The complete chloroplast genome sequence of Rhododendron farrerae Tate ex Sweet (Ericaceae).

Rhododendron farrerae Tate ex Sweet 1831 is a species of ornamental plant found in southern China. In the present study, the complete chloroplast genome of R. farrerae was sequenced. The genome was 149,453 bp in length and lacked the typical quadripartite structure. The plastid genome contained 112 genes, including 74 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. The overall GC content of the genome was 35.65%. Phylogenetic analysis of 25 chloroplast genomes revealed that R. farrerae was closely related to Rhododendron huadingense. This study could provide fundamental information for the distribution, utilization, and phylogenomics of Rhododendron.

Transcriptome and photosynthetic analyses provide new insight into the molecular mechanisms underlying heat stress tolerance in Rhododendron × pulchrum Sweet.

Rhododendron species provide excellent ornamental use worldwide, yet heat stress (HS) is one of the major threats to their cultivation. However, the intricate mechanisms underlying the photochemical and transcriptional regulations associated with the heat stress response in Rhododendron remain relatively unexplored. In this study, the analyses of morphological characteristics and chlorophyll fluorescence (ChlF) kinetics showed that HS (40 °C/35 °C) had a notable impact on both the donor's and acceptor's sides of photosystem II (PSII), resulting in reduced PSII activity and electron transfer capacity. The gradual recovery of plants observed following a 5-day period of culture under normal conditions indicates the reversible nature of the HS impact on Rhododendron × pulchrum. Analysis of transcriptome data unveiled noteworthy trends: four genes associated with photosynthesis-antenna protein synthesis (LHCb1, LHCb2 and LHCb3) and the antioxidant system (glutamate-cysteine ligase) experienced significant down-regulation in the leaves of R. × pulchrum during HS. Conversely, aseorbate peroxidase and glutathione S-transferase TAU 8 demonstrated an up-regulated pattern. Furthermore, six down-regulated genes (phos-phoenolpyruvate carboxylase 4, sedoheptulose-bisphosphatase, ribose-5-phosphate isomerase 2, high cyclic electron flow 1, beta glucosidase 32 and starch synthase 2) and two up-regulated genes (beta glucosidase 2 and UDP-glucose pyrophosphorylase 2) implicated in photosynthetic carbon fixation and starch/sucrose metabolism were identified during the recovery process. To augment these insights, a weighted gene co-expression network analysis yielded a co-expression network, pinpointing the hub genes correlated with ChlF dynamics' variation trends. The cumulative results showed that HS inhibited the synthesis of photosynthesis-antenna proteins in R. × pulchrum leaves. This disruption subsequently led to diminished photochemical activities in both PSII and PSI, albeit with PSI exhibiting heightened thermostability. Depending on the regulation of the reactive oxygen species scavenging system and heat dissipation, photoprotection sustained the recoverability of R. × pulchrum to HS.

Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum.

Rhododendron × pulchrum, an important horticultural species, is widely distributed in Europe, Asia, and North America. To analyze the phylogenetic and organelle genome information of R. × pulchrum and its related species, the organelle genome of R. × pulchrum was sequenced and assembled. The complete mitochondrial genome showed lineage DNA molecules, which were 816,410 bp long and contained 64 genes, namely 24 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 37 protein-coding genes. The chloroplast genome of R. × pulchrum was reassembled and re-annotated; the results were different from those of previous studies. There were 42 and 46 simple sequence repeats (SSR) identified from the mitochondrial and chloroplast genomes of R. × pulchrum, respectively. Five genes (nad1, nad2, nad4, nad7, and rps3) were potentially useful molecular markers. The R. × pulchrum mitochondrial genome collinear alignment among five species of the Ericaceae showed that the mitochondrial genomes of these related species have a high degree of homology with R. × pulchrum in this gene region, and the most conservative genes were trnC-GCA, trnD-GUC, trnM-CAU, trnN-GUU, trnY-GUA, atp4, nad4, nad2, nad5, ccmC, and rrn26. The phylogenetic trees of mitochondrial genome showed that R. simsii was a sister to R. × pulchrum. The results verified that there was gene rearrangement between R. × pulchrum and R. simsii mitochondrial genomes. The codon usage bias of 10 Ericaceae mitochondrial genes and 7 Rhododendron chloroplast genes were influenced by mutation, while other genes codon usages had undergone selection. The study identified 13 homologous fragments containing gene sequences between the chloroplast and mitochondrial genomes of R. × pulchrum. Overall, our results illustrate the organelle genome information could explain the phylogenetics of plants and could be used to develop molecular markers and genetic evolution. Our study will facilitate the study of population genetics and evolution in Rhododendron and other genera in Ericaceae.

Comparative transcriptome analysis identified ChlH and POLGAMMA2 in regulating yellow-leaf coloration in Forsythia.

Leaf color is one of the most important features for plants used for landscape and ornamental purposes. However, the regulatory mechanism of yellow leaf coloration still remains elusive in many plant species. To understand the complex genetic mechanism of yellow-leaf Forsythia, we first compared the pigment content and leaf anatomical structure of yellow-leaf and green-leaf accessions derived from a hybrid population. The physiological and cytological analyses demonstrated that yellow-leaf progenies were chlorophyll deficient with defected chloroplast structure. With comparative transcriptome analysis, we identified a number of candidate genes differentially expressed between yellow-leaf and green-leaf Forsythia plants. Among these genes, we further screened out two candidates, ChlH (magnesium chelatase Subunit H) and POLGAMMA2 (POLYMERASE GAMMA 2), with consistent relative-expression pattern between different colored plants. To verify the gene function, we performed virus-induced gene silencing assays and observed yellow-leaf phenotype with total chlorophyll content reduced by approximately 66 and 83% in ChlH-silenced and POLGAMMA2-silenced plants, respectively. We also observed defected chloroplast structure in both ChlH-silenced and POLGAMMA2-silenced Forsythia. Transient over-expression of ChlH and POLGAMMA2 led to increased chlorophyll content and restored thylakoid architecture in yellow-leaf Forsythia. With transcriptome sequencing, we detected a number of genes related to chlorophyll biosynthesis and chloroplast development that were responsive to the silencing of ChlH and POLGAMMA2. To summarize, ChlH and POLGAMMA2 are two key genes that possibly related to yellow-leaf coloration in Forsythia through modulating chlorophyll synthesis and chloroplast ultrastructure. Our study provided insights into the molecular aspects of yellow-leaf Forsythia and expanded the knowledge of foliage color regulation in woody ornamental plants.

The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis.

Carya cathayensis, an important economic nut tree, is narrowly endemic to eastern China in the wild. The complete cp genome of C. cathayensis was sequenced with NGS using an Illumina HiSeq2500, analyzed, and compared to its closely related species. The cp genome is 160,825 bp in length with an overall GC content of 36.13%, presenting a quadripartite structure comprising a large single copy (LSC; 90,115 bp), a small single copy (SSC; 18,760 bp), and a pair of inverted repeats (IRs; 25,975 bp). The genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 252 simple sequence repeats (SSRs) and 55 long repeats were identified. Gene selective pressure analysis showed that seven genes (rps15, rpoA, rpoB, petD, ccsA, atpI, and ycf1-2) were possibly under positive selection compared with the other Juglandaceae species. Phylogenetic relationships of 46 species inferred that Juglandaceae is monophyletic, and that C. cathayensis is sister to Carya kweichowensis and Carya illinoinensis. The genome comparison revealed that there is a wide variability of the junction sites, and there is higher divergence in the noncoding regions than in coding regions. These results suggest a great potential in phylogenetic research. The newly characterized cp genome of C. cathayensis provides valuable information for further studies of this economically important species.

Molecular and Photosynthetic Performance in the Yellow Leaf Mutant of Torreya grandis According to Transcriptome Sequencing, Chlorophyll a Fluorescence, and Modulated 820 nm Reflection.

To study the photosynthetic energy mechanism and electron transfer in yellow leaves, transcriptomics combined with physiological approaches was used to explore the mechanism of the yellow leaf mutant Torreya grandis 'Merrillii'. The results showed that chlorophyll content, the maximal photochemical efficiency of PSII (Fv/Fm), and the parameters related to the OJ phase of fluorescence (φEo, φRo) were all decreased significantly in mutant-type T. grandis leaves. The efficiency needed for an electron to be transferred from the reduced carriers between the two photosystems to the end acceptors of the PSI (δRo) and the quantum yield of the energy dissipation (φDo) were higher in the leaves of mutant-type T. grandis compared to those in wild-type leaves. Analysis of the prompt fluorescence kinetics and modulated 820 nm reflection showed that the electron transfer of PSII was decreased, and PSI activity was increased in yellow T. grandis leaves. Transcriptome data showed that the unigenes involved in chlorophyll synthesis and the photosynthetic electron transport complex were downregulated in the leaves of mutant-type T. grandis compared to wild-type leaves, while there were no observable changes in carotenoid content and biosynthesis. These findings suggest that the downregulation of genes involved in chlorophyll synthesis leads to decreased chlorophyll content, resulting in both PSI activity and carotenoids having higher tolerance when acting as photo-protective mechanisms for coping with chlorophyll deficit and decrease in linear electron transport in PSII.

Selection and validation of appropriate reference genes for gene expression studies in Forsythia.

The qRT-PCR method has been widely used to detect gene expression level in plants, helping to understand the molecular mechanisms. However, there are few researches which focus on the selection of the internal reference genes in Forsythia. To select the appropriate reference genes of Forsythia aimed at qRT-PCR normalization, twelve candidate reference genes were selected from our transcriptome data. Their expression was assessed by RT-PCR analysis in 47 Forsythia samples, including 12 species cultivars, different organs and tissues. GeNorm, NormFinder, and BestKeeper software were used to select the appropriate reference genes, AG and PSY were used to verify the accuracy of the outcome. The results showed that UKN1 was a stable reference gene in leaves of twelve Forsythia germplasms and in different developmental stages of fruits. MTP, ABCT + MTP, and ABCT + MTP + TIP were stable reference genes in different organs. ACT and SDH were stable reference genes in different flower tissues and different developmental stages of the flower buds. When Forsythia plants were stressed with PEG or ABA, SDH + UKN1 + G6PD was the stable reference gene group for qRT-PCR. The results provided the basis for investigating the physiological and biochemical processes of Forsythia related to medicinal and ornamental properties, and drought-resistance in the level of gene expression.