Transcriptional Sequencing and Gene Expression Analysis of Various Genes in Fruit Development of Three Different Black Pepper (Piper nigrumL.) Varieties

Abstract

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.

Drought responsiveness in black pepper (Piper nigrum L.): Genes associated and development of a web‐genomic resource

“…Many belonged to the purine metabolism, followed by thiamine metabolism and antibiotics biosynthesis. The over-representation of purine metabolism was also reported in the fruit transcriptome analysis of black pepper (Khew et al, 2020). This confirmed the role of purine metabolites in drought tolerance as reported in Arabidopsis (Watanabe et al, 2010) and almond-peach rootstock (Bielsa et al, 2018).…”

Comparative metabolite analysis of Piper sarmentosum organs approached by LC–MS-based metabolic profiling

“…These enzymes add an activated sugar unit to the aglycone in the cytosol of the plant cell [ 64 – 66 ]. Recently, the analysis of the 7-deoxyloganetin glucosyltransferase-like (GGT) gene during fruit development of various Piper nigrum L. varieties revealed that increased GGT expression in Piper fruits correlated with up-regulation of volatile and nonvolatile metabolites [ 67 ]. Interestingly, some of the glycosides detected in this study contain 3-hydroxy-3-methylglutaryl residues as also found in flavonoids in this species (see chapter 2.4.2.1.)…”

De novo transcriptome profiling unveils the regulation of phenylpropanoid biosynthesis in unripe Piper nigrum berries

“…An enzyme can be responsible for synthesizing more than one metabolite that may be related to each other structurally [ 37 ].The complete information on the set of enzymes active at a particular stage can be uncovered using NGS technology. NGS technology helps in the identification of potential candidates that can be targeted to enhance the quality of fruits in P. nigrum [ 38 ].…”

“…Gene expression analysis helps to confirm the results obtained from RNA-Seq data [ 38 ]. The expression of selected genes was analysed in different developmental stages using qRT-PCR experiment.…”