Transcriptome Sequencing and Screening of Anthocyanin-Related Genes in the Leaves of Acer truncatum Bunge.

Acer truncatum Bunge is generally used as an ornamental tree because of its autumn leaves, although the viewing period is short-approximately 7-15 days. Color improvement of ornamental trees has consistently been an important research topic because color partially determines the value of the commodity; however, a lack of genomic data have limited the progress of molecular breeding research in this area. The purposes of this study were to obtain a transcriptome database for A. truncatum, screen anthocyanin biosynthesis-related genes, and reveal the mechanisms underlying leaf color transformation to provide a basis for increasing the viewing period or breeding cultivars that display red leaves throughout the growing season via gene regulation. In this study, although the use of an Illumina HiSeq 2000 platform and systematic bioinformatics analysis using both young and mature leaves as experimental materials, 233,912,882 clean reads were generated and 121,287 unique transcripts were retrieved. We selected 16 color-related genes (from the transcriptome results) for qRT-PCR to validate the results, and the expression trends of the selected genes were largely consistent with the transcriptome analysis results, with a consistency of 0.875. According to the results of the transcriptome analysis, the validation, and previous studies, we obtained sequences of genes related to anthocyanins, including CHS, CHI, ANS, UFGT, UGT75c1, DFR, BZ1, F3H, F3'H, LAR, ANR, FLS, and those of several transcription factors, including MYB1, BHLH, and WD40. Verifying specific regulation by one or several of these genes in the control of leaf color requires further research. The acquisition of transcriptomic information, especially information concerning anthocyanin biosynthesis-related genes and their base sequences, can provide a theoretical basis for the study of the molecular mechanisms determining changes in leaf color in Acer and is of great importance to the breeding of new cultivars.

Transcriptome sequencing and flavonoid metabolism analysis in the leaves of three different cultivars of Acer truncatum.

Young and mature leaves of three Acer truncatum varieties with different leaf colors were examined. Transcriptome sequencing and flavonoid metabolism were used to analyze the differential gene expression associated with different leaf colors and growth stages and the relationships between gene expression and flavonoid and anthocyanin contents to improve ornamental value and develop flavonoid-rich A. truncatum. Kyoto Encyclopedia of Genes and Genomes database annotation of differentially expressed genes indicated that the following genes were related to flavonoid synthesis: phenylpropanoid biosynthesis genes (PAL, C4H, 4CL and CHS), flavonoid biosynthesis genes (E2.1.1.104, CHI, FLS, F3'5'H and ANR), anthocyanin biosynthesis genes (ANS, DFR, HCT, BZ1, GT1, and UGT79B1), isoflavonoid biosynthesis genes (HIDH and CYP81E17), and their transcriptional regulator (MYB). A total of 234 types of flavonoids were detected. The types and contents of anthocyanins in the red-leaf varieties 'Hong Jingling' and 'Caidie Fanfei' were significantly higher than those in the green leaf cultivar 'Lv Baoshi', especially morning glory 3-O-glucoside, delphinidin 3-O-glucoside, and pelargonium-3-O-glucoside, which were not detected in 'Lv Baoshi'. Combined omics analysis showed that downregulated expression of C4H, CHS and F3'5'H and upregulated expression of FLS reduced the supply of raw materials for anthocyanin synthesis, and downstream ANR upregulation converted anthocyanins to procyanidins, increasing the total flavonoid content. F3'5'H expression was downregulated in the leaves of each variety with development, resulting in the accumulation of catechins and the gradual greening of the leaves. F3'5'H was significantly depleted in the young leaves of 'Hong Jingling' and 'Caidie Fanfei' compared with the young leaves of 'Lv Baoshi', while ANS and BZ1 were enriched significantly. It is concluded that F3'5'H, BZ1, and ANS are the key genes needed for breeding red A. truncatum and that ANR is the key gene needed for breeding varieties with a high flavonoids contens. These results may facilitate genetic modification or selection for further improvement of the ornamental qualities and flavonoid content of A. truncatum.

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.

Construction of Pseudomolecules for the Chinese Chestnut (Castanea mollissima) Genome.

The Chinese chestnut (Castanea mollissima Bl.) is a woody nut crop with a high ecological value. Although many cultivars have been selected from natural seedlings, elite lines with comprehensive agronomic traits and characters remain rare. To explore genetic resources with aid of whole genome sequence will play important roles in modern breeding programs for chestnut. In this study, we generated a high-quality C. mollissima genome assembly by combining 90× Pacific Biosciences long read and 170× high-throughput chromosome conformation capture data. The assembly was 688.93 Mb in total, with a contig N50 of 2.83 Mb. Most of the assembled sequences (99.75%) were anchored onto 12 chromosomes, and 97.07% of the assemblies were accurately anchored and oriented. A total of 33,638 protein-coding genes were predicted in the C. mollissima genome. Comparative genomic and transcriptomic analyses provided insights into the genes expressed in specific tissues, as well as those associated with burr development in the Chinese chestnut. This highly contiguous assembly of the C. mollissima genome provides a valuable resource for studies aiming at identifying and characterizing agronomical-important traits, and will aid the design of breeding strategies to develop more focused, faster, and predictable improvement programs.

[Effects of hydrogen sulfide on mitochondrial function in sweet cherry stigma and ovary under low temperature stress]. / 硫化氢对低温胁迫下甜樱桃柱头和子房线粒体功能的影响.

To investigate the effects of H2S on mitochondrial functions under low temperature stress, we analyzed the effects of 0.05 mmol·L-1 NaHS and 15 µmmol·L-1 HT (hypotaurine and H2S scavenger) on mitochondria antioxidant enzyme activities and mitochondrial permeability transition pore, mitochondrial membrane fluidity, mitochondrial membrane potential, Cyt c/a ratio and H+-ATPase activity in sweet cherry stigma and ovary with sweet cherry variety Zaodaguo under -2 ℃ low temperature stress. The results showed that low temperature stress increased the concentrations of mitochondrial H2O2 and MDA, enhanced the mitochondrial membrane permeability, but decreased the mitochondrial membrane fluidity, membrane potential, Cyt c/a and H+-ATPase acti-vity. Application of NaHS at 0.05 mmol·L-1 could effectively reduce the concentrations of H2O2 and MDA, and keep higher activities of SOD, POD and CAT of mitochondrial for longer time. Furthermore, application of 0.05 mmol·L-1 NaHS could decrease mitochondrial membrane permeability while increase mitochondrial membrane fluidity, membrane potential, Cyt c/a and H+-ATPase activity in stigma and ovary under low temperature stress. The effects of NaHS were completely offset by HT addition. The results suggested that exogenous H2S could alleviate the oxidative damage on stigma and ovary stress through decreasing H2O2 accumulation, regulating mitochondria antioxidant system, increasing H+-ATPase activity, and mitigating mitochondria function under low temperature.

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.

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.

Molecular Link between Leaf Coloration and Gene Expression of Flavonoid and Carotenoid Biosynthesis in Camellia sinensis Cultivar 'Huangjinya'.

'Huangjinya' is an excellent albino tea germplasm cultivated in China because of its bright color and high amino acid content. It is light sensitive, with yellow leaves under intense light while green leaves under weak light. As well, the flavonoid and carotenoid levels increased after moderate shading treatment. However, the mechanism underlying this interesting phenomenon remains unclear. In this study, the transcriptome of 'Huangjinya' plants exposed to sunlight and shade were analyzed by high-throughput sequencing followed by de novo assembly. Shading 'Huangjinya' made its leaf color turn green. De novo assembly showed that the transcriptome of 'Huangjinya' leaves comprises of 127,253 unigenes, with an average length of 914 nt. Among the 81,128 functionally annotated unigenes, 207 differentially expressed genes were identified, including 110 up-regulated and 97 down-regulated genes under moderate shading compared to full light. Gene ontology (GO) indicated that the differentially expressed genes are mainly involved in protein and ion binding and oxidoreductase activity. Antioxidation-related pathways, including flavonoid and carotenoid biosynthesis, were highly enriched in these functions. Shading inhibited the expression of flavonoid biosynthesis-associated genes and induced carotenoid biosynthesis-related genes. This would suggest that decreased flavonoid biosynthetic gene expression coincides with increased flavonoids (e.g., catechin) content upon moderate shading, while carotenoid levels and biosynthetic gene expression are positively correlated in 'Huangjinya.' In conclusion, the leaf color changes in 'Huangjinya' are largely determined by the combined effects of flavonoid and carotenoid biosynthesis.