Identification of a PTC-containing DlRan transcript and its differential expression during somatic embryogenesis in Dimocarpus longan

Comparative transcriptome analysis reveals different functions of Kandelia obovata superoxide dismutases in regulation of cadmium translocation

Kandelia obovata is a dominant mangrove species in southeastern of China. This species has a high tolerance to heavy metal stress that is mainly ascribed to the thickening of the secondary exodermis and high activity of superoxide dismutase (SOD) enzymes in the roots. The thickened exodermis inhibits entry of heavy metals into the roots, and oxidative stress due to Cd can be reduced efficiently by SOD activity. Although there are several proposed mechanisms by which genes encoding SODs in K. obovata (KoSODs) could induce lignification that contributes to thickening of the root exodermis, the exact functions of FeSOD2 (KoFSD2) and Cu/ZnSOD3 (KoCSD3) remain unclear. In this study we investigated the role of a thickened exodermis in K. obovata root tissues in response to Cd treatment, and determined functions of KoFSD2 and KoCSD3 by performing comparative transcriptome analysis on tobacco lines that overexpress these two enzymes. we found that a thickened exodermis can reduce Cd uptake, and that exposure to high concentrations Cd can promote secondary thickening processes in K. obovata roots exodermis. Transgenic Nicotiana benthamiana overexpressing of KoFSD2 or KoCSD3 exhibit different responses to Cd stress. KoCSD3 can promote thickening of the secondary cell wall of root vascular tissues to impede Cd entry. Meanwhile, KoFSD2 and KoCSD3 can also regulate translocation of copper and iron in response to Cd accumulation. Taken together, our results expand our understanding of the physiological roles of SODs in K. obovata against Cd stress.

Alternative splicing and its regulatory role in woody plants

Alternative splicing (AS) is an important post-transcriptional process to enhance proteome diversity in eukaryotic organisms. In plants, numerous reports have primarily focused on AS analysis in model plant species or herbaceous plants, leading to a notable lack of research on AS in woody plants. More importantly, emerging evidence indicates that many important traits, including wood formation and stress resistance, in woody plants are controlled by AS. In this review article, we summarize the current progress of all kinds of AS studies in different tree species at various stages of development and in response to various stresses, revealing the significant role played by AS in woody plants, as well as the similar properties and differential regulation within their herbaceous counterparts. Furthermore, we propose several potential strategies to facilitate the functional characterization of splicing factors in woody plants and evaluate a general pipeline for the systematic characterization of splicing isoforms in a complex AS regulatory network. The utilization of genetic studies and high-throughput omics integration approaches to analyze AS genes and splicing factors is likely to further advance our understanding of AS modulation in woody plants.

SODs involved in the hormone mediated regulation of H2O2 content in Kandelia obovata root tissues under cadmium stress

Cadmium (Cd) pollution in mangrove wetlands has received increasing attention as urbanization expands rapidly. As a dominant mangrove species, Kandelia obovata is highly tolerant to Cd toxicity. Plant hormones and superoxide dismutase (SODs) play critical roles in the response to heavy metal stress in K. obovata roots. Although theirs important influence have been reported, the regulation mechanism between SODs and plant hormones in Cd detoxification by K. obovata roots remains limited. Here, we investigated relationships among SOD, plant hormones, and Cd tolerance in K. obovata roots exposed to Cd. We found that Cd was retained in the epidermis and exodermis of roots, and the epidermis and exodermis had highest hydrogen peroxide (H₂O₂) content and SOD activity. Similarly, SOD isozymes also exhibited distinct activity in the different parts of root. Overexpressed KoCSD3 and KoFSD2 individually in Nicotiana benthamiana revealed that different SOD members contributed to H₂O₂ content regulation by promote the activity of downstream antioxidant enzymes under Cd treatment. In addition, assays on the effects of hormones showed that increased endogenous indole-3-acetic acid (IAA) was observed in the cortex and stele, whereas the abscisic acid (ABA) content was enhanced in the epidermis and exodermis in roots during Cd treatment. The results of exogenous hormones treatment indicated that KoFSD2 upregulated under ABA and IAA treatment, but KoCSD3 only induced by ABA stimulation. Taken together, our results reveal the relationship between SODs and plant hormones, which expands the knowledge base regarding KoSODs response to plant hormones and mediating H₂O₂ concentration under Cd stress.

Identification of candidate genes involved in anthocyanin accumulation in the peel of jaboticaba (Myrciaria cauliflora) fruits by transcriptomic analysis

Jaboticaba is a grape-like fruit that accumulates high levels of anthocyanins in the peel and is proposed as a good source of functional pigments. However, the molecular mechanisms underlying anthocyanin accumulation in jaboticaba peel remains to be elucidated. In this study, we employed RNA-seq technique to compare the transcriptomic differences between green-colored and black-colored jaboticaba peels. Over 5 million high-quality reads were assembled into 62,190 unigenes with an average length of 737 bp, 29,320 (47.15%) of them were annotated by public databases. 2152 unigenes were found to be differentially expressed (830 upregulated and 1322 downregulated). Gene ontology analysis and pathway enrichment annotation revealed that 18 differentially expressed genes encode phenylalanine ammonialyase, 4-coumaroyl:CoA-ligase, chalcone synthase, flavanone 3-hydroxylase, flavonoid 3'-hydroxylase, anthocyanidin synthase, UDP-glucose: flavonoid 3-O-glucosyltransferase, glutathione S-transferase, Cytochrome b5 were associated with anthocyanin biosynthesis. Additionally, 54 differentially expressed transcription factors were identified. Furthermore, the expression of genes involved in biosynthesis and signal transduction of ethylene and abscisic acid were negatively and positively correlated with that of anthocyanin pathway genes and anthocyanin accumulation, respectively. Quantitative reverse transcription PCR analysis of candidate genes showed trends similar to those in the RNA-seq analysis. McMYB, a homolog of AtMYB113, induced anthocyanin accumulation in tobacco leaves when co-infiltrated PsbHLH3. These results will contribute to further understanding of the molecular mechanisms regulating anthocyanin accumulation in jaboticaba peel.

Molecular cloning, structural and expression profiling of DlRan genes during somatic embryogenesis in Dimocarpus longan Lour

To clone and examine expression profiles of DlRan genes during somatic embryogenesis in Dimocarpus longan Lour. Thirty cDNA sequences and two genomic sequences encoding DlRan proteins were isolated from longan embryogenic cultures. Structural analysis of DlRan genes revealed that the longan Ran gene family is more expanded than that of Arabidopsis. Expression analysis of DlRan genes during somatic embryogenesis uncovered a high abundance of DlRan genes in early embryogenic cultures and heart- and torpedo-shaped embryos. The expression of DlRan genes in embryogenic calli was affected by exogenous 2,4-dichlorophenoxyacetic acid treatment. DlRan is involved in 2,4-D induced somatic embryogenesis and development of somatic embryos in longan.

Identification of Candidate Anthocyanin-Related Genes by Transcriptomic Analysis of 'Furongli' Plum (Prunus salicina Lindl.) during Fruit Ripening Using RNA-Seq

Anthocyanins are important pigments and are responsible for red coloration in plums. However, little is known about the molecular mechanisms underlying anthocyanin accumulation in plum fruits. In this study, the RNA-seq technique was used to analyze the transcriptomic changes during fruit ripening in the red-fleshed plum (Prunus salicina Lindl.) cultivar 'Furongli'. Over 161 million high-quality reads were assembled into 52,093 unigenes and 49.4% of these were annotated using public databases. Of these, 25,681 unigenes had significant hits to the sequences in the NCBI Nr database, 17,203 unigenes showed significant similarity to known proteins in the Swiss-Prot database and 5816 and 8585 unigenes had significant similarity to existing sequences in the Kyoto Encyclopedia of Genes and Genomes and the Cluster of Orthologous Groups databases, respectively. A total of 3548 unigenes were differentially expressed during fruit ripening and 119 of these were annotated as involved in "biosynthesis of other secondary metabolites." Biological pathway analysis and gene ontology term enrichment analysis revealed that 13 differentially expressed genes are involved in anthocyanin biosynthesis. Furthermore, transcription factors such as MYB and bHLH, which may control anthocyanin biosynthesis, were identified through coexpression analysis of transcription factors, and structural genes. Real-time qPCR analysis of candidate genes showed good correlation with the transcriptome data. These results contribute to our understanding of the molecular mechanisms underlying anthocyanin biosynthesis in plum flesh. The transcriptomic data generated in this study provide a basis for further studies of fruit ripening in plum.