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The mitogen-activated protein kinase (MAPK) cascade is a highly conserved signaling transduction module that transduces extracellular stimuli into intracellular responses in plants. Early studies of plant MAPKs focused on their functions in model plants. Based on the results of whole-genome sequencing, many MAPKs have been identified in horticultural plants, such as tomato and apple. Recent studies revealed that the MAPK cascade also plays crucial roles in the biotic and abiotic stress responses of horticultural plants. In this review, we summarize the composition and classification of MAPK cascades in horticultural plants and recent research on this cascade in responses to abiotic stresses (such as drought, extreme temperature and high salinity) and biotic stresses (such as pathogen infection). In addition, we discuss the most advanced research themes related to plant MAPK cascades, thus facilitating research on MAPK cascade functions in horticultural plants.

Background Punica granatum is a fundamentally important fruit tree that has important economic, medicinal and ornamental properties. At present, there are few reports on the mitochondrial genome of pomegranate. Hence, in this study the P. granatum mitogenome was sequenced and assembled to further understanding of organization, variation, and evolution of mitogenomes of this tree species. Results The genome structure was multi-chromosomes with seven circular contigs, measuring 382,774 bp in length with a 45.91% GC content. It contained 74 genes, including 46 protein-coding genes, 25 tRNA genes, and three rRNA genes. There were 188 pairs of dispersed repeats with lengths of 30 or greater, primarily consisting of reverse complementary repeats. The mitogenome analysis identified 114SSRs and 466 RNA editing sites. Analyses of codon usage, nucleotide diversity and gene migration from chloroplast to mitochondrial were also conducted. The collinear and comparative analysis of mitochondrial structures between P. granatum and its proximal species indicated that P. granatum ‘Taishanhong’ was closely related to P. granatum ‘Qingpitian’ and Lagerstroemia indica. Phylogenetic examination based on the mitogenome also confirmed the evolutionary relationship. Conclusion The results offered crucial information on the evolutionary biology of pomegranate and highlighted ways to promote the utilization of the species’ germplasm.

Background Prunus cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast genome of P. cistena and compared it with related species of the genus Prunus based on the chloroplast genome. Results The complete chloroplast genome of P. cistena is a 157,935 bp long typical tetrad structure, with an overall GC content of 36.72% and higher GC content in the in the inverted repeats (IR) regions than in the large single-copy (LSC) and small single-copy (SSC) regions. It contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes have two introns, with the longest intron in the trnK-UUU gene in the LSC region. Moreover, the genome has a total of 253SSRs, with the mononucleotide SSRs being the most abundant. The chloroplast sequences and gene arrangements of P. cistena are highly conserved, with the overall structure and gene order similar to other Prunus species. The atpE , ccsA , petA , rps8 , and matK genes have undergone significant positive selection in Prunus species. P. cistena has a close evolutionary relationship with P. jamasakura . The coding and IR regions are more conserved than the noncoding regions, and the chloroplast DNA sequences are highly conserved throughout the genus Prunus . Conclusions The current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of the genus Prunus .

Background Light is the main source of energy and, as such, is one of the most important environmental factors for plant growth, morphogenesis, and other physiological responses. MicroRNAs (miRNAs) are endogenous non-coding RNAs that contain 21–24 nucleotides (nt) and play important roles in plant growth and development as well as stress responses. However, the role of miRNAs in the light response is less studied. We used tomato seedlings that were cultured in red light then transferred to blue light for 2 min to identify miRNAs related to light response by high-throughput sequencing. Results A total of 108 known miRNAs and 141 predicted novel miRNAs were identified in leaf samples from tomato leaves treated with the different light qualities. Among them, 15 known and 5 predicted novel miRNAs were differentially expressed after blue light treatment compared with the control (red light treatment). KEGG enrichment analysis showed that significantly enriched pathways included zeatin biosynthesis (ko00908), homologous recombination (ko03440), and plant hormone signal transduction (ko04075). Zeatin biosynthesis and plant hormone signal transduction are related to plant hormones, indicating that plant hormones play important roles in the light response. Conclusion Our results provide a theoretical basis for further understanding the role of miRNAs in the light response of plants.

Self-rooted pomegranate seedlings are widely used in the horticultural industry to cut costs and time. However, these seedlings produce shallow roots that exhibit poor cold resistance. Thus, deeper adventitious roots generated through gravitropism are imperative for seedling survival, and understanding the molecular mechanisms of gravitropism can facilitate improved breeding techniques. We hypothesized that gravitropism in pomegranate is partially controlled by pomegranate FOUR LIPS (PgFLP), an R2R3-MYB protein that interacts with and controls the transcriptional expression of PgPIN10 , which facilitates transmembrane auxin signaling. We studied subcellular localization of PgFLP, quantified auxin levels, and measured gravitropic set-point angle (GSA) to investigate the underlying mechanisms regulating PgPIN10 expression during the formation of GSA in pomegranate adventitious roots. We found that PgFLP was localized to the nucleus based on use of green florescent proteins, suggesting that this protein is a transcription factor. When using the tractable 35S::PgFLP , we observed stronger gravitational response in overexpression lines leading to a narrower GSA than in the wild-type Arabidopsis , and the expression of PgFLP and PgPIN10 in ‘Lanbaoshi’ (LBS; a deep-rooted cultivar) was higher than that in ‘Taishanhong’ (TSH; a shallow-rooted cultivar), which indicates that PgFLP may participate in regulating the GSA of adventitious roots via PgPIN10 in pomegranate. Taken together, our results indicate that the pomegranate R2R3-MYB transcription factor, PgFLP, plays a vital role in setting the GSA of adventitious roots in this crop species.

Pomegranate (Punica granatum) is a well-known fruit tree species and a significant pioneer ecological species on saline–alkali land with moderate resistance to salt stress. To explore its response mechanism to salt stress could provide valuable insights into the molecular and physiological strategies plants employ to adapt and survive in high-salt environments. In this study, changes in physiological parameters and gene expressions were examined following salt treatment. After 72 h of salt treatment, change patterns of SOD and POD differed between high and low salt concentrations. Similar changes were found in the contents of proline and total soluble sugar. RNA-Seq analysis of fifteen samples detected 32,630 genes from the pomegranate genome data. A total of 6571 DEGs, including 374 TFs, were identified across different treatments. Six special modules and 180 hub genes were obtained by WGCNA analysis. Functional annotation highlighted signaling pathways and the accumulation of primary and secondary metabolites as significant pathways. These findings could reveal the salt tolerance mechanism in pomegranate leaves, offering a theoretical foundation for enhancing plant salt tolerance through genetic engineering.

Malus spectabilis 'Guanghui' is an important ornamental plant, which complete chloroplast genome (Accession: MT501657) was sequenced, assembled and annotated. The genome size is 1601,230 bp and the overall GC content is 36.50%, with large single-copy (LSC, 89,310bp) regions, small single-copy (SSC, 19,196 bp) regions, and two inverted repeat regions (IRs, 23,632bp each). A total of 129 genes are successfully annotated, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic relationships showed that Malus spectabilis 'Guanghui' is closely related to the species of Malus sieversii.

The Quercus robur 'Fastigiata' is an important ornamental plant, in which the complete chloroplast genome (accession no. MN562095) was identified and sequenced. The genome size is 161,172 bp, with a large single-copy (LSC, 90,505 bp) region, a small single-copy (SSC, 18,997 bp) region, and two inverted repeat regions (IRs, 25,835 bp each). A total of 134 genes are successfully annotated, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic relationships inferred that Q. robur 'Fastigiata' is closely related to Quercus mongolica, Quercus wutaishanica, and Quercus dentata.

Punica granatum 'Luqing1' is an important d fruit tree with high quality and strong cold-resistance. The complete chloroplast genome (Accession: MN630638) was sequenced, assembled, and annotated. The size of chloroplast genome was 158,638 bp with large single-copy (LSC, 89,021 bp) regions, small single-copy (SSC, 18,685 bp) regions, and two inverted repeat regions (IRs, 25,466 bp each). A total of 130 genes were successfully annotated, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic relationships showed that P. granatum 'Luqing1' was closely related with different pomegranate cultivars.

Cercis canadensis 'Forest Pansy' is a tree species with high ornamental value, which complete chloroplast (cp) genome was sequenced, assembled, and annotated. The genome size is 158,960 bp with a total GC content of 36.17%. The cp genome is made up of a large single-copy region (88,114 bp), a small single-copy region (19,590 bp), and two inverted repeat regions (25,628 bp each). It contains 128 genes, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Eighteen genes were duplicated in IRs. The maximum-likelihood (ML) phylogenetic analysis indicated that the Leguminosae species are grouped together, and C. canadensis 'Forest Pansy' is closely related to C. canadensis. The result would provide valuable information for genetic studies on Cercis genus.