Abstract Litchi is a perennial fruit crop with a highly heterozygous genome and complex transcripts. Although fruit senescence and pericarp browning have been extensively studied, the underlying regulatory mechanisms are still poorly understood. In this study, we used long-read sequencing technology in combination with RNA-seq analysis to investigate the diversity and complexity of the litchi transcriptome, as well as differential express of transcripts during litchi fruit storage. We obtained a reference transcriptome with 50,808 unique full-length isoforms, including 41,290 coding sequences (CDS), 1658 transcription factors, 22,100 simple sequence repeats, 2434 long noncoding RNAs, and 151 alternative splicing (AS) events. In addition, 41,290 isoforms had transmembrane helical structure, 33,579 isoforms contained Pfam protein domains, 14,348 isoforms contained SMART protein domains, 4180 isoforms had signal-peptide structure, 19,183 isoforms contained glycosylation sites, and 30,436 isoforms contained furin protease cleavage sites. Using this transcriptome, 1272 isoforms were found to be differentially expressed in litchi fruit pericarp during postharvest storage. The postharvest storage could be divided into a ‘senescence onset’ stage and a subsequent ‘browning’ stage according to RNA-seq data. During the ‘senescence onset’ stage, the expression of isoforms related to senescence and stress response was significantly up-regulated. During the ‘browning’ stage, the expression of isoforms related to cell wall degradation, oxidation, and disease response was significantly up-regulated. In addition, qPCR analysis showed that the expression changes of 30 isoforms during the postharvest storage of both ‘Huaizhi’ and ‘Guiwei’ fruit were consistent with the RNA-seq results, indicating high reliability of our results and inferences.

中文翻译：

---

通过单分子长读长测序揭示荔枝转录组和果皮褐变的复杂性

摘要 荔枝是一种具有高度杂合基因组和复杂转录本的多年生水果作物。尽管果实衰老和果皮褐变已被广泛研究，但其潜在的调控机制仍知之甚少。在本研究中，我们使用长读长测序技术结合RNA-seq分析来研究荔枝转录组的多样性和复杂性，以及荔枝果实贮藏过程中转录本的差异表达。我们获得了具有 50,808 个独特全长亚型的参考转录组，包括 41,290 个编码序列 (CDS)、1658 个转录因子、22,100 个简单序列重复、2434 个长非编码 RNA 和 151 个可变剪接 (AS) 事件。此外，41,290 个异构体具有跨膜螺旋结构，33,579 个异构体包含 Pfam 蛋白结构域，14 个，348 个异构体包含 SMART 蛋白结构域，4180 个异构体具有信号肽结构，19,183 个异构体包含糖基化位点，30,436 个异构体包含弗林蛋白酶裂解位点。使用该转录组，发现 1272 种异构体在采后储存期间在荔枝果皮中差异表达。根据 RNA-seq 数据，收获后储存可分为“衰老开始”阶段和随后的“褐变”阶段。在“衰老开始”阶段，与衰老和应激反应相关的异构体的表达显着上调。在“褐变”阶段，与细胞壁降解、氧化和疾病反应相关的异构体的表达显着上调。此外，