Comprehensive assembly and comparative examination of the full mitochondrial genome in Castanea mollissima Blume.

The Chinese chestnut, Castanea mollissima Blume, a nut-bearing tree native to China and North Korea, belongs to the Fagaceae family. As an important genetic resource, C. mollissima is vital in enhancing edible chestnut varieties and offers significant insights into the origin and evolution of chestnut species. While the chloroplast genome of C. mollissima has been sequenced, its mitochondrial genome (mitogenome) remains largely uncharted. In this study, we have characterized the C. mollissima mitogenome, assembling it utilizing reads from both BGI and Nanopore sequencing platforms, and conducted a comparative analysis with the mitochondrial genomes of closely related species. The mitogenome of C. mollissima manifests a polycyclic structure consisting of two circular molecules measuring 363,232 bp and 24,806 bp, respectively. This genome encompasses 35 unique protein-coding genes, 19 tRNA genes, and three rRNA genes. A total of 139 SSRs were identified throughout the entire C. mollissima mitogenome. Furthermore, the combined length of homologous fragments between the chloroplast and mitochondrial genomes was 5766 bp, constituting 1.49% of the mitogenome. We also predicted 484 RNA editing sites in C. mollissima, demonstrating C-to-U RNA editing. Phylogenetic analysis of related species' mitogenomes showed that C. mollissima was closely related to Lithocarpus litseifolius (Hance) Chun and Quercus acutissima Carruth. Interestingly, the mitogenome sequences of C. mollissima, L. litseifolius, Q. acutissima, Fagus sylvatica L., and Juglans mandshurica Maxim did not show conservation in their alignments, indicating frequent genome reorganization. This report marks the inaugural study of the C. mollissima mitogenome, serving as a benchmark genome for economically significant plants within the Castanea genus. Moreover, it supplies invaluable information that can guide future molecular breeding efforts and contribute to the broader understanding of chestnut genomics.

Comparative Transcriptome and Metabolome Profiling Reveal Mechanisms of Red Leaf Color Fading in Populus × euramericana cv. 'Zhonghuahongye'.

Anthocyanins are among the flavonoids that serve as the principal pigments affecting the color of plants. During leaf growth, the leaf color of 'Zhonghuahongye' gradually changes from copper-brown to yellow-green. At present, the mechanism of color change at different stages has not yet been discovered. To find this, we compared the color phenotype, metabolome, and transcriptome of the three leaf stages. The results showed that the anthocyanin content of leaves decreased by 62.5% and the chlorophyll content increased by 204.35%, 69.23%, 155.56% and 60%, respectively. Differential metabolites and genes were enriched in the pathway related to the synthesis of 'Zhonghuahongye' flavonoids and anthocyanins and to the biosynthesis of secondary metabolites. Furthermore, 273 flavonoid metabolites were detected, with a total of eight classes. DFR, FLS and ANS downstream of anthocyanin synthesis may be the key structural genes in reducing anthocyanin synthesis and accumulation in the green leaf of 'Zhonghuahongye'. The results of multi-omics analysis showed that the formation of color was primarily affected by anthocyanin regulation and its related synthesis-affected genes. This study preliminarily analyzed the green regression gene and metabolic changes in 'Zhonghuahongye' red leaves and constitutes a reference for the molecular breeding of 'Zhonghuahongye' red leaves.

Metabolome analysis reveals flavonoid changes during the leaf color transition in Populus × euramericana 'Zhonghuahongye'.

Introduction: To investigate the mechanism of leaf color change at different stages in Populus × euramericana 'Zhonghuahongye' ('Zhonghong' poplar). Methods: Leaf color phenotypes were determined and a metabolomic analysis was performed on leaves at three stages (R1, R2 and R3). Results: The a*, C* and chromatic light values of the leaves decreased by 108.91%, 52.08% and 113.34%, while the brightness L values and chromatic b* values gradually increased by 36.01% and 13.94%, respectively. In the differential metabolite assay, 81 differentially expressed metabolites were detected in the R1 vs. R3 comparison, 45 were detected in the R1 vs. R2 comparison, and 75 were detected in the R2 vs. R3 comparison. Ten metabolites showed significant differences in all comparisons, which were mostly flavonoid metabolites. The metabolites that were upregulated in the three periods were cyanidin 3,5-O-diglucoside, delphinidin, and gallocatechin, with flavonoid metabolites accounting for the largest proportion and malvidin 3- O-galactoside as the primary downregulated metabolite. The color shift of red leaves from a bright purplish red to a brownish green was associated with the downregulation of malvidin 3-O-glucoside, cyanidin, naringenin, and dihydromyricetin. Discussion: Here, we analyzed the expression of flavonoid metabolites in the leaves of 'Zhonghong' poplar at three stages and identified key metabolites closely related to leaf color change, providing an important genetic basis for the genetic improvement of this cultivar.

Metabolome combined with transcriptome profiling reveals the dynamic changes in flavonoids in red and green leaves of Populus × euramericana 'Zhonghuahongye'.

Flavonoids are secondary metabolites that have economic value and are essential for health. Poplar is a model perennial woody tree that is often used to study the regulatory mechanisms of flavonoid synthesis. We used a poplar bud mutant, the red leaf poplar variety 2025 (Populus × euramericana 'Zhonghuahongye'), and green leaves as study materials and selected three stages of leaf color changes for evaluation. Phenotypic and biochemical analyses showed that the total flavonoid, polyphenol, and anthocyanin contents of red leaves were higher than those of green leaves in the first stage, and the young and tender leaves of the red leaf variety had higher antioxidant activity. The analyses of widely targeted metabolites identified a total of 273 flavonoid metabolites (114 flavones, 41 flavonols, 34 flavonoids, 25 flavanones, 21 anthocyanins, 18 polyphenols, 15 isoflavones, and 5 proanthocyanidins). The greatest difference among the metabolites was found in the first stage. Most flavonoids accumulated in red leaves, and eight anthocyanin compounds contributed to red leaf coloration. A comprehensive metabolomic analysis based on RNA-seq showed that most genes in the flavonoid and anthocyanin biosynthetic pathways were differentially expressed in the two types of leaves. The flavonoid synthesis genes CHS (chalcone synthase gene), FLS (flavonol synthase gene), ANS (anthocyanidin synthase gene), and proanthocyanidin synthesis gene LAR (leucoanthocyanidin reductase gene) might play key roles in the differences in flavonoid metabolism. A correlation analysis of core metabolites and genes revealed several candidate regulators of flavonoid and anthocyanin biosynthesis, including five MYB (MYB domain), three bHLH (basic helix-loop-helix), and HY5 (elongated hypocotyl 5) transcription factors. This study provides a reference for the identification and utilization of flavonoid bioactive components in red-leaf poplar and improves the understanding of the differences in metabolism and gene expression between red and green leaves at different developmental stages.

Complex Physical Structure of Complete Mitochondrial Genome of Quercus acutissima (Fagaceae): A Significant Energy Plant.

Quercus acutissima Carruth. is a Chinese important energy plant with high ecological and economic values. While the species chloroplast genome has been reported, its mitochondrial genome (mitogenome) is still unexplored. Here, we assembled and annotated the Q. acutissima mitogenome, and we compared its characteristic differences with several closely related species. The Q. acutissima mitogenome's main structure is branched with three distinguished contigs (linear molecule 1, circular molecule 2, and circular molecule 3) with 448,982 bp total length and 45.72% GC content. The mitogenome contained 51 genes, including 32 protein-coding, 16 tRNA and 3 rRNA genes. We examined codon usage, repeated sequences, genome recombination, chloroplast to mitochondrion DNA transformation, RNA editing, and synteny in the Q. acutissima mitogenome. Phylogenetic trees based on 29 species mitogenomes clarified the species classification. Our results provided comprehensive information of Q. acutissima mitogenome, and they are expected to provide valuable information for Fagaceae evolutionary biology and to promote the species germplasm utilization.

Phosphorus influence Cd phytoextraction in Populus stems via modulating xylem development, cell wall Cd storage and antioxidant defense.

The soils in mining lands with cadmium (Cd) contamination usually are deficient in nutrients. Disclosing how P nutrition and N:P stoichiometric ratio influences Cd accumulation and stress tolerance in stems of Populus spp. will facilitate the phytoremediation of mining sites polluted by Cd. In this study, investigations at the anatomical and physiological levels were conducted using a clone of Populus × euramericana. Both phosphorus deficiency and cadmium exposure inhibited xylem development via reducing cell layers in the xylem. Under P-sufficient condition, appropriate P status and balanced N:P ratio in stem promoted xylem development under Cd exposure via stimulating cell division, which enhanced Cd accumulation in stems. Cd accumulation in cell walls of collenchyma tissues of the stem was enhanced by P application due to increased polysaccharide production and cell wall affinity for Cd. The low P concentrations (0.3-0.4 mg g-1) and imbalanced N:P ratio under P deficiency inhibited the production of APX and ascorbate-GSH cycle, which increased oxidative stress and lipid peroxidation as indicated by high MDA concentration in stem. Under P-sufficient condition, the interactions between phytohormones and antioxidants play crucial roles in the process of antioxidant defense under Cd exposure. In conclusions, appropriate P addition and balanced N:P ratio enhanced secondary xylem development and promoted cadmium accumulation and stress tolerance in Populus stems, which can benefit the phytoextraction of Cd from Cd-contaminated soil.

Ectopic expression of EuWRI1, encoding a transcription factor in E. ulmoides, changes the seeds oil content in transgenic tobacco.

The WRINKLED1 (WRI1) gene is a well-established key transcriptional regulator involved in the regulation of fatty acid biosynthesis in developing seeds. In this study, a new WRI1 gene was isolated from seeds of Eucommia ulmoides and named EuWRI1. A close link between gibberellins signaling and EuWRI1 gene expression was suggested in this study. Functional characterization of EuWRI1 was elucidated through seed-specific expression in tobacco. In transgenic tobacco, the expression of EuWRI1 in eight independent transgenic lines was detected by semiquantitative RT-PCR. The relative mRNA accumulation of genes encoding enzymes involved in fatty acid biosynthesis (biotin carboxyl carrier protein and keto-ACP synthase 1) was also assayed in tobacco seeds. Analysis of the seeds oil content and starch content indicated that the transgenic lines showed a significant increase in seeds oil content, whereas starch content decreased significantly. Further analysis of the fatty acid composition revealed that palmitic acid (16:0), linoleic acid (18:2) and linolenic acid (18:3) increased significantly in seeds of transgenic tobacco lines, but stearic acid (18:0) levels significantly declined. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:337-346, 2018.

The Hardy Rubber Tree Genome Provides Insights into the Evolution of Polyisoprene Biosynthesis.

Eucommia ulmoides, also called hardy rubber tree, is an economically important tree; however, the lack of its genome sequence restricts the fundamental biological research and applied studies of this plant species. Here, we present a high-quality assembly of its ∼1.2-Gb genome (scaffold N50 = 1.88 Mb) with at least 26 723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which was obtained using an integrated strategy combining Illumina sequencing, PacBio sequencing, and BioNano mapping. As a sister taxon to lamiids and campanulids, E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication in the last ∼125 million years. E. ulmoides exhibits high expression levels and/or gene number expansion for multiple genes involved in stress responses and the biosynthesis of secondary metabolites, which may account for its considerable environmental adaptability. In contrast to the rubber tree (Hevea brasiliensis), which produces cis-polyisoprene, E. ulmoides has evolved to synthesize long-chain trans-polyisoprene via farnesyl diphosphate synthases (FPSs). Moreover, FPS and rubber elongation factor/small rubber particle protein gene families were expanded independently from the H. brasiliensis lineage. These results provide new insights into the biology of E. ulmoides and the origin of polyisoprene biosynthesis.