Black pepper (Piper nigrum) is a vital spice crop with uses ranging from culinary to pharmacological applications. However, limited genetic information has constrained the understanding of the molecular regulation of flower and fruit development in black pepper. In this study, a comparison among three different black pepper varieties, Semengok Aman (SA), Kuching (KC), and Semengok 1 (S1), with varying fruit characteristics was used to provide insight on the genetic regulation of flower and fruit development. Next-generation sequencing (NGS) technology was used to determine the flower and fruit transcriptomes by sequencing on an Illumina HiSeq 2500 platform followed by de novo assembly using SOAPdenovo-Trans. The high-quality assembly of 66,906 of unigenes included 64.4% of gene sequences (43,115) with similarity to one or more protein sequences from the GenBank database. Annotation with Blast2Go assigned 37,377 genes to one or more Gene Ontology terms. Of these genes, 5,874 genes were further associated with the biological pathways recorded in the KEGG database. Comparison of flower and fruit transcriptome data from the three different black pepper varieties revealed a large number of DEGs between flower and fruit of the SA variety. Gene Ontology (GO) enrichment analysis further supports functions of DEGs between flower and fruit in the categories of carbohydrate metabolic processes, embryo development, and DNA metabolic processes while the DEGs in fruit relate to biosynthetic process, secondary metabolic process, and catabolic process. The enrichment of DEGs in KEGG pathways was also investigated, and a large number of genes were found to belong to the nucleotide metabolism and carbohydrate metabolism categories. Gene expression profiling of flower formation-related genes reveals that other than regulating the flowering in black pepper, the flowering genes might also be implicated in the fruit development process. Transcriptional analysis of sugar transporter and carbohydrate metabolism genes in different fruit varieties suggested that the carbohydrate metabolism in black pepper fruit is developmentally regulated, and some genes might serve as potential genes for future crop quality improvement. Study on the piperine-related gene expression analysis suggested that lysine-derived products might present in all stages of fruit development, but the transportation was only active at the early stage of fruit development. These results indicate several candidate genes related to the development of flower and fruit in black pepper and provide a resource for future functional analysis and potentially for future crop improvement.

中文翻译：

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三种不同黑胡椒（Piper nigrum L.）品种果实发育过程中各基因的转录测序和基因表达分析。


黑胡椒（ Piper nigrum ）是一种重要的香料作物，用途广泛，从烹饪到药理学应用。然而，有限的遗传信息限制了对黑胡椒花和果实发育分子调控的理解。在这项研究中，对具有不同果实特性的三种不同黑胡椒品种 Semengok Aman (SA)、Kuching (KC) 和 Semengok 1 (S1) 进行了比较，以深入了解花和果实发育的遗传调控。新一代测序 (NGS) 技术用于通过在 Illumina HiSeq 2500 平台上进行测序，然后使用 SOAPdenovo-Trans从头组装来确定花和果实转录组。 66,906 个 unigene 的高质量组装包括 64.4% 的基因序列 (43,115) 与 GenBank 数据库中的一个或多个蛋白质序列相似。使用 Blast2Go 注释将 37,377 个基因分配给一个或多个基因本体术语。在这些基因中，有 5,874 个基因与 KEGG 数据库中记录的生物学途径进一步相关。对三个不同黑胡椒品种的花和果实转录组数据的比较揭示了SA品种的花和果实之间存在大量DEG。基因本体（GO）富集分析进一步支持花和果实之间的DEG在碳水化合物代谢过程、胚胎发育和DNA代谢过程等类别中的功能，而果实中的DEG与生物合成过程、次生代谢过程和分解代谢过程相关。还研究了KEGG通路中DEG的富集，发现大量基因属于核苷酸代谢和碳水化合物代谢类别。 花形成相关基因的基因表达谱表明，除了调节黑胡椒的开花外，开花基因还可能与果实发育过程有关。对不同水果品种糖转运蛋白和碳水化合物代谢基因的转录分析表明，黑胡椒果实的碳水化合物代谢受到发育调控，某些基因可能作为未来作物品质改良的潜在基因。胡椒碱相关基因表达分析表明，赖氨酸衍生产物可能存在于果实发育的各个阶段，但运输仅在果实发育的早期活跃。这些结果表明了与黑胡椒花和果实发育相关的几个候选基因，并为未来的功能分析和未来作物改良提供了资源。