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The response of plants to abiotic stress is intricately mediated by PYR/PYL/RCARs, key components within the ABA signal transduction pathway. Despite the widespread identification of PYL genes across diverse plant species, the evolutionary history and structural characteristics of these genes within the pomegranate (Punica granatum L.) remained unexplored. In this study, we uncovered, for the first time, 12 PgPYLs from the whole genome dataset of 'Tunisia', mapping them onto five chromosomes and categorizing them into three distinct subgroups (Group I, Group II, and Group III) through phylogenetic analysis. Detailed examination of the composition of these genes revealed similar conserved motifs and exon–intron structures among genes within the same subgroup. Fragment duplication emerged as the primary mechanism driving the amplification of the PYL gene family, as evidenced by intra-species collinearity analysis. Furthermore, inter-species collinearity analysis provided insights into potential evolutionary relationships among the identified PgPYL genes. Cis-acting element analysis revealed a rich repertoire of stress and hormone response elements within the promoter region of PgPYLs, emphasizing their putative roles in diverse signaling pathways. Upon treatment with 100 μmol/L ABA, we investigated the expression patterns of the PgPYL gene family, and the qRT-PCR data indicated a significant up-regulation in the majority of PYL genes. This suggested an active involvement of PgPYL genes in the plant's response to exogenous ABA. Among them, PgPYL1 was chosen as a candidate gene to explore the function of the gene family, and the CDS sequence of PgPYL1 was cloned from pomegranate leaves with a full length of 657 bp, encoding 218 amino acids. Tobacco transient expression analysis demonstrated a consistent trend in the expression levels of pBI121-PgPYL1 and the related genes of the ABA signaling pathway, both of which increased initially before declining. This study not only contributes to the elucidation of the genomic and structural attributes of PgPYL genes but also provides a foundation for understanding their potential functions in stress responses. The identified conserved motifs, evolutionary relationships, and expression patterns under ABA treatment pave the way for further research into the PgPYL gene family's role in pomegranate biology, offering valuable insights for future studies on genetic improvement and stress resilience in pomegranate cultivation. [ABSTRACT FROM AUTHOR]

Petaloidy leads to a plump floral pattern and increases the landscape value of ornamental pomegranates; however, research on the mechanism of petaloidy in ornamental pomegranates is limited. In this study, we aimed to screen candidate genes related to petaloidy. We performed transcriptomic and proteomic sequencing of the stamens and petals of single-petal and double-petal flowers of ornamental pomegranates. Briefly, 24,567 genes and 5865 proteins were identified, of which 5721 genes were quantified at both transcriptional and translational levels. In the petal and stamen comparison groups, the association between differentially abundant proteins (DAPs) and differentially expressed genes (DEGs) was higher than that between all genes and all proteins, indicating that petaloidy impacts the correlation between genes and proteins. The enrichment results of transcriptome, proteome, and correlation analyses showed that cell wall metabolism, jasmonic acid signal transduction, redox balance, and transmembrane transport affected petaloidy. Nine hormone-related DEGs/DAPs were selected, among which ARF, ILR1, LAX2, and JAR1 may promote petal doubling. Sixteen transcription factor DEGs/DAPs were selected, among which EREBP, LOB, MEF2, MYB, C3H, and trihelix may promote petal doubling. Our results provide transcriptomic and proteomic data on the formation mechanism of petaloidy and a theoretical basis for breeding new ornamental pomegranate varieties. [ABSTRACT FROM AUTHOR]

Expansins, which are important components of plant cell walls, act as loosening factors to directly induce turgor-driven cell wall expansion, regulate the growth and development of roots, leaves, fruits, and other plant organs, and function essentially under environmental stresses. In multiple species, many expansin genes (EXPs) have been cloned and functionally validated but little is known in pomegranate. In this study, a total of 33 PgEXPs were screened from the whole genome data of 'Taishanhong' pomegranate, belonging to the EXPA(25), EXPB(5), EXLA(1), and EXLB(2) subfamilies. Subsequently, the composition and characteristics were analyzed. Members of the same branch shared similar motif compositions and gene structures, implying they had similar biological functions. According to cis-acting element analysis, PgEXPs contained many light and hormone response elements in promoter regions. Analysis of RNA-seq data and protein interaction network indicated that PgEXP26 had relatively higher transcription levels in all pomegranate tissues and might be involved in pectin lyase protein synthesis, whilst PgEXP5 and PgEXP31 might be involved in the production of enzymes associated with cell wall formation. Quantitative real-time PCR (qRT-PCR) results revealed that PgEXP expression levels in fruit peels varied considerably across fruit developmental phases. PgEXP23 was expressed highly in the later stages of fruit development, suggesting that PgEXP23 was essential in fruit ripening. On the other hand, the PgEXP28 expression level was minimal or non-detected. Our work laid a foundation for further investigation into pomegranate expansin gene functions. [ABSTRACT FROM AUTHOR]

The double-petal varieties of ornamental pomegranate have higher ornamental value and garden development potential than the single-petal varieties but there has been no study on the genomic variation between them. This study aimed to determine the genomic variation between the two kinds of varieties and the relationship between the variation and phenotype by identifying the DNA variation of three single-petal varieties and three double-petal varieties using re-sequencing technology. The results showed that the variation number of each variety was in the order of single nucleotide polymorphisms (SNPs) > insertions and deletions (InDels) > structural variations (SVs) > copy number variations (CNVs). The number of SNPs and InDels in the double-petal varieties was significantly higher than that in the single-petal varieties, and there was no significant difference in the number of SVs and CNVs. The number of non-synonymous SNPs in the coding region (Nonsyn_CDS_SNPs) and InDels with a 3X length in the coding region (3X_shiftMutation_CDS_InDel) was significantly higher in the double-petal varieties than that in the single-petal varieties. The number of the two variants was strongly positively correlated with each morphological index that was related to the phenotypic difference between the two varieties. Nonsyn_CDS_SNPs and 3X_shiftMutation_CDS_InDel were enriched in the cell membrane system, cell periphery, and signal transduction, from which 15 candidate genes were screened. Our results provide genomic data for the study of the formation mechanism of the double-petal flower and lay a theoretical foundation for new variety breeding of ornamental pomegranate. [ABSTRACT FROM AUTHOR]

The ubiquitination pathway is essential for several developmental phases in plants, and the U-box protein family of ubiquitin ligases plays an important role in this process. However, little is known about pomegranate's PUB genes. In this investigation, the pomegranate U-box gene family was identified using whole-genome sequencing data. We identified a total of 56 members of the pomegranate U-box family based on the U-box domain, and the PgPUBs were classified into four groups. Chromosomal localization, phylogenetic analysis, motif distribution, gene duplications, cis-acting elements, and expression profiling were also investigated. The PgPUB genes were unevenly distributed among the eight pomegranate chromosomes, and collinear duplicated genes were identified between the Arabidopsis thaliana genome and the Punica granatum genome. Furthermore, the gene expression analysis revealed that expression of U-box genes in pomegranate was induced by abiotic stressors. Collectively, our findings provide insight into the U-box gene family and will assist in understanding the functional divergence of U-box genes in Punica granatum L. [ABSTRACT FROM AUTHOR]

Pomegranates (Punica granatum L.) are one of the most fashionable fruits and can be cultivated in both tropical and subtropical regions of the world. It is a shiny and attractive pome due to its cultivation. It belongs to the Lythraceae family. In this study, we analyzed the chloroplast genome of wild pomegranate based on whole genome shotgun sequences. In wild pomegranate, we found 158,645 bp in size, 132 genes containing 84 protein genes, 37 tRNA genes, 8 rRNA genes, and 36.92% of GC content, one infA and two duplicated ycf15 pseudogenes. Moreover, 21 chloroplast genes contained intros that are detected in a large single copy (LSC), small single copy (SSC), and two inverted repeats (IRA and IRB) regions, 17 of which were involved in single introns, while four genes (ycf3, rps12, clpP and rsp12) located in LSC, IRA, and IRB region. In total, 26,272 codons are found in protein-coding genes (PCGs); relative synonymous codon usage (RSCU) analysis revealed that the most abundant amino acid is leucine containing 2773 codons (10.55%), less abundant is methionine amino acid containing 1 codon (0.0032) in the PCGs. Furthermore, a total of 233 cpSSRs were identified in the wild pomegranate cp genome, and their distribution was analyzed in three regions, namely IR, LSC, and SSC. However, 155 cpSSR were found in the LSC (66.5%), followed by 40 cpSSR in the SSC (17.2%) and 38 cpSSR in the IR (16.3%) regions. Phylogenetic validation revealed that wild pomegranate is close to the pemphis acidula species. We believe that the cp genome allocates significant information promising for breeding research of wild pomegranate to Lythraceae. [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]

Based on the genome and small-RNA sequencing of pomegranate, miRNA167 and three target genes PgARF6 were identified in "Taishanhong" genome. Three PgARF6 genes and their corresponding protein sequences, expression patterns in pomegranate flower development and under exogenous hormones treatments were systematically analyzed in this paper. We found that PgARF6s are nuclear proteins with conserved structures. However, PgARF6s had different protein structures and expression profiles in pomegranate flower development. At the critical stages of pomegranate ovule sterility (8.1–14.0 mm), the expression levels of PgARF6s in bisexual flowers were lower than those in functional male flowers. Interestingly, PgARF6c expression level was significantly higher than PgARF6a and PgARF6b. Under the treatment of exogenous IBA and 6-BA, PgARF6s were down-regulated, and the expression of PgARF6c was significantly inhibited. PgmiR167a and PgmiR167d had the binding site on PgARF6 genes sequences, and PgARF6a has the directly targeted regulatory relationship with PgmiR167a in pomegranate. At the critical stage of ovule development (8.1–12.0 mm), exogenous IBA and 6-BA promoted the content of GA and ZR accumulation, inhibited BR accumulation. There was a strong correlation between the expression of PgARF6a and PgARF6b. Under exogenous hormone treatment, the content of ZR, BR, GA, and ABA were negatively correlated with the expressions of PgARF6 genes. However, JA was positively correlated with PgARF6a and PgARF6c under IBA treatment. Thus, our results provide new evidence for PgARF6 genes involving in ovule sterility in pomegranate flowers. [ABSTRACT FROM AUTHOR]

The cultivated apple (Malus domestica Borkh.) is one of the most important crop fruits with high-economic values in the world. In the present study, we characterized the complete chloroplast (cp) genome sequence of apple cultivar 'Yantai Fuji 8'. The complete cp genome is 160,062 bp in length with a typical quadripartite structure. A total of 112 unique genes were found in the newly sequenced genome, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. Of these, 7 protein-coding genes, 7 tRNA genes, and all 4 rRNA genes are duplicated in the inverted regions. A maximum likelihood phylogenetic tree was reconstructed using the full length of cp genome to show the relationships among species in Rosaceae. The complete cp genome will be potential genetic resources for apple breeding programs. [ABSTRACT FROM AUTHOR]

Summary: Pomegranate (Punica granatum L.) has an ancient cultivation history and has become an emerging profitable fruit crop due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin‐based compounds in its peel and aril. However, the limited genomic resources have restricted further elucidation of genetics and evolution of these interesting traits. Here, we report a 274‐Mb high‐quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336‐Mb genome, consists of 2177 scaffolds with an N50 size of 1.7 Mb and contains 30 903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate and Eucalyptus grandis share the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin‐based compounds, the colour formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence provides an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding. [ABSTRACT FROM AUTHOR]

Members of the sugars will eventually be exported transporter (SWEET) family regulate the transport of different sugars through the cell membrane and control the distribution of sugars inside and outside the cell. The SWEET gene family also plays important roles in plant growth and development and physiological processes. So far, there are no reports on the SWEET family in pomegranate. Meanwhile, pomegranate is rich in sugar, and three published pomegranate genome sequences provide resources for the study of the SWEET gene family. 20 PgSWEETs from pomegranate and the known Arabidopsis and grape SWEETs were divided into four clades (Ⅰ, Ⅱ, Ⅲ and Ⅳ) according to the phylogenetic relationships. PgSWEETs of the same clade share similar gene structures, predicting their similar biological functions. RNA-Seq data suggested that PgSWEET genes have a tissue-specific expression pattern. Foliar application of tripotassium phosphate significantly increased the total soluble sugar content of pomegranate fruits and leaves and significantly affected the expression levels of PgSWEETs. The plant growth hormone regulator assay also significantly affected the PgSWEETs expression both in buds of bisexual and functional male flowers. Among them, we selected PgSWEET17a as a candidate gene that plays a role in fructose transport in leaves. The 798 bp CDS sequence of PgSWEET17a was cloned, which encodes 265 amino acids. The subcellular localization of PgSWEET17a showed that it was localized to the cell membrane, indicating its involvement in sugar transport. Transient expression results showed that tobacco fructose content was significantly increased with the up-regulation of PgSWEET17a, while both sucrose and glucose contents were significantly down-regulated. The integration of the PgSWEET phylogenetic tree, gene structure and RNA-Seq data provide a genome-wide trait and expression pattern. Our findings suggest that tripotassium phosphate and plant exogenous hormone treatments could alter PgSWEET expression patterns. These provide a reference for further functional verification and sugar metabolism pathway regulation of PgSWEETs. [ABSTRACT FROM AUTHOR]

Apple is one of the most important fruit crops in international trade. In this study, we presented the complete mitochondrial genome sequence of apple cultivar 'Yantai Fuji 8'. The complete mitochondrial genome is 396947 bp in length with an overall GC content of 45.40%. It contains 57 genes including 33 protein-coding genes, 4 rRNAs, and 20 tRNAs. The phylogenetic analysis showed that 'Yantai Fuji 8' was clustered with the Malus of Rosaceae family. [ABSTRACT FROM AUTHOR]

Prunus cerasifera Ehrh. 'Pissardii', is a widespread ornamental and fruit tree. Here, we reported the complete chloroplast (cp) genome of P. cerasifera 'Pissardii' (GenBank accession number: MN418903). The total cp genome is 157,952 bp in length, displayed a typical quadripartite structure, including a large single copy region (LSC) of 86,286 bp and a small single copy region (SSC) of 18,926 bp, which are separated by a pair of inverted repeat (IR) regions of 26,370 bp. The overall guanine-cytosine (GC) content of the genome sequence is 36.7%. The cp genome encodes 134 unique genes, including 84 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of 27 chloroplast genomes showed that P. cerasifera 'Pissardii' was closely related to P. humilis in Rosaceae. [ABSTRACT FROM AUTHOR]

Spiraea blumei G. Don is an ornamental shrub widely distributed in Eastern Asia. Here, we reported and characterized the complete chloroplast (cp) genome sequence of S. blumei (GenBank accession number: MN418904) to provide genomic resources for promoting its conservation. The total chloroplast genome is 155,957 bp in length and contains the typical chloroplast structure, including two inverted repeat (IR) regions of 26,343 bp, a large single-copy (LSC) region of 84,384 bp, and a small single-copy (SSC) region of 18,887 bp. The overall guanine-cytosine (GC) content of the S. blumei chloroplast genome is 36.8%. The cp genome encodes 133 unique genes, including 85 protein-coding genes (PCGs), 40 tRNA genes, and 8 rRNA genes. We used the cp genome of S. blumei and 26 other cp genomes to perform a phylogenetic analysis, which indicated that S. blumei was closely related to S. martini in Rosaceae. [ABSTRACT FROM AUTHOR]

Kerria japonica (L.) DC., a monotypic species endemic to China and Japan, is an important ornamental shrub. In this study, we reported the complete chloroplast genome sequence of K. japonica (L.) DC. 'pleniflora' (GenBank accession number: MN418902) to provide genomic resources for its conservation. The total chloroplast (cp) genome is 160,007 bp in length, including a large single-copy region (LSC) of 87,672 bp and a small single-copy region (SSC) of 19,461 bp, which are separated by two inverted repeat (IR) regions of 26,437 bp. The overall guanine-cytosine (GC) content of the genome sequence is 34.0%. The cp genome encodes 132 unique genes, including 84 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of 25 cp genomes showed that K. japonica 'pleniflora' was most closely related to K. japonica and then had a close genetic relationship with Neviusia cliftonii in Rosaceae. [ABSTRACT FROM AUTHOR]

Calycanthaceae is a perennial shrub endemic to China with important ornamental and medicinal values. In this study, Chimonanthus praecox cv. concolor chloroplast (cp) genome was characterized using Illumina paired-end reads data. In total, whole cp genome is 153,254 bp long and contains a small single-copy region of 19,769 bp, a pair of repeat (IRa and IRb) regions of 23,286 bp each, and a large single-copy region of 86,913 bp. This genome contains 129 genes, including 84 protein-genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis based on 19 cp genomes showed that C. praecox cv. concolor is closely related to Chimonanthus praecox and Chimonanthus nitens. [ABSTRACT FROM AUTHOR]

Malus baccata var. xiaojinensis belonging to Rosaceae is not only an ornamental tree but also an apple genotype that is highly tolerant to Fe deficiency. In this study, we reported the complete chloroplast (cp) genome of M. baccata var. xiaojinensis using ILLUMINA sequencing. The whole cp genome is 160,067 bp in length, containing a pair of inverted repeats (IRs) of 26,358 bp, a large single copy (LSC) region of 88,157 bp and a small single copy (SSC) region of 19,194 bp. And, the overall GC content of the cp genome was 36.56%. A total of 110 unique genes were found in the cp genome. 17 genes were duplicated in the IRs, including six protein-coding genes, seven tRNA genes, and four rRNA genes. Fourteen genes contained one intron, whereas three genes (rps12, clpP, and ycf3) contained two introns. The phylogenetic analysis demonstrated a close relationship between M. baccata var. xiaojinensis and Malus hupehensis. [ABSTRACT FROM AUTHOR]

The European wild apple (Malus sylvestris L.) is an important economical fruit crop. In this present study, we characterized the complete chloroplast (cp) genome sequence of Malus sylvestris L. The complete cp genome is 159,926 bp in length with a typical quadripartite structure, containing a large single-copy region (88,064 bp), a small single-copy region (26,353 bp) and a pair of inverted repeat regions (19,157 bp each). A total of 110 unique genes were found in the newly sequenced genome, including 78 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. Of these, 6 protein-coding genes, 7 tRNA genes, and all 4 rRNA genes are duplicated in the inverted regions. A phylogenetic tree was reconstructed using the neighbor-joining method based on the full length of cp genomes within genus Malus. The result showed that M. sylvestris L. was clustered together with the cultivated apple. The complete cp genome could provide valuable information for understanding the phylogenetic relationships within the genus Malus. [ABSTRACT FROM AUTHOR]

The dwarf M9 (Malus domestica 'M9') rootstock is the most widely available Malus rootstock, here we report the complete chloroplast (cp) genome of 'M9' rootstock. The size of the complete cp genome was 159,926 bp, with the large-copy (LSC, 88,065 bp) regions, small single-copy (SSC, 19,157 bp) regions, and two inverted repeat regions (IRs, 26,352 bp each). It contained 110 genes, including 78 protein-coding genes, 28 transfer RNA genes (tRNA), and 4 ribosomal RNA genes (rRNA). A phylogenetic tree demonstrated that 'M9' rootstock was closely related to M. hupehensis, M. baccata, M. prunifolia, M. micromalus, and M. tschonoskii. [ABSTRACT FROM AUTHOR]

Fruit cracking is a physiological disease that occurs during fruit development, which limits the quality and marketability of the fruit and causes great economic losses. Fruit cracking is affected by physiological, genetic and environmental factors. In this paper, the mechanism of fruit cracking was elaborated from cutin and cell wall, especially the gene families related to cell wall metabolism, including the polygalacturonase (PG) gene family, xylologlucan endotransglucosylase/hydrolase (XTH) gene family and expansin gene family. In addition, due to the advancement of high-throughput sequencing technology, an increasing number of horticultural plants have completed genome sequencing. This paper expounds the application of omics, including transcriptome, proteome, metabolomics and integrative omics in fruit cracking. The measures to reduce fruit cracking include using plastic rain covers and bagging, and spraying mineral and plant growth regulators. In this paper, the mechanisms of fruit cracking are reviewed at the molecular level, and the problems needing to be solved in fruit cracking research are put forward. [ABSTRACT FROM AUTHOR]

Sweet cherry (Prunus avium L.) is one of the two major species of cherries in world trade. In this study, we determined the complete mitochondrial genome of sweet cherry cultivar 'summit' using whole genome sequencing data. The genome was 389,709 bp in size. Totally, 44 genes were predicted, including 25 protein-coding, 16 tRNA, and 3 rRNA genes. A maximum-likelihood phylogenetic tree was reconstructed based on the complete mitochondrial genome sequences of eight species within Rosales. The result indicated that P. avium was clustered together with other Rosaceae species with high support value. The complete mitochondrial genome sequence of P. avium could provide valuable information for understanding the phylogenetic relationships within the Rosaceae family. [ABSTRACT FROM AUTHOR]

Pomegranate (Punica granatum), as one of the most important fruit trees, is widely cultivated in the tropical and subtropical of the world. In our present study, we assembled a complete chloroplast genome of an important pomegranate cultivar 'Bhagwa' using whole genome sequencing data previously reported. The complete cp genome is 158,641 bp in length. A total of 112 unique genes were annotated, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on complete cp genomes of Myrtales supported that P. granatum belongs to the Lythraceae 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]

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]

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]

Mitogen-activated protein kinase (MAPK) cascade is involved in the regulation of a series of biological processes in organisms, which are composed of MAPKKKs, MAPKKs, and MAPKs. Although genome-wide analyses of it has been well described in some species, little is known about MAPK and MAPKK genes in pomegranates. In this study, we identified 18 PgMAPKs, 9 PgMAPKKs through a genome-wide search. Chromosome localization showed that 27 genes are distributed on 7 chromosomes with different densities. Multiple sequence alignment and phylogenetic analysis revealed that PgMAPKs and PgMAPKKs could be divided into 4 subfamilies (groups A, B, C, and D), respectively. In addition, exon-introns structural analysis of each candidate gene has indicated high levels of conservation within and between phylogenetic groups. Cis-acting element analysis predicted that PgMAPKs and PgMAPKKs were widely involved in the growth, development, stress and hormone response of pomegranate. Expression profile analyses of PgMAPKs and PgMAPKKs were performed in different tissues (root, leaf, flower and fruit), and PgMAPK13 was significantly expressed in all tissues. To our knowledge, this is the first genome-wide analysis of the MAPK and MAPKK gene family in pomegranate. This study provides valuable information for understanding the classification and functions of pomegranate MAPK signal. [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]

Pomegranate (Punica granatum L.) is widely grown in arid and semiarid regions, where the salinization may have developed through irrigation. A greenhouse experiment was conducted to investigate NaCl stress on growth, photosynthesis, and nutrients of 18 pomegranate cultivars. One group was irrigated twice a week with a nutrient solution. The other group was watered twice a week with the same nutrient solution and 200 mM NaCl for five weeks. Dry weight, shoot length, new shoot number, root length and number, leaf area, leaf relative water content, and net photosynthesis of salt-treated plants were negatively impacted by salt stress, and there was a significant difference among cultivars. Few foliar damages were observed. Na content of plants significantly increased in all cultivars, while P, S, K, Ca, Mg, Si, Al, Zn content of plants decreased under salt stress. Fe, Mn, and Cu content increased in most cultivars. Pomegranate accumulated supraoptimal Na mostly in roots and transported more K and Ca to shoots, which was attributed to maintaining a higher ratio of K/Na and Ca/Na in the aerial part of plants. Ten of the 18 cultivars were considered salt-tolerant, which would offer a reference for pomegranate cultivation on saline lands. [ABSTRACT FROM AUTHOR]

Pomegranates (Punica granatum L.) are one of the most popular fruit trees cultivated in arid and semi-arid tropics and subtropics. In this study, we determined and characterized three complete chloroplast (cp) genomes of P. granatum cultivars with different phenotypes using the genome skimming approach. The complete cp genomes of three pomegranate cultivars displayed the typical quadripartite structure of angiosperms, and their length ranged from 156,638 to 156,639 bp. They encoded 113 unique genes and 17 are duplicated in the inverted regions. We analyzed the sequence diversity of pomegranate cp genomes coupled with two previous reports. The results showed that the sequence diversity is extremely low and no informative sites were detected, which suggests that cp genome sequences may be not be suitable for investigating the genetic diversity of pomegranate genotypes. Further, we analyzed the codon usage pattern and identified the potential RNA editing sites. A comparative cp genome analysis with other species within Lythraceae revealed that the gene content and organization are highly conserved. Based on a site-specific model, 11 genes with positively selected sites were detected, and most of them were photosynthesis-related genes and genetic system-related genes. Together with previously released cp genomes of the order Myrtales, we determined the taxonomic position of P. granatum based on the complete chloroplast genomes. Phylogenetic analysis suggested that P. granatum form a single clade with other species from Lythraceae with a high support value. The complete cp genomes provides valuable information for understanding the phylogenetic position of P. gramatum in the order Myrtales. [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]