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.

中文翻译：

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辣椒果实在转录本变异数据库开发和构建过程中的全长转录组测序


辣椒是一种重要的香料，也是水果发育研究的模式植物。继续收集有关辣椒植物发育的大规模组学信息，以了解发育以及辣椒素的生物合成。在这项研究中，使用 Oxford Nanopore 长读长测序方法生成了 8 个辣椒组织在 5 个生长阶段的全谱转录组数据。在 485 351 个转录本中，35 336 个记录为参考转录本（基因），而 450 015 个是新的，包括编码、lnc 和其他非编码 RNA。这些新的转录本属于未知/基因间 （347703），那些保留的内含子 （26336），并且具有至少一个连接匹配的多外显子 （20333）。在选择性剪接方面，保留的内含子比例最高 （14795）。组织特异性表达转录本的数量范围为 22 925 （茎） 至 40 289 （花）。详细讨论了水果和胎盘发育过程中的表达变化。在整个胎盘发育过程中整合基因表达和辣椒素含量定量阐明，辣椒中辣椒素的生物合成主要来源于缬氨酸、亮氨酸和异亮氨酸降解以及柠檬酸盐循环和/或嘧啶代谢途径。最重要的是，已经开发了用户友好的 Pepper 全长转录组变异数据库 （PFTVD 1.0） （http://pepper-database.cn/）。PFTVD 1.0 提供转录组学和基因组学信息，并允许用户使用实施的各种工具分析数据。这项工作强调了长读长测序在植物发育生物学中发现新基因和转录本及其多样性的潜力。