/URGI and an individualized peptidogenomic database were identified. Unlike conventional peptides, these NCPs derived mainly from intergenic, intronic, upstream ORF, 5′UTR, 3′UTR, and downstream ORF regions. These results show that unannotated regions are translated more broadly than we thought. We also found that most NCPs were derived from regions related to phenotypic variations, LTR retrotransposons, and domestication selection, indicating that the NCPs have an important function in complex biological processes. We also found that the NCPs were developmentally specific and had transient and specific functions in grape berry development. In summary, our study is the first to extensively identify NCPs in grape. It demonstrated that there was a large amount of translation in the genome. These results lay a foundation for studying the functions of NCPs and also provide a reference for the discovery of new functional genes in grape.