Transcriptomics and metabolomics analyses identified key genes associated with sugar and acid metabolism in sweet and sour pomegranate cultivars during the developmental period.

Pomegranate (Punica granatum), an important fruit tree in the world, is rich in bioactive substances and has broad prospects for development. In this study, gene expression levels and the concentrations of metabolites involved in the metabolism of soluble sugars and organic acids were investigated in sweet and sour pomegranate cultivars at the S1 (July 25) stage, S2 (August 26) stage, and S3 (September 24) stage. The results showed that glucose, fructose, citric acid, and malic acid were predominantly present in pomegranate. The expression of invertase 2 (INV2), INV1, FRK2, FRK7, PFK2, PFK7, and HK1 was closely correlated with the fructose and glucose contents during different developmental stages, whereas the expression of sucrose synthase 3 (SUS3) and INV1 was negatively correlated with the sucrose content. The expression of MDH (c28468_g3) and WRKY42 (c20711_g1) genes were closely related to the content of sucrose, malic acid, citric acid, and succinic acid during different developmental stages. Gene expression and metabolite concentrations varied between the two cultivars. The results provide valuable information for gene discovery, marker-assisted selection, and investigation of metabolism mechanisms in pomegranate fruits.

The role of RNA-binding protein, microRNA and alternative splicing in seed germination: a field need to be discovered.

Seed germination is the process through which a quiescent organ reactivates its metabolism culminating with the resumption cell divisions. It is usually the growth of a plant contained within a seed and results in the formation of a seedling. Post-transcriptional regulation plays an important role in gene expression. In cells, post-transcriptional regulation is mediated by many factors, such as RNA-binding proteins, microRNAs, and the spliceosome. This review provides an overview of the relationship between seed germination and post-transcriptional regulation. It addresses the relationship between seed germination and RNA-binding proteins, microRNAs and alternative splicing. This presentation of the current state of the knowledge will promote new investigations into the relevance of the interactions between seed germination and post-transcriptional regulation in plants.

The first complete chloroplast genome of Hovenia acerba Lindl.

Hovenia acerba Lindl. is an important medicinal plant, for which complete chloroplast genome (Accession: MN782301) was sequenced, assembled and annotated. The genome size is 161,668 bp and the overall GC content is 36.69%, with large single-copy (LSC, 89,451bp) regions, small single-copy (SSC, 18,979 bp) regions, and two inverted repeat regions (IRs, 26,619 bp each). A total of 130 genes are successfully annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic relationships showed that H. acerba is closely related to the species of Ziziphus genus.

Characterization of the complete chloroplast genome of Malus spectabilis 'Guanghui'.

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 complete chloroplast genome of Quercus robur 'Fastigiata'.

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.

Characterization and phylogenetic analysis of the complete chloroplast genome of Cercis canadensis 'Forest Pansy'.

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.

Comparative genome analysis of jujube witches'-broom Phytoplasma, an obligate pathogen that causes jujube witches'-broom disease.

BACKGROUND: JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the genome of a JWB phytoplasma isolate jwb-nky was sequenced and compared with other phytoplasmas enabled us to explore the mechanisms of genomic rearrangement. RESULTS: The complete genome sequence of JWB phytoplasma (jwb-nky) was determined, which consisting of one circular chromosome of 750,803 bp with a GC content of 23.3%. 694 protein-encoding genes, 2 operons for rRNA genes and 31 tRNA genes as well as 4 potential mobile units (PMUs) containing clusters of DNA repeats were identified. Based on PHIbaes analysis, a large number of genes were genome-specific and approximately 13% of JWB phytoplasma genes were predicted to be associated with virulence. Although transporters for maltose, dipeptides/oligopeptides, spermidine/putrescine, cobalt, Mn/Zn and methionine were identified, KEGG pathway analysis revealed the reduced metabolic capabilities of JWB phytoplasma. Comparative genome analyses between JWB phytoplasma and other phytoplasmas shows the occurrence of large-scale gene rearrangements. The low synteny with other phytoplasmas indicated that the expansion of multiple gene families/duplication probably occurred separately after differentiation. CONCLUSIONS: In this study, the complete genome sequence of a JWB phytoplasma isolate jwb-nky that causing JWB disease was reported for the first time and a number of species-specific genes were identified in the genome. The study enhanced our understandings about genomic basis and the pathogenicity mechanism of this pathogen, which will aid in the development of improved strategies for efficient management of JWB diseases.