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

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外文摘要：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 22925(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.

作者：

Zhoubin Liu、Bozhi Yang、Tianyuan Zhang、Hao Sun、Lianzhen Mao、Sha Yang、Xiongze Dai、Huan Suo、Zhuqing Zhang、Wenchao Chen、Hu Chen、Wangjie Xu、Komivi Dossa、Xuexiao Zou、Lijun Ou

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作者单位：

Engineering Research Center of Education,Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops,Key Laboratory for Vegetable Biology of Hunan Province,College of Horticulture,Hunan Agricultural University,Changsha 410125,China

Vegetable Institution of Hunan Academy of Agricultural Science,Changsha 410125,China

Wuhan Benagen Technology Co.,Ltd.,Wuhan 430075,China

CIRAD,UMR AGAP Institut,97170 Petit Bourg,Guadeloupe,France

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出版年：

2024

DOI：

10.1093/hr/uhae198

园艺研究(英文)

CSTPCD

ISSN：

年,卷(期)：2024.11(9)