Genome-wide identification of microRNAs in pomegranate (Punica granatum L.) by high-throughput sequencing
© The Author(s). 2016
Received: 16 December 2015
Accepted: 17 May 2016
Published: 26 May 2016
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, 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.
Our 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.
Pomegranate (Punica granatum L.), one of the two species within the genus Punica, producing a non-climacteric fruit with a low respiration rate , is a tropical and subtropical attractive deciduous shrub. 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, although it is native to Iran [2–4]. Although pomegranate is widely cultivated, the five major producers are India, Iran, China, the United States and Turkey .
The plant is tolerant of various soil conditions and grows well under sunlight and mild winters . The fruit is a round or spherical in shape, with a fleshy, tubular calyx and leathery skin often deep pink or rich red in color . 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].
In recent years, pomegranate has become popular for its medicinal properties and its nutritional benefit in the human diet. Pomegranate is a nutrient-dense food source rich in phytochemical compounds. It contains high levels of flavonoids and polyphenols, potent antioxidants offering protection against heart disease and cancer. Because of the health-promoting traits from both the edible and nonedible parts of the fruit in treating a wide range of human diseases such as cancer, diabetes, obesity, Alzheimer disease, and hypertension, pomegranate is considered an important commercial and valuable fruit crop across the world [8, 9]. Metabolome analysis revealed that parts of pomegranate including the fruit peel, juice, root and bark, flowers, leaves and seed contain almost 40 biochemical compounds that are beneficial in different therapies . The compounds include gallotannins, ellagic acid, flavonoids, antioxidants, terpenoids and alkaloids [11–13].
The color of the pomegranate fruit including arils develops from the presence of anthocyanins, water-soluble flavonoid pigments, mostly orange to red and purple/blue . In addition to playing significant roles in plant defense mechanisms , anthocyanins are considered valuable to human health because of high antioxidant activity , and fruit arils, the edible part of pomegranate, contain the highest quantity of anthocyanins . The biochemical pathway of anthocyanin production has been well documented in numerous plant species, with the involvement of chalcone synthase, chalcone isomerase, and leucoanthocyanidin .
In Arabidopsis, the anthocyanin pathway is regulated at the transcription level by transcriptional regulators such as the R2R3-MYB domain, WD40 repeat, and a basic helix-loop-helix (bHLH) [19–21]. The WD40-repeat gene is a functional homologue of Arabidopsis TTG1 and is involved in regulating anthocyanin biosynthesis during pomegranate fruit development . Recently, anthocyanin biosynthetic genes in red and white pomegranate were cloned and characterized  and the expression of key regulatory genes of anthocyanin biosynthesis in pomegranate was analyzed .
Plants have two major classes of small regulatory non-coding RNAs. They are small interfering RNAs (siRNAs) and microRNAs (miRNAs), both generated from double-stranded RNA precursors into 20- to 24-nt molecules with the help of Dicers or Dicer-like (DCL) . Many basic aspects of plant development and stresses are controlled by miRNA families . Most of the miRNAs are coded by genes spanning 100–400 nt and further processed by the RNA-induced silencing complex containing Argonaute (AGO) proteins. At the end of processing, depending on the presence of the type of AGO effector protein, the targets can be degraded at the mRNA level or inhibited at the translation level . Bioinformatics analyses revealed at least 21 conserved miRNA families, including miR156, miR159, and miR160, in angiosperms. Plants contain more non-conserved than conserved miRNAs , and high-throughput sequencing led to the discovery of non-conserved miRNAs from divergent plant species such as cucurbits, grape, barley and apple [29–34]. miRNAs play key roles in different crops for development and stress response, regulation of anthocyanin accumulation in tomato , mediation of nitrogen starvation adaptation in Arabidopsis thaliana , and elongation of fiber in cotton .
Although pomegranate is an important fruit crop with many medicinal properties, the information on miRNAs in pomegranate is lacking. In this study, we report the profiling of miRNAs from seedling to fruit with use of Illumina HiSeq 2000 RNA sequencing and expression analysis of specific miRNAs in leaves, flowers and during fruit development. miR157 was the most abundant miRNA, followed by miR156, miR166, and others. Among different small RNAs (sRNAs), those of 24 nt were most abundant. We found 28 novel miRNAs along with predicted precursor structures and participating pathways. The results from this study could provide valuable information to further reveal the regulatory roles in pomegranate.
Collection of arils from mature fruits to grow seedlings
Arils of physiologically mature ‘Al-sirin-nar’ fruits were removed by gently opening the fruits and extracting the arils with the help of air and water. The extracted pomegranate arils were immersed in a bath of cold water, and all other elements of the fruit were washed away. All extracted arils were separated from all other fruit parts, leaving them pristine, whole, and untouched, and then were washed and air-dried. The arils were sown in peat moss pads to grow young seedlings.
Total RNA from 10-day-old seedlings was extracted as described  by using TRIzol reagent (Invitrogen, Carlsbad, CA) and the RNA MiniPrep kit (Zymo Research, Irvine, CA). Total RNA from leaves, flowers and fruits of different developmental stages was extracted using a modified CTAB-LiCl method . For fruit samples, we used only separated arils for all developmental stages. About 200 mg of finely ground sample in liquid nitrogen for each tissue was used for extraction. Extraction buffer I, II and other solutions were prepared as suggested . The chloroform: isoamyl alcohol (24:1) and LiCl steps were repeated three times. Finally, the RNA pellet was dissolved in 40 μL RNase-free water. All RNA samples were purified with use of the RNA Clean & Concentrator kit with on-column digestion of genomic DNA by using DNase I (Zymo Research, Irvine, CA). RNA integrity number > 8.0 was confirmed by use of the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). For global miRNA transcriptome profiling, an equimolar concentration of total RNA extracted from three biological replications of all samples was pooled and sent for RNA sequencing. Total RNA from all three biological replications was independently used in stem-loop RT-qPCR.
Small RNA sequencing
sRNA samples were sequenced by the Beijing Genomics Institute (BGI, Hong Kong) with the Illumina HiSeq 2000 platform. The construction of the sRNA library and sequencing consisted of the following steps . After extracting the total RNA from the samples, sRNAs of 18 ~ 30 nt were gel-purified, 5’ RNA adapter-ligated and gel-purified, 3’ RNA adapter-ligated and gel-purified, then underwent RT-PCR and gel purification. Finally, the library products were ready for sequencing by using Illumina HiSeq 2000.
sRNAs from deep sequencing covered almost every kind of RNA, including miRNAs, siRNAs, piwi-interacting RNAs (piRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), repeat-associated sRNAs and degraded tags of exons or introns. The sRNA digitization analysis based on high-throughput sequencing involved use of sequencing by synthesis (SBS), which can decrease the loss of nucleotides caused by the secondary structure. This HiSeq method is robust and also strong because of its requirement for small sample quantity, high throughput, and high accuracy with a simply operated automatic platform. Such analysis resulted in millions of sRNA sequence tags from the pomegranate RNA sample.
RNA-seq bioinformatics analysis and miRNA prediction
After sequencing, raw sequence reads (FASTQ files) were processed into clean reads, then filtered to discard low-quality adapter contaminative tags, and the remaining reads with lengths < 18 nt were discarded. Usually, the sRNA is 18 to 30 nt (miRNA, 21 or 22 nt; siRNA, 24 nt; and piRNA, 30 nt). All unique clean reads, specifically non-redundant ones, were considered for further analysis, including non-coding RNA identification and proper annotation. First, clean reads of sRNAs such as rRNAs, small cytoplasmic RNAs (scRNAs), snoRNAs, snRNAs, and tRNAs were identified by a BLASTall search against the Rfam (v10.1) and GenBank databases. miRNAs were identified by mapping sRNA reads against poplar genome sequences by using SOAP2 . The SOAP2 output was filtered with use of in-house filter tool to identify the candidate sequences as miRNA precursors by analyzing a mapping pattern of one or more blocks of aligned small RNAs with perfect matches . The secondary structures of candidate sequences were checked by applying stringent criteria as suggested . To determine conserved miRNAs, clean reads were compared with known plant miRNAs deposited at miRBase . Those with non-perfect matches were considered variants of known miRNAs. Other sequences that did not map to known miRNAs and other kinds of sRNAs were considered un-annotated sequences for novel miRNA prediction. To obtain the miRNA predicted precursor structure, the sequences were analyzed by using TurboFold  http://rna.urmc.rochester.edu/RNAstructure.html) and guide and star sequences were obtained.
Target prediction, functional annotation and pathway analysis
The target prediction method involved loading miRNA reads in a FASTA format file containing sRNA sequences to search for targets from a known poplar (Populus trichocarpa) transcript database by using the suggested rules [46, 47]. Specifically, criteria for choosing miRNA/target duplexes were 1) less than four mismatches between sRNA and the target, 2) less than two adjacent mismatches in the miRNA/target duplex, 3) no adjacent mismatches in positions 2–12 of the miRNA/target duplex (5’ of miRNA), 4) no mismatches in positions 10–11 of the miRNA/target duplex, 5) less than 2.5 mismatches in positions 1–12 of the miRNA/target duplex (5’ of miRNA), and 6) minimum free energy (MFE) of the miRNA/target duplex ≥74 % of the MFE of the miRNA bound to its perfect complement. To investigate the putative functions of potential target genes, the target sequences from poplar were annotated by using the databases Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) [48, 49]. The GO results were classified into three independent groups: cellular component, molecular function, and biological process. KO pathways were grouped into different metabolism functions and signal transduction.
Validation of miRNA variants and novel miRNAs by stem-loop RT-qPCR
Stem-loop RT-qPCR was used to confirm the differential expression of miRNAs and their variants across leaves, flowers, and fruit developmental stages. About 1 μg DNA-free total RNA was hybridized with miRNA-specific stem-loop RT primers for six miRNA families and six novel miRNAs, and the hybridized molecules were reverse-transcribed into cDNAs with use of the Superscript III kit (Thermo Fisher Scientific, Waltham, MA USA). The forward miRNA-specific primer for the mature miRNA sequences and the universal reverse primer for the stem-loop sequences were designed (Additional file 1: Table S8). For each reaction, 1 μL cDNA, 10 μL 2X FastStart SYBR Green (Roche), and primers were mixed. PCR runs were 95 °C for 10s, 60 °C for 30s with the StepOnePlus Real-Time PCR System (Applied Biosystems, Foster City, CA, USA). The expression of miRNAs was normalized to that in leaves in all three biological replications. 5.8S ribosomal RNA was used as reference to calculate relative gene expression by the 2-ΔΔCt method .
Results and discussion
Pomegranate fruit contains a variety of natural compounds such as phenolics, alkaloids, terpenoids, and fatty acids and has a role in numerous health-promoting activities . Both fruit peels and arils are used to extract natural compounds such as punicalagin (derivative of gallic acid and glucose) and anthocyanins (class of water-soluble phenolic compounds responsible for the pink to red fruit) . 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. In this study, we profiled the conserved and novel miRNAs in pomegranate and discuss their different biochemical pathways.
Fruit development and collection of tissues
Pomegranate fruit development is divided into different stages. The fruit growth pattern depends on the cultivar as well as location and season [53, 54]. We divided the developmental stages of Al-sirin-nar as follows (Fig. 1): stage 1, approximately 8–10 days from initial flowering (petal drop stage); stage 2, approximately 10 days from stage 1 (fruit has begun to expand, but no color change); stage 3, approximately 12–15 days later (fruit has swelled more and is just starting to change from red to green); stage 4, approximately 15–18 days later (fruit has expanded from pear shape to more rounded shape, more green from red); stage 5, approximately 15 days later (continued expansion of fruit, color continues to change from red to green); and stage 6, approximately 15 days later (continued expansion of fruit, color continues to change from red to green), the calyx remains red, referred to as the “lipstick” stage. The process takes 75 to 85 days from initial flowering to stage 6. After stage 6, the fruit becomes glossy red and contains rosy-pink arils with a sweet tart taste. To profile the overall miRNA expression, we collected leaves, male and female flowers and fruit tissues from different stages. Throughout the fruit developmental stages, the color development of the peel (fading of dark red) and arils inside the fruit (accumulation of dark red) is the reverse. So, the anthocyanin is increasingly accumulating in arils during the later stages of fruit development.
During fruit development, pomegranate accumulates a variety of phytochemical compounds  that function as a defense mechanism. The edible part is 50 % of the fruit: 40 % and 10 % are arils and seeds, respectively. Arils contain mostly water (85 %), 10 % sugar (glucose and fructose), organic acids (citric acid, ascorbic acid, malic acid), and the bioactive compounds anthocyanins (phenolics and flavonoids) . In addition, the seed cover contains six types of glucosides, with delphinidin-3,5-diglucoside the main anthocyanin in juice . Pigmentation of fruit peel and arils is an important quality indicator of fruit. Al-sirin-nar fruit peel is rosy-red as compared with dark red for ‘Wonderful’, and the color of peel and arils is not related .
High-throughput sequencing and annotation of small RNAs
Overview of miRNA sequencing reads
Identification of conserved miRNAs in pomegranate
Details of conserved miRNA families in pomegranate
Because of their high sequence similarity and conserved targets, miR156 and miR157 were grouped into a single family. Cleavage of the Squamosa promoter binding protein-like (SPL) by miR156/157 has been confirmed in different crops including Arabidopsis  and rice [64, 65]. In our studies, miR157 was the largest miRNA family among all families. This finding contrasts with recent reports of pear fruit development  and peanut , showing miR156 as the most abundant. MiR157 may have unique targets and common targets between miR156/miR157. In addition to families, variants of each family showed differential expression. The number of miRNAs was counted and normalized to total reads of sRNAs. The total counts for each family variant varied greatly. The expression of miRNA families of miR157a, miR156, miR157b, miR156a, miR156g, miR159a and miR160b was high in our pooled pomegranate sample. In contrast, a few other families and variants showed less expression (Additional file 3: Table S2). The abundance of each family also varied. When the miRNAs were predicted from miRBase, different family members exactly matched known miRNAs from different plants such as Arabidopsis, rice, grapes, poplar tree, maize, and soybean.
Novel miRNAs and their identification in pomegranate
Predicted novel miRNAs in pomegranate
Validation of high-throughput RNA-sequencing in different tissues
Prediction of miRNA target genes, gene ontology (GO) and KEGG pathway analysis
Most of the targets of miRNA are conserved across several plants including Arabidopsis, rice, poplar, and wheat [73–76]. Majority of them are various transcription factors including SQUAMOSA promoter binding protein-like (SPB/SPL) (miR156), NAM (miR164), MYB (miR159, miR172, miR319) that regulate plant development and phytohormone signaling . SPL is one of the miR156 targets in Arabidopsis , with expression inversely related to that of miR156. SPL, which shows abundant expression in the absence of miR156 expression in early stages of fruit development, may destabilize the MYB-bHLH-WD40 complex to repress the anthocyanin biosynthetic pathway and further accumulation . Keeping this hypothesis in mind, with increased SPL expression being a negative regulator of anthocyanin accumulation, the anthocyanin content in pomegranate might be still under the detectable level with increased flavonol quantity in early aril developmental stages. However, SPL expression may be decreased during later stages of maturity to accumulate anthocyanin with increased PgmiR156 expression. Although this conclusion is premature without quantifying SPL accumulation in different fruit stages, the increased expression of PgmiR156/PgmiR157 we observed might have a positive effect on increasing anthocyanin and proanthocynidin or tannin levels in mature pomegranate.
To better understand the functions of identified novel miRNAs in pomegranate, we predicted putative candidate genes by using bioinformatic analyses [79, 80]. A total of 288 target genes were identified for ten novel miRNAs and gene ontology with annotation details have been found (Additional file 7: Table S6). Consistent with previous reports, most of the novel miRNA targets belong to plant-specific transcription factors, (AP2, MYB, ARF, GRAS, PHD, and bZIP), followed by regulators of metabolic processes (protein kinases, LRR kinase, RLKs, etc.) and hormone signaling. In addition, there are several other targets whose functions are largely unknown. The targets of PgmiR08 ARFs, bHLH, SecY protein, TIR1 F-box, and auxin signaling F-box2 (AFB2) are shown to be involved in root and fruit development, anthocyanin accumulation as well as in abiotic stress. In contrast to climacteric fruits (apple, banana, tomato), notably little is known about the hormonal control of ripening in non-climacteric fruits such as pomegranate, grape, and strawberry  and it has been proven that even ethylene levels or respiration was considerably low during ripening of non-climacteric fruit . That could be one possibility that we did not find any major ethylene pathway candidates in our target identification. Anthocyanin biosynthesis is a branch of the flavonoid pathway and genes involved in anthocyanin biosynthesis and regulation have been discovered and studied in several fruits, such as bHLH in apple , and MYB and bHLH in peach . To support this notion, ARF10 plays key role in anthocyanin biosynthesis of pomegrante. The GO (Additional file 7: Table S6) shows that MYB transcription factor, the target of PgmiR14, PgmiR22 and PgmiR31 is involved in multiple hormone signaling including gibberellic acid, ethylene and salicylic acid during fruit development and ripening .
In addition, GRAS transcription factor (PgmiR25), and nuclear transcription factor Y (PgmiR22), copper transporter (PgmiR09), disease resistance protein TIR-NBS-LRR, and LRR protein kinase (PgmiR31) are the targets of few novel miRNAs. Recently, genes coding for GRAS transcription factors were identified as targets of miRNAs during fruit development and ripening of tomato  and grapevine . Moreover, F-box family proteins play vital roles in the signal transduction pathways of different hormones  and 166 F-box genes were identified during maturation and fruit ripening in apple . Group of F-box genes targeted by PgmiR08 and PgmiR20 might participate mostly in auxin signaling pathway towards fruit ripening. During fruit development, synthesized sucrose in the leaf is transported to sink tissues such as fruits where it is directly used for metabolism or translocated into storage tissues for the synthesis of major storage products through carbohydrate metabolism . Mutants of sucrose transporters (SUT) exclusively affected tomato fruit and seed development . SUT2, the target of PgmiR31 and the key player in sucrose:hydrogen symporter activity, might be a key player in normal fruit development. The seed development is part of fruit maturity and ripening, and the development of both occurs simultaneously. In pomegranate, seeds which are inside the arils are surrounded by juice. A nuclear transcription factor Y subunit A-1 (NF-YA1) targeted by novel miRNAs PgmiR22 and PgmiR23, and a bZIP transcription factor targeted by PgmiR31 seem to involve in seed maturation and dormancy in the arils of pomegranate fruits.
Above all, tissue integrity and cation binding to the cell wall during fruit senescence is very important, and pectin methylesterase (PME) activity modifies tissue integrity in ripening tomato . As an ubiquitous plant enzyme, PME catalyzes the deesterification of galactosyluronate methyl esters of pectin to their free carboxylic groups, and has been suggested to cause transesterification to uronoyl-sugar crosslinks . PME has been implicated in various processes in ripening fruits including textural changes, formation of abscission zones and cell wall growth, maturation, and extensibility. Alongside, invertases may involve in the long-distance transport of sucrose and take part in phloem loading and unloading . From our transcriptome and GO analysis, we believe that plant invertase/pectin methylesterase inhibitor could be targeted by PgmiR31 to aid in fruit ripening process. Overall, the known and unknown targets of novel microRNAs participate in pomegranate fruit development and further ripening process.
We used small RNA-sequencing of pomegranate with Illumina Hiseq2000 sequencing and identified 10 novel miRNAs. We reveal the differential expression of a few predominately expressed miRNAs and their variants in different developmental stages of fruit. This is the first report to investigate sRNAs in pomegranate, with a large number found as known and novel miRNAs. By searching the poplar genome, 288 putative target genes were predicted for the 10 novel miRNAs and then annotated by using GO and KEGG databases to explore their putative functions in different metabolic pathways. We revealed several fruit development pathways including sugar and acid, and plant hormone signaling. This identification of novel miRNAs in pomegranate will be valuable for further understanding the functions and regulatory mechanisms of miRNAs in other related plant species.
This project was supported by the USDA-NIFA grant (Proposal no. 2013-04023) and additionally supported by the Indian Council of Agricultural Research (ICAR). The authors thank the National Agricultural Innovation Project, ICAR, for sponsoring visits of Nripendra V. Singh and Ramajayam Devarajan. We are also grateful to Guru Jagadeeswaran for his suggestions to improve the quality of the manuscript significantly.
Availability of data and materials
The sequencing data for the small RNA library and other analyzed datasets are available under NCBI-GEO accession number GSE78498. All the supporting data are included as additional files.
TS, PN and UR designed the study and drafted the manuscript. TS, AB and NVS extracted and cleaned total RNA using different methods. NVS and RD extracted arils from mature fruit. ST analyzed and interpreted the RNA-seq data. ST and AB performed RT-qPCR experiments. MJ and MA maintained the materials and collected tissues at various stages. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Consent to publish
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