Khew Choy Yuen, Harikrishna Jennifer Ann, Wee Wei Yee, Lau Ee Tiing, Hwang Siaw San
Department of Research and Quality Development, Malaysian Pepper Board, Lot 1115, Jalan Utama, Pending Industrial Area, 93450 KC, Sarawak, Malaysia.
School of Chemical Engineering and Science, Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Jalan Simpang Tiga, 93350 KC, Sarawak, Malaysia.
Int J Genomics. 2020 Mar 27;2020:1540915. doi: 10.1155/2020/1540915. eCollection 2020.
Black pepper () 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 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.
黑胡椒（ ）是一种重要的香料作物，其用途涵盖烹饪和药理学应用等多个领域。然而，有限的遗传信息限制了我们对黑胡椒花和果实发育分子调控的理解。在本研究中，通过比较三个具有不同果实特征的黑胡椒品种，即诗梦谷阿曼（SA）、古晋（KC）和诗梦谷1号（S1），来深入了解花和果实发育的遗传调控。利用下一代测序（NGS）技术，在Illumina HiSeq 2500平台上进行测序，随后使用SOAPdenovo-Trans进行组装，以确定花和果实的转录组。高质量组装得到的66,906个单基因中，有64.4%（43,115个）的基因序列与GenBank数据库中一个或多个蛋白质序列具有相似性。通过Blast2Go注释，37,377个基因被分配到一个或多个基因本体（Gene Ontology）术语。在这些基因中，有5,874个基因进一步与KEGG数据库中记录的生物途径相关。对三个不同黑胡椒品种的花和果实转录组数据进行比较，发现SA品种的花和果实之间存在大量差异表达基因（DEGs）。基因本体（GO）富集分析进一步支持了花和果实之间差异表达基因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，而果实中的差异表达基因与生物合成过程、次生代谢过程和分解代谢过程相关。还研究了KEGG途径中差异表达基因的富集情况，发现大量基因属于核苷酸代谢和碳水化合物代谢类别。花形成相关基因的表达谱分析表明，除了调控黑胡椒的开花外，开花基因可能还参与果实发育过程。对不同果实品种中糖转运蛋白和碳水化合物代谢基因的转录分析表明，黑胡椒果实中的碳水化合物代谢受到发育调控一些基因可能成为未来作物品质改良的潜在基因。对胡椒碱相关基因表达分析的研究表明，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早期活跃。这些结果表明了几个与黑胡椒花和果实发育相关的候选基因，并为未来的功能分析以及潜在的作物改良提供了资源。
