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Backgrounds: Pomegranate is an excellent tree species with nutritional, medicinal, ornamental and ecological values. Studies have confirmed that SPL factors play an important role in floral transition and flower development. Results: Used bioinformatics methods, 15 SPL (SQUAMOSA promoter-binding protein-like) genes were identified and analyzed from the 'Taishanhong' pomegranate (P. granatum L.) genome. Phylogenetic analysis showed that PgSPLs were divided into six subfamilies (G1 ~ G6). PgSPL promoter sequences contained multiple cis-acting elements associated with abiotic stress or hormonal response. Based on the transcriptome data, expression profiles of different tissues and different developmental stages showed that PgSPL genes had distinct temporal and spatial expression characteristics. The expression analysis of miR156 in small RNA sequencing results showed that miR156 negatively regulated the expression of target genes. qRT-PCR analysis showed that the expression levels of PgSPL2, PgSPL3, PgSPL6, PgSPL11 and PgSPL14 in leaves were significantly higher than those in buds and stems (p < 0.05). The expression levels of PgSPL5, PgSPL12 and PgSPL13 in flower buds were significantly higher than that in leaves and stems (p < 0.05). The full-length of coding sequence of PgSPL5 and PgSPL13 were obtained by homologous cloning technology. The full length of PgSPL5 is 1020 bp, and PgSPL13 is 489 bp, which encodes 339 and 162 amino acids, respectively. Further investigation revealed that PgSPL5 and PgSPL13 proteins were located in the nucleus. Exogenous plant growth regulator induction experiments showed that PgSPL5 was up-regulated in leaves and stems. PgSPL13 was up-regulated in leaves and down-regulated in stems. When sprayed with 6-BA, IBA and PP333 respectively, PgSPL5 and PgSPL13 were up-regulated most significantly at P2 (bud vertical diameter was 5.1 ~ 12.0 mm) stage of bisexual and functional male flowers. Conclusions: Our findings suggested that PgSPL2, PgSPL3, PgSPL6, PgSPL11 and PgSPL14 played roles in leaves development of pomegranate. PgSPL5, PgSPL12 and PgSPL13 played roles in pomegranate flower development. PgSPL5 and PgSPL13 were involved in the response process of different plant hormone signal transduction in pomegranate development. This study provided a robust basis for further functional analyses of SPL genes in pomegranate. [ABSTRACT FROM AUTHOR]

Backgrounds: Pomegranate (Punica granatum L.) is an important commercial fruit tree, with moderate tolerance to salinity. The balance of Cl− and other anions in pomegranate tissues are affected by salinity, however, the accumulation patterns of anions are poorly understood. The chloride channel (CLC) gene family is involved in conducting Cl−, NO3−, HCO3− and I−, but its characteristics have not been reported on pomegranate. Results: In this study, we identified seven PgCLC genes, consisting of four antiporters and three channels, based on the presence of the gating glutamate (E) and the proton glutamate (E). Phylogenetic analysis revealed that seven PgCLCs were divided into two clades, with clade I containing the typical conserved regions GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), whereas clade II not. Multiple sequence alignment revealed that PgCLC-B had a P [proline, Pro] residue in region I, which was suspected to be a NO3−/H+ exchanger, while PgCLC-C1, PgCLC-C2, PgCLC-D and PgCLC-G contained a S [serine, Ser] residue, with a high affinity to Cl−. We determined the content of Cl−, NO3−, H2PO4−, and SO42− in pomegranate tissues after 18 days of salt treatments (0, 100, 200 and 300 mM NaCl). Compared with control, the Cl− content increased sharply in pomegranate tissues. Salinity inhibited the uptake of NO3− and SO42−, but accelerated H2PO4− uptake. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of three antiporters PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves might be contributed to sequestrating Cl− into the vacuoles. However, the low expression levels of PgCLCs in roots might be associated with the exclusion of Cl− from root cells. Also, the up-regulated PgCLC-B in leaves indicated that more NO3− was transported into leaves to mitigate the nitrogen deficiency. Conclusions: Our findings suggested that the PgCLC genes played important roles in balancing of Cl− and NO3− in pomegranate tissues under salt stress. This study established a theoretical foundation for the further functional characterization of the CLC genes in pomegranate. [ABSTRACT FROM AUTHOR]

• Pomegranate flowers develop into two types on the same tree: bisexual flowers and functional male flowers. • The plant-specific YABBY transcription factors have important biological roles in plant morphogenesis, growth and development. • PgINO may play a critical role in regulating the differentiation of bisexual flowers during the development of pomegranate. The plant-specific YABBY transcription factors have important biological roles in plant morphogenesis, growth and development. In this study, we identified six YABBY genes in pomegranate (Punica granatum) and characterized their expression pattern during flower development. Six PgYABBY genes were divided into five subfamilies (YAB1/3, YAB2, INO, CRC, and YAB5), based on protein sequence, motifs and similarity of exon-intron structure. Next, analysis of putative cis -acting element showed that PgYABBY s contained lots of hormone response and stress response elements. Subsequently, gene function prediction and protein-protein network analysis showed that PgYABBYs were associated with the development of apical meristem, flower, carpel, and ovule. Analysis of PgYABBY genes expression in various structures and organs suggested that PgYABBYs were highly activated in flower, leaf and seed coat. Analysis of expression during flower development in pomegranate showed that PgINO might play critical role in regulating the differentiation of flowers. This study provided a theoretical basis for function research and utilization of YABBY genes in pomegranate. [ABSTRACT FROM AUTHOR]

MADS-box is a critical transcription factor regulating the development of floral organs and plays essential roles in the growth and development of floral transformation, flower meristem determination, the development of male and female gametophytes, and fruit development. In this study, 36 MIKC-type MADS-box genes were identified in the 'Taishanhong' pomegranate genome. By utilizing phylogenetic analysis, 36 genes were divided into 14 subfamilies. Bioinformatics methods were used to analyze the gene structure, conserved motifs, cis-acting elements, and the protein interaction networks of the MIKC-type MADS-box family members in pomegranate, and their expressions pattern in different tissues of pomegranate were analyzed. Tissue-specific expression analysis revealed that the E-class genes (PgMADS03, PgMADS21, and PgMADS27) were highly expressed in floral tissues, while PgMADS29 was not expressed in all tissues, indicating that the functions of the E-class genes were differentiated. PgMADS15 of the C/D-class was the key gene in the development network of pomegranate flower organs, suggesting that PgMADS15 might play an essential role in the peel and inner seed coat development of pomegranate. The results in this study will provide a reference for the classification, cloning, and functional research of pomegranate MADS-box genes. [ABSTRACT FROM AUTHOR]

4-Coumarate:CoA ligase (4CL, EC6.2.1.12), located at the end of the phenylpropanoid metabolic pathway, regulates the metabolic direction of phenylpropanoid derivatives and plays a pivotal role in the biosynthesis of flavonoids, lignin, and other secondary metabolites. In order to understand the molecular characteristics and potential biological functions of the 4CL gene family in the pomegranate, a bioinformatics analysis was carried out on the identified 4CLs. In this study, 12 Pg4CLs were identified in the pomegranate genome, which contained two conserved amino acid domains: AMP-binding domain Box I (SSGTTGLPKGV) and Box II (GEICIRG). During the identification, it was found that Pg4CL2 was missing Box II. The gene cloning and sequencing verified that this partial amino acid deletion was caused by genome sequencing and splicing errors, and the gene cloning results corrected the Pg4CL2 sequence information in the 'Taishanhong' genome. According to the phylogenetic tree, Pg4CLs were divided into three subfamilies, and each subfamily had 1, 1, and 10 members, respectively. Analysis of cis-acting elements found that all the upstream sequences of Pg4CLs contained at least one phytohormone response element. An RNA-seq and protein interaction network analysis suggested that Pg4CL5 was highly expressed in different tissues and may participate in lignin synthesis of pomegranate. The expression of Pg4CL in developing pomegranate fruits was analyzed by quantitative real-time PCR (qRT-PCR), and the expression level of Pg4CL2 demonstrated a decreasing trend, similar to the trend of flavonoid content, indicating Pg4CL2 may involve in flavonoid synthesis and pigment accumulation. Pg4CL3, Pg4CL7, Pg4CL8, and Pg4CL10 were almost not expressed or lowly expressed, the expression level of Pg4CL4 was higher in the later stage of fruit development, suggesting that Pg4CL4 played a crucial role in fruit ripening. The expression levels of 4CL genes were significantly different in various fruit development stages. The results laid the foundation for an in-depth analysis of pomegranate 4CL gene functions. [ABSTRACT FROM AUTHOR]

Many fruit trees have been whole-genome sequenced, and these genomic resources provide us with valuable resources of genes related to interesting fruit traits (e.g., fruit color, size and taste) and help to facilitate the breeding progress. Pomegranate (Punica granatum L.), one economically important fruit crop, has attracted much attention for its multiple colors, sweet and sour taste, soft seed and nutraceutical properties. In recent years, the phylogenesis of pomegranate has been revised which belongs to Lythraceae. So far, three published pomegranate genomes including 'Taishanhong', 'Tunisia' and 'Dabenzi' have been released on NCBI with open availability. This article analyzed and compared the assembly and annotation of three published pomegranate genomes. We also analyzed the evolution-development of anthocyanin biosynthesis and discussed pomegranate population genetics for soft seed breeding. These provided some references for horticultural crop breeding on the basis of genomic resources, especially pomegranate. [ABSTRACT FROM AUTHOR]

The three-amino-acid-loop-extension (TALE) gene family is a pivotal transcription factor that regulates the development of flower organs, flower meristem formation, organ morphogenesis and fruit development. A total of 17 genes of pomegranate TALE family were identified and analyzed in pomegranate via bioinformatics methods, which provided a theoretical basis for the functional research and utilization of pomegranate TALE family genes. The results showed that the PgTALE family genes were divided into eight subfamilies (KNOX-Ⅰ, KNOX-Ⅱ, KNOX-Ⅲ, BELL-Ⅰ, BELL-Ⅱ, BELL-Ⅲ, BELL-Ⅳ, and BELL-Ⅴ). All PgTALEs had a KNOX domain or a BELL domain, and their structures were conservative. The 1500 bp promoter sequence had multiple cis-elements in response to hormones (auxin, gibberellin) and abiotic stress, indicating that most of PgTALE were involved in the growth and development of pomegranates and stress. Function prediction and protein-protein network analysis showed that PgTALE may participate in regulating the development of apical meristems, flowers, carpels, and ovules. Analysis of gene expression patterns showed that the pomegranate TALE gene family had a particular tissue expression specificity. In conclusion, the knowledge of the TALE gene gained in pomegranate may be applied to other fruit as well. [ABSTRACT FROM AUTHOR]

Pomegranate (Punica granatum L.) is widely grown in arid and semi-arid soils, with constant soil salinization. To elucidate its molecular responses to salt stress on mRNA levels, we constructed 18 cDNA libraries of pomegranate roots and leaves from 0 (controls), 3, and 6 days after 200 mM NaCl treatment. In total, we obtained 34,047 genes by mapping to genome, and then identified 2255 DEGs (differentially expressed genes), including 1080 up-regulated and 1175 down-regulated genes. We found that the expression pattern of most DEGs were tissue-specific and time-specific. Among root DEGs, genes associated with cell wall organization and transmembrane transport were suppressed, and most of metabolism-related genes were over-represented. In leaves, 41.29% of DEGs were first suppressed and then recovered, including ions/metal ions binding-related genes. Also, ion transport and oxidation-reduction process were restricted. We found many DEGs involved in ABA, Ca2+-related and MAPK signal transduction pathways, such as ABA-receptors, Ca2+-sensors, MAPK cascades, TFs, and downstream functional genes coding for HSPs, LEAs, AQPs and PODs. Fifteen genes were selected to confirm the RNA-seq data using qRT-PCR. Our study not only illuminated pomegranate molecular responses to salinity, but also provided references for selecting salt-tolerant genes in pomegranate breeding processes. [ABSTRACT FROM AUTHOR]

Gene duplication is the major resource with which to generate new genes, which provide raw material for novel functions evolution. Thus, to elucidate the gene family evolution after duplication events is of vital importance. Anthocyanin O-methyltransferases (AOMTs) have been recognized as being capable of anthocyanin methylation, which increases anthocyanin diversity and stability and improves the protection of plants from environmental stress. Meanwhile, no detailed identification or genome-wide analysis of the AOMT gene family members in pomegranate (Punicagranatum) have been reported. Three published pomegranate genome sequences offer substantial resources with which to explore gene evolution based on the whole genome. Altogether, 58 identified OMTs from pomegranate and five other species were divided into the AOMT group and the OMT group, according to their phylogenetic tree and AOMTs derived from OMTs. AOMTs in the same subclade have a similar gene structure and protein conserved motifs. The PgAOMT family evolved and expanded primarily via whole-genome duplication (WGD) and tandem duplication. PgAOMTs expression pattern in peel and aril development by qRT-PCR verification indicated that PgAOMTs had tissue-specific patterns. The main fates of AOMTs were neo- or non-functionalization after duplication events. High expression genes of PgOMT04 and PgOMT09 were speculated to contribute to "Taishanhong" pomegranate's bright red peel color. Finally, we integrated the above analysis in order to infer the evolutionary scenario of AOMT family. [ABSTRACT FROM AUTHOR]

Most cultivated lands are suffering from soil salinization, which is a global problem affecting agricultural development and economy. High NaCl concentrations in the soil result in the accumulation of toxic Cl− and Na+ in plants. Na+/H+ antiporter (NHX) can regulate Na+ compartmentalization or efflux to reduce Na+ toxicity. This study aims to identify the NHX genes in pomegranate (Punica granatum L.) from the genome sequences and investigate their expression patterns under different concentrations of NaCl stress. In this study, we used the sequences of PgNHXs to analyze the physicochemical properties, phylogenetic evolution, conserved motifs, gene structures, cis-acting elements, protein tertiary structure and expression pattern. A total of 10 PgNHX genes were identified, and divided into three clades. Conserved motifs and gene structures showed that most of them had an amiloride-binding site (FFI/LY/FLLPPI), except for the members of clade III. There were multiple cis-acting elements involved in abiotic stress in PgNHX genes. Additionally, protein-protein interaction network analysis suggested that PgNHXs might play crucial roles in keeping a balance of Na+ in cells. The qRT-PCR analysis suggested that PgNHXs had tissue-specific expressional patterns under salt stress. Overall, our findings indicated that the PgNHXs could play significant roles in response to salt stress. The theoretical foundation was established in the present study for the further functional characterization of the NHX gene family in pomegranate. [ABSTRACT FROM AUTHOR]