PepperHub, an Informatics Hub for the Chili Pepper Research Community

Abstract

Pepper belongs to the Solanaceae family, which includes many important vegetable crops such as tomato, potato, and eggplant. Not only widely used as vegetables and spicy ingredients, pepper also has diverse applications in pharmaceutics, natural coloring agents, cosmetics, defense repellents, and as ornamental plants (Kim et al., 2014;Qin et al., 2014). Pepper is among the most widely cultivated and consumed vegetables in the world, with annual production reaching to 38 million tons in 2011 (www.fao. org). Pepper fruits have significant diversity in morphology and color, and they provide good models for fruit developmental biology (Paran and van der Knaap, 2007;Rivera et al., 2016). Like all other crops, pepper plants are often confronted with different pathogens and pests (Pernezny et al., 2003), and diverse abiotic stress conditions, which necessitate basic studies on the mechanisms of pepper plants responding to various stimuli to facilitate breeding efforts for tolerant cultivars.

The zinc‐finger transcription factor CcLOL1 controls chloroplast development and immature pepper fruit color in Capsicum chinense and its function is conserved in tomato

“…However, expression remained at similar level at the ripe fruit stage (Table S4). Similar expression profiles were observed in the PepperHub database (http://pepperhub.hzau.edu.cn; Liu et al ., ).…”

Full‐length mRNA sequencing and gene expression profiling reveal broad involvement of natural antisense transcript gene pairs in pepper development and response to stresses

“…Assembly of the full-length pepper transcriptome using PacBio sequencing technology For better annotation of the pepper genome, we conducted PacBio sequencing for the pepper transcriptome ( Figure 1). Three cDNA libraries of different lengths (A:1~2 kb; B: 2~3 kb and C:3~6 kb) were prepared and sequenced using the PacBio Iso-seq platform, using mixed RNA samples derived from pepper samples of different developmental stages and subjected to various treatments (Data S1; Liu et al, 2017). These libraries were sequenced using six Isoseq chips, and approximately 20-300 thousand reads were obtained from each chip (Figure 1, step I), and more than 85% of the reads from each chip passed initial filtering and constituted full-length and non-chimeric circular consensus sequence (FLCCS) reads (Figure 1, step II).…”

“…In plants, the first functional cis-NAT pair was discovered in Arabidopsis during salt stress response, in which the two genes showed opposite expression patterns during the stress response (Borsani et al, 2005). To select potential functional cis-NAT genes involved in stress or hormone treatment or various developmental processes in pepper, gene expression profiles of the cis-NATs were analyzed using published pepper gene expression data (Liu et al, 2017). These datasets were generated for pepper samples of different tissues/organs at different developmental stages or at different time points after different stress or hormone treatments (Liu et al, 2017).…”

“…To select potential functional cis-NAT genes involved in stress or hormone treatment or various developmental processes in pepper, gene expression profiles of the cis-NATs were analyzed using published pepper gene expression data (Liu et al, 2017). These datasets were generated for pepper samples of different tissues/organs at different developmental stages or at different time points after different stress or hormone treatments (Liu et al, 2017). The cis-NAT pairs with one gene expression going up and the other going down during a treatment or developmental process were considered responsive to the treatment or developmental process.…”

“…Pepper is an important crop both as a vegetable of great economic value and rich nutrients and as raw material for industrial use (Liu et al, 2017). Pepper is also an important model plant for fruit development due to its rich diversity in fruit morphology and biochemical activities of special metabolites, such as capsanthin and capsaicin (Paran and van der Knaap, 2007;Mazourek et al, 2009).…”