Abstract
ATP-binding cassette (ABC) transporter genes act as transporters for different molecules across biological membranes and are involved in a diverse range of biological processes. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC transporter proteins in three Capsicum species, i.e., Capsicum annuum, Capsicum baccatum and Capsicum chinense. Capsicum is a valuable horticultural crop worldwide as an important constituent of many foods while containing several medicinal compounds including capsaicin and dihydrocapsaicin. Our results identified the presence of a total of 200, 185 and 187 ABC transporter genes in C. annuum, C. baccatum and C. chinense genomes, respectively. Capsaicin and dihydrocapsaicin content were determined in green pepper fruits (16 dpa). Additionally, we conducted different bioinformatics analyses including ABC genes classification, gene chromosomal location, Cis elements, conserved motifs identification and gene ontology classification, as well as profile expression of selected genes. Based on phylogenetic analysis and domain organization, the Capsicum ABC gene family was grouped into eight subfamilies. Among them, members within the ABCG, ABCB and ABCC subfamilies were the most abundant, while ABCD and ABCE subfamilies were less abundant throughout all species. ABC members within the same subfamily showed similar motif composition. Furthermore, common cis-elements involved in the transcriptional regulation were also identified in the promoter regions of all Capsicum ABC genes. Gene expression data from RNAseq and reverse transcription-semi-quantitative PCR analysis revealed development-specific stage expression profiles in placenta tissues. It suggests that ABC transporters, specifically the ABCC and ABCG subfamilies, may be playing important roles in the transport of secondary metabolites such as capsaicin and dihydrocapsaicin to the placenta vacuoles, effecting on their content in pepper fruits. Our results provide a more comprehensive understanding of ABC transporter gene family in different Capsicum species while allowing the identification of important candidate genes related to capsaicin content for subsequent functional validation.
Highlights
Pepper (Capsicum spp.) is a member of the Solanaceae family and is closely related to potato, tomato, eggplant, tobacco and petunia
The ATP-binding cassette (ABC) transporter gene superfamily has been widely studied among extant organisms including plants, the present study is the first to report the presence of 572 putative ABC transporter proteins in the entire pepper genome sequences of three different Capsicum species
Our results provide fundamental and exhaustive information about the pepper ABC transporters by performing a comprehensive genome-wide identification and expression patterns of these proteins family
Summary
Pepper (Capsicum spp.) is a member of the Solanaceae family and is closely related to potato, tomato, eggplant, tobacco and petunia. Pepper fruits have been widely used as a coloring agent, food flavoring, cosmetic and pharmaceutical ingredient, and as an ornamental product. It has nutrimental value by containing vitamins A, B, C, and E, as well as phytochemicals such as phenolic compounds, carotenoids, and capsaicin. Pepper genotypes exhibit a wide range of capsaicinoid accumulation as a result of both environmental and genetic variability. Nimmakayala et al [5] determined that the major markers linked to capsaicinoid synthesis are ankyrin-like protein, the IKI3 protein family and the ATP-binding cassette (ABC) transporter family, which suggests that their activity may be involved in the pungency modulations in pepper. Some ABC proteins act as regulators of ion channels, receptors and proteins involved in mRNA translation and ribosome biogenesis [9]
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