Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants.

Camellia plants include more than 200 species of great diversity and immense economic, ornamental, and cultural values. We sequenced the transcriptomes of 116 Camellia plants from almost all sections of the genus Camellia. We constructed a pan-transcriptome of Camellia plants with 89 394 gene families and then resolved the phylogeny of genus Camellia based on 405 high-quality low-copy core genes. Most of the inferred relationships are well supported by multiple nuclear gene trees and morphological traits. We provide strong evidence that Camellia plants shared a recent whole genome duplication event, followed by large expansions of transcription factor families associated with stress resistance and secondary metabolism. Secondary metabolites, particularly those associated with tea quality such as catechins and caffeine, were preferentially heavily accumulated in the Camellia plants from section Thea. We thoroughly examined the expression patterns of hundreds of genes associated with tea quality, and found that some of them exhibited significantly high expression and correlations with secondary metabolite accumulations in Thea species. We also released a web-accessible database for efficient retrieval of Camellia transcriptomes. The reported transcriptome sequences and obtained novel findings will facilitate the efficient conservation and utilization of Camellia germplasm towards a breeding program for cultivated tea, camellia, and oil-tea plants.

The soybean GmNFY-B1 transcription factor positively regulates flowering in transgenic Arabidopsis.

Nuclear Factor Y (NF-Y) gene family regulates numbers of flowering processes. Two independent transgenic Arabidopsis lines overexpressing (OX) GmNFY-B1 and GmNFYB1-GR (GmNFYB1 fused with the glucocorticoid receptor) were used to investigate the function of NFY-B1 in flowering. Furthermore, GmNFYB1-GR lines were chemically treated with dexamethasone (Dex, synthetic steroid hormone), cycloheximide (Cyc, an inhibitor of protein biosynthesis), and ethanol to examine their effects on different flowering related marker genes. Our results indicated that the transgenic lines produced longer hypocotyl lengths and had fewer numbers of rosette leaves compared to the wild-type and nf-yb1 mutant plants under both long and short-day (LD and SD) conditions. The qRT-PCR assays revealed that transcript levels of all flowering time regulating genes, i.e. SOC, FLC, FT, TSF, LFY, GI2, AGL, and FCA showed higher transcript abundance in lines OX GmNFYB1-GR. However, FT and GI genes showed higher transcript levels under Dex and Dex/Cyc treatments compared to Cyc and ethanol. Additionally, 24 differentially expressed genes were identified and verified through RNA-seq and RT-qPCR in GmNF-YB1-GR lines under Cyc and Dex/Cyc treatments from which 14 genes were up-regulated and 10 were down-regulated. These genes are involved in regulatory functions of circadian rhythm, regulation of flower development in photoperiodic, and GA pathways. The overexpression of GmNF-YB1 and GmNF-YB1-GR promote flowering through the higher expression of flowering-related genes. Further GmNF-YB1 and its attachment with the GR receptor can regulate its target genes under Dex/Cyc treatment and might act as flowering inducer under LD and SD conditions.

Recent progress and perspectives on physiological and molecular mechanisms underlying cold tolerance of tea plants.

Tea is one of the most consumed and widely planted beverage plant worldwide, which contains many important economic, healthy, and cultural values. Low temperature inflicts serious damage to tea yields and quality. To cope with cold stress, tea plants have evolved a cascade of physiological and molecular mechanisms to rescue the metabolic disorders in plant cells caused by the cold stress; this includes physiological, biochemical changes and molecular regulation of genes and associated pathways. Understanding the physiological and molecular mechanisms underlying how tea plants perceive and respond to cold stress is of great significance to breed new varieties with improved quality and stress resistance. In this review, we summarized the putative cold signal sensors and molecular regulation of the CBF cascade pathway in cold acclimation. We also broadly reviewed the functions and potential regulation networks of 128 cold-responsive gene families of tea plants reported in the literature, including those particularly regulated by light, phytohormone, and glycometabolism. We discussed exogenous treatments, including ABA, MeJA, melatonin, GABA, spermidine and airborne nerolidol that have been reported as effective ways to improve cold resistance in tea plants. We also present perspectives and possible challenges for functional genomic studies on cold tolerance of tea plants in the future.

Cloning and in silico characterization of an abiotic stress-inducible U-box domain-containing protein gene GsPUB8 from Glycine soja.

The ubiquitination pathway is involved in the posttranslational modification of cellular proteins. However, the role of E3 ubiquitin ligase family proteins under abiotic stress conditions remains unclear, particularly in soybean. The core objective of the current study was to isolate and functionally characterize the GsPUB8 protein gene from wild soybean (Glycine soja) by using a homologous cloning method to investigate its abiotic stress responses. The GsPUB8 is a 40,562 Da molecular weight protein with 373 amino acid residues. The sequence alignment revealed the presence of U-box domain while the phylogenetic analysis showed an abundance of PUB8 proteins in both monocot and dicot plants. Analysis of gene structure predicted the absence of introns along with the presence of one exon. Furthermore, the activity of the GsPUB8 protein was anticipated in the plasma membrane and its expression was persuaded with NaCl, ABA, PEG6000, and NaHCO3 treatments with considerably higher manifestation in roots than leaves although, expressed in both vegetative and reproductive parts of G. soja. GsPUB8 protein showed 54% and 32% sequence identity to U-box domain containing 8 and 12 proteins from Arabidopsis thaliana and Oryza sativa subsp. japonica, respectively. GsPUB8 exhibited relatively higher expression under saline and drought stress particularly in roots. Whereas, the 3D model of GsPUB8 protein was generated using the SWISS-MODEL. This study can be used to manipulate the GsPUB8 protein or GsPUB8 gene for transformation purposes and its functional characterization under abiotic stress conditions.

The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation.

Tea plant is an important economic crop, which is used to produce the world's oldest and most widely consumed tea beverages. Here, we present a high-quality reference genome assembly of the tea plant (Camellia sinensis var. sinensis) consisting of 15 pseudo-chromosomes. LTR retrotransposons (LTR-RTs) account for 70.38% of the genome, and we present evidence that LTR-RTs play critical roles in genome size expansion and the transcriptional diversification of tea plant genes through preferential insertion in promoter regions and introns. Genes, particularly those coding for terpene biosynthesis proteins, associated with tea aroma and stress resistance were significantly amplified through recent tandem duplications and exist as gene clusters in tea plant genome. Phylogenetic analysis of the sequences of 81 tea plant accessions with diverse origins revealed three well-differentiated tea plant populations, supporting the proposition for the southwest origin of the Chinese cultivated tea plant and its later spread to western Asia through introduction. Domestication and modern breeding left significant signatures on hundreds of genes in the tea plant genome, particularly those associated with tea quality and stress resistance. The genomic sequences of the reported reference and resequenced tea plant accessions provide valuable resources for future functional genomics study and molecular breeding of improved cultivars of tea plants.

GmPLP1, a PAS/LOV protein, functions as a possible new type of blue light photoreceptor in soybean.

Light is one of the most important environmental factors for the growth and development of plants. To adapt to changes in day length, the photoreception and transmission of the light signals in plants mainly depend on the various light receptor proteins. The PAS/LOV protein (PLP) has a PAS domain in the N-terminal and LOV domain in the C-terminal and has been confirmed as a new type of blue light receptor in Arabidopsis thaliana. However, the role of its counterpart in soybean remains largely unclear. In this study, the expression pattern of the GmPLP1 under different light qualities was determined by real-time RT-PCR analysis using the cultivar 'DongNong 42', a photosensitive soybean cultivar, suggesting that GmPLP1 was affected by the circadian clock and was a dark-induced gene. Moreover, the mRNA abundance increased significantly under blue light. Further analysis revealed that overexpression of GmPLP1 displayed the inhibition of hypocotyl elongation under blue light, and the expression of CRY1, CRY2, CKL3, CKL4, BIT1, and HY5 were simultaneously increased in GmPLP1-transgenic Arabidopsis, suggesting that the shortened hypocotyl was associated with the up-regulation of these genes. Taken together, our results suggest that GmPLP1, which is a new possible type of blue light photoreceptor in soybean, plays an important role in the blue light signaling pathway.

GsSNAP33, a novel Glycine soja SNAP25-type protein gene: Improvement of plant salt and drought tolerances in transgenic Arabidopsis thaliana.

The N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) superfamily, specifically the SNAP25-type proteins and t-SNAREs, have been proposed to regulate cellular processes and plant resistance mechanisms. However, little is known about the role of SNAP25-type proteins in combating abiotic stresses, specifically in wild soybean. In the current study, the isolation and functional characterization of the putative synaptosomal-associated SNAP25-type protein gene GsSNAP33 from wild soybean (Glycine soja) were performed. GsSNAP33 has a molecular weight of 33,311 Da and comprises 300 amino acid residues along with Qb-Qc SNARE domains. Multiple sequence alignment revealed the highest similarity of the GsSNAP33 protein to GmSNAP33 (91%), VrSNAP33 (89%), PvSNAP33 (86%) and AtSNAP33 (63%). Phylogenetic studies revealed the abundance of SNAP33 proteins mostly in dicotyledons. Quantitative real-time PCR assays confirmed that GsSNAP33 expression can be induced by salt, alkali, ABA and PEG treatments and that GsSNAP33 is highly expressed in the pods, seeds and roots of Glycine soja. Furthermore, the overexpression of the GsSNAP33 gene in WT Arabidopsis thaliana resulted in increased germination rates, greater root lengths, improved photosynthesis, lower electrolyte leakage, higher biomass production and up-regulated expression levels of various stress-responsive marker genes, including KINI, COR15A, P5Cs, RAB18, RD29A and COR47 in transgenic lines compared with those in WT lines. Subcellular localization studies revealed that the GsSNAP33-eGFP fusion protein was localized to the plasma membrane, while eGFP was distributed throughout whole cytoplasm of onion epidermal cells. Collectively, our findings suggest that GsSNAP33, a novel plasma membrane protein gene of Glycine soja, might be involved in improving plant responses to salt and drought stresses in Arabidopsis.