Abstract
BackgroundMicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression post-transcriptionally, play multiple key roles in plant growth and development and in biotic and abiotic stress response. Knowledge and roles of miRNAs in pomegranate fruit development have not been explored.ResultsPomegranate, which accumulates a large amount of anthocyanins in skin and arils, is valuable to human health, mainly because of its antioxidant properties. In this study, we developed a small RNA library from pooled RNA samples from young seedlings to mature fruits and identified both conserved and pomegranate-specific miRNA from 29,948,480 high-quality reads. For the pool of 15- to 30-nt small RNAs, ~50 % were 24 nt. The miR157 family was the most abundant, followed by miR156, miR166, and miR168, with variants within each family. The base bias at the first position from the 5’ end had a strong preference for U for most 18- to 26-nt sRNAs but a preference for A for 18-nt sRNAs. In addition, for all 24-nt sRNAs, the nucleotide U was preferred (97 %) in the first position. Stem-loop RT-qPCR was used to validate the expression of the predominant miRNAs and novel miRNAs in leaves, male and female flowers, and multiple fruit developmental stages; miR156, miR156a, miR159a, miR159b, and miR319b were upregulated during the later stages of fruit development. Higher expression of miR156 in later fruit developmental may positively regulate anthocyanin biosynthesis by reducing SPL transcription factor. Novel miRNAs showed variation in expression among different tissues. These novel miRNAs targeted different transcription factors and hormone related regulators. Gene ontology and KEGG pathway analyses revealed predominant metabolic processes and catalytic activities, important for fruit development. In addition, KEGG pathway analyses revealed the involvement of miRNAs in ascorbate and linolenic acid, starch and sucrose metabolism; RNA transport; plant hormone signaling pathways; and circadian clock.ConclusionOur first and preliminary report of miRNAs will provide information on the synthesis of biochemical compounds of pomegranate for future research. The functions of the targets of the novel miRNAs need further investigation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0807-3) contains supplementary material, which is available to authorized users.
Highlights
MicroRNAs, a class of small non-coding endogenous RNAs that regulate gene expression post-transcriptionally, play multiple key roles in plant growth and development and in biotic and abiotic stress response
Many reports describe the benefits of pomegranate natural products for humans, but lack of genomic information is a major bottleneck in genomic research of pomegranate
We divided the developmental stages of Al-sirin-nar as follows (Fig. 1): stage 1, approximately 8–10 days from initial flowering; stage 2, approximately 10 days from stage 1; stage 3, approximately 12–15 days later; stage 4, approximately 15–18 days later; stage 5, approximately 15 days later; and stage 6, approximately 15 days later, the calyx remains red, referred to as the “lipstick” stage
Summary
MicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression post-transcriptionally, play multiple key roles in plant growth and development and in biotic and abiotic stress response. Knowledge and roles of miRNAs in pomegranate fruit development have not been explored. Pomegranate was previously placed within its own family Punicaceae, but recent phylogenetic studies have shown that it belongs to Lythraceae. It is one of the oldest edible fruits and has grown naturally from Iran to the Himalayas in northern India since ancient times, it is native to Iran [2,3,4]. The inside of the fruit is separated by membranous walls into compartments packed with sac-like structures filled with fleshy juicy, red, pink or whitish pulp called arils, and each aril sac contains one white or red, angular, soft or hard seed [6, 7]
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