Publications by authors named "Diyang Zhang"

16 Publications

  • Page 1 of 1

The Cymbidium genome reveals the evolution of unique morphological traits.

Hortic Res 2021 Dec 1;8(1):255. Epub 2021 Dec 1.

Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a chromosome-scale assembly of the genome of Cymbidium ensifolium (Jianlan) is presented. Comparative genomic analysis showed that C. ensifolium has experienced two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, while the older event was the τ event shared by most monocots. The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation, and flower shape mutations in C. ensifolium were shown to be associated with the abnormal expression of MADS-box genes. The most abundant floral scent components identified included methyl jasmonate, acacia alcohol and linalool, and the genes involved in the floral scent component network of C. ensifolium were determined. Furthermore, the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves, while the increased expression of MADS-box genes in leaves led to perianth-like leaves. Our results provide fundamental insights into orchid evolution and diversification.
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http://dx.doi.org/10.1038/s41438-021-00683-zDOI Listing
December 2021

The camphor tree genome enhances the understanding of magnoliid evolution.

J Genet Genomics 2021 Nov 16. Epub 2021 Nov 16.

College of Forestry, Fujian Agriculture and Forestry, Fuzhou 350002, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address:

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http://dx.doi.org/10.1016/j.jgg.2021.11.001DOI Listing
November 2021

The Melastoma dodecandrum genome and the evolution of Myrtales.

J Genet Genomics 2021 Oct 28. Epub 2021 Oct 28.

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China. Electronic address:

Melastomataceae have abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the first chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size was 299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum, Eucalyptus grandis and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. We found that the SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.
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http://dx.doi.org/10.1016/j.jgg.2021.10.004DOI Listing
October 2021

R2R3-MYB genes coordinate conical cell development and cuticular wax biosynthesis in Phalaenopsis aphrodite.

Plant Physiol 2021 Sep 2. Epub 2021 Sep 2.

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Petals of the monocot Phalaenopsis aphrodite (Orchidaceae) possess conical epidermal cells on their adaxial surfaces, and a large amount of cuticular wax is deposited on them to serve as a primary barrier against biotic and abiotic stresses. It has been widely reported that subgroup 9A members of the R2R3-MYB gene family, MIXTA and MIXTA-like in eudicots, act to regulate the differentiation of conical epidermal cells. However, the molecular pathways underlying conical epidermal cell development and cuticular wax biosynthesis in monocot petals remain unclear. Here, we characterized two subgroup 9A R2R3-MYB genes, PaMYB9A1 and PaMYB9A2 (PaMYB9A1/2), from P. aphrodite through the transient overexpression of their coding sequences and corresponding chimeric repressors in developing petals. We showed that PaMYB9A1/2 function to coordinate conical epidermal cell development and cuticular wax biosynthesis. In addition, we identified putative targets of PaMYB9A1/2 through comparative transcriptome analyses, revealing that PaMYB9A1/2 acts to regulate the expression of cell wall-associated and wax biosynthetic genes. Furthermore, a chemical composition analysis of cuticular wax showed that even-chain n-alkanes and odd-chain primary alcohols are the main chemical constituents of cuticular wax deposited on petals, which is inconsistent with the well-known biosynthetic pathways of cuticular wax, implying a distinct biosynthetic pathway occurring in P. aphrodite flowers. These results reveal that the function of subgroup 9A R2R3-MYB family genes in regulating the differentiation of epidermal cells is largely conserved in monocots and dicots. Furthermore, both PaMYB9A1/2 have evolved additional functions controlling the biosynthesis of cuticular wax.
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http://dx.doi.org/10.1093/plphys/kiab422DOI Listing
September 2021

Frequent germplasm exchanges drive the high genetic diversity of Chinese-cultivated common apricot germplasm.

Hortic Res 2021 Oct 1;8(1):215. Epub 2021 Oct 1.

Liaoning Institute of Pomology, Yingkou, 115009, China.

The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement. However, little is known about the factors that shape and maintain genetic diversity. Here, we assembled a high-quality chromosome-level reference of the Chinese common apricot 'Yinxiangbai', and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries. We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries. We also detected seven migration events among different apricot groups, where 27% of the genome was identified as being introgressed. Remarkably, we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups. Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.
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http://dx.doi.org/10.1038/s41438-021-00650-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8484454PMC
October 2021

The Euscaphis japonica genome and the evolution of malvids.

Plant J 2021 Dec 5;108(5):1382-1399. Epub 2021 Nov 5.

College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the γ event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.
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http://dx.doi.org/10.1111/tpj.15518DOI Listing
December 2021

Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution.

Hortic Res 2021 Sep 1;8(1):183. Epub 2021 Sep 1.

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

As one of the largest families of angiosperms, the Orchidaceae family is diverse. Dendrobium represents the second largest genus of the Orchidaceae. However, an assembled high-quality genome of species in this genus is lacking. Here, we report a chromosome-scale reference genome of Dendrobium chrysotoxum, an important ornamental and medicinal orchid species. The assembled genome size of D. chrysotoxum was 1.37 Gb, with a contig N50 value of 1.54 Mb. Of the sequences, 95.75% were anchored to 19 pseudochromosomes. There were 30,044 genes predicted in the D. chrysotoxum genome. Two whole-genome polyploidization events occurred in D. chrysotoxum. In terms of the second event, whole-genome duplication (WGD) was also found to have occurred in other Orchidaceae members, which diverged mainly via gene loss immediately after the WGD event occurred; the first duplication was found to have occurred in most monocots (tau event). We identified sugar transporter (SWEET) gene family expansion, which might be related to the abundant medicinal compounds and fleshy stems of D. chrysotoxum. MADS-box genes were identified in D. chrysotoxum, as well as members of TPS and Hsp90 gene families, which are associated with resistance, which may contribute to the adaptive evolution of orchids. We also investigated the interplay among carotenoid, ABA, and ethylene biosynthesis in D. chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers. The reference D. chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.
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http://dx.doi.org/10.1038/s41438-021-00621-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8408244PMC
September 2021

Wolfberry genomes and the evolution of Lycium (Solanaceae).

Commun Biol 2021 06 3;4(1):671. Epub 2021 Jun 3.

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.
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http://dx.doi.org/10.1038/s42003-021-02152-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8175696PMC
June 2021

Genome-Wide Identification of the Gene Family in Seven Species of Magnoliids and Expression Analysis in .

Plants (Basel) 2020 Dec 24;10(1). Epub 2020 Dec 24.

College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

The gene family, specific to seed plants, encodes a class of transcription factors in the lamina maintenance and development of lateral organs. Magnoliids are sisters to the clade-containing eudicots and monocots, which have rapidly diversified among the common ancestors of these three lineages. However, prior to this study, information on the function of the genes in magnoliids was extremely limited to the third major clades and the early diverging lineage of Mesangiospermae. In this study, the sum of 55 genes including five genes in , six in , eight in , 22 in , and 14 in clade were identified from seven magnoliid plants. Sequence analysis showed that all encoded YABBY protein sequences possess the highly conserved YABBY domain and C2C2 zinc-finger domain. Gene and protein structure analysis indicates that a certain number of exons were highly conserved and similar in the same class, and genes encode proteins of 71-392 amino acids and an open reading frame of 216-1179 bp in magnoliids. Additionally, the predicted molecular weight and isoelectric point of YABBY proteins in three species ranged from 7689.93 to 43578.13 and from 5.33 to 9.87, respectively. Meanwhile, the gene homolog expression of was detected at a temporal and spatial level during various developmental stages of leaf and reproductive tissues. This research could provide a brief overview of gene family evolution and its differential expression in magnoliids. Therefore, this comprehensive diversification analysis would provide a new insight into further understanding of the function of genes in seven magnoliids.
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http://dx.doi.org/10.3390/plants10010021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824534PMC
December 2020

Genome-Wide Identification of Genes in Orchidaceae and Their Expression Patterns in Orchid.

Genes (Basel) 2020 08 19;11(9). Epub 2020 Aug 19.

Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.

The plant transcription factors are key regulators in the lamina development of lateral organs. Orchid is one of the largest families in angiosperm and known for their unique floral morphology, reproductive biology, and diversified lifestyles. However, nothing is known about the role of genes in orchids, although biologists have never lost their fascination with orchids. In this study, a total of 54 genes, including 15 genes in CRC/DL, eight in INO, 17 in YAB2, and 14 in FIL clade, were identified from the eight orchid species. A sequence analysis showed that all protein sequences encoded by these YABBY genes share the highly conserved C2C2 zinc-finger domain and YABBY domain (a helix-loop-helix motif). A gene structure analysis showed that the number of exons is highly conserved in the same clades. The genes in YAB2 clade have six exons, and genes in CRC/DL, INO, and FIL have six or seven exons. A phylogenetic analysis showed all 54 orchid genes could be classified into four major clades, including CRC/DL, INO, FIL, and YAB2. Many of orchid species maintain more than one member in CRC/DL, FIL, and YAB2 clades, implying functional differentiation among these genes, which is supported by sequence diversification and differential expression. An expression analysis of genes revealed that members in the CRC/DL clade have concentrated expressions in the early floral development stage and gynostemium, the fused male and female reproductive organs. The expression of is consistent with the biological role it played in ovule integument morphogenesis. Transcripts of members in the FIL clade could be obviously detected at the early developmental stage of the flowers. The expression of three genes, , and , in the YAB2 clade could be revealed both in vegetative and reproductive tissues, and was transcribed at a relatively higher level than that of and . Together, this comprehensive analysis provides the basic information for understanding the function of the gene in Orchidaceae.
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http://dx.doi.org/10.3390/genes11090955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563141PMC
August 2020

The genome sequence of star fruit ().

Hortic Res 2020 1;7(1):95. Epub 2020 Jun 1.

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.

Oxalidaceae is one of the most important plant families in horticulture, and its key commercially relevant genus, , has diverse growth habits and fruit types. Here, we describe the assembly of a high-quality chromosome-scale genome sequence for (star fruit). distribution analysis showed that underwent a whole-genome triplication event, i.e., the gamma event shared by most eudicots. Comparisons between and other angiosperms also permitted the generation of Oxalidaceae gene annotations. We identified unique gene families and analyzed gene family expansion and contraction. This analysis revealed significant changes in MADS-box gene family content, which might be related to the cauliflory of . In addition, we identified and analyzed a total of 204 nucleotide-binding site, leucine-rich repeat receptor (NLR) genes and 58 WRKY genes in the genome, which may be related to the defense response. Our results provide insights into the origin, evolution and diversification of star fruit.
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http://dx.doi.org/10.1038/s41438-020-0307-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261771PMC
June 2020

The complete chloroplast genome sequence of (Orchidaceae).

Mitochondrial DNA B Resour 2019 Jul 11;4(2):2223-2224. Epub 2019 Jul 11.

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.

is a terrestrial orchid distributes in southwestern China. In this study, we reported the first complete chloroplast genome of . The whole genome was 158,329 bp, consisting of a pair of inverted repeats (IR 27,043 bp), a large single-copy region (LSC 85,950 bp), and a small single-copy region (SSC 18,293 bp). The complete genome contained 132 genes, including 77 protein-coding genes, 38 tRNA, and 8 rRNA genes. The overall GC content of the whole genome was 36.9%. A maximum-likelihood phylogenetic analysis demonstrated a close relationship between and .
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http://dx.doi.org/10.1080/23802359.2019.1624638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7687627PMC
July 2019

Correction: Isolated Fe and Co dual active sites on nitrogen-doped carbon for a highly efficient oxygen reduction reaction.

Chem Commun (Camb) 2018 05;54(38):4882

Department of Chemistry, Tsinghua University, Beijing 100084, China.

Correction for 'Isolated Fe and Co dual active sites on nitrogen-doped carbon for a highly efficient oxygen reduction reaction' by Diyang Zhang et al., Chem. Commun., 2018, DOI: 10.1039/c8cc00988k.
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http://dx.doi.org/10.1039/c8cc90183jDOI Listing
May 2018

Isolated Fe and Co dual active sites on nitrogen-doped carbon for a highly efficient oxygen reduction reaction.

Chem Commun (Camb) 2018 Apr;54(34):4274-4277

Department of Chemistry, Tsinghua University, Beijing 100084, China.

We successfully prepared Fe and Co isolated single atoms on metal-organic framework derived nitrogen-doped carbon (FeCo-ISAs/CN) by an adsorption-calcination strategy. The obtained FeCo-ISAs/CN exhibited top-level catalytic reactivity for the alkaline oxygen reduction reaction (ORR) with a half-wave potential of 0.920 V, which was 70 mV more positive than that of commercial Pt/C. Moreover, the catalyst was durable and showed negligible activity decay in the alkaline ORR during 5000 voltage cycles.
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http://dx.doi.org/10.1039/c8cc00988kDOI Listing
April 2018

Platinum-nickel frame within metal-organic framework fabricated in situ for hydrogen enrichment and molecular sieving.

Nat Commun 2015 Sep 22;6:8248. Epub 2015 Sep 22.

Department of Chemistry and Collaborative Innovation Center for Nanomaterial Science and Engineering, Tsinghua University, Beijing 100084, China.

Developing catalysts that provide the effective activation of hydrogen and selective absorption of substrate on metal surface is crucial to simultaneously improve activity and selectivity of hydrogenation reaction. Here we present an unique in situ etching and coordination synthetic strategy for exploiting a functionalized metal-organic framework to incorporate the bimetallic platinum-nickel frames, thereby forming a frame within frame nanostructure. The as-grown metal-organic framework serves as a 'breath shell' to enhance hydrogen enrichment and activation on platinum-nickel surface. More importantly, this framework structure with defined pores can provide the selective accessibility of molecules through its one-dimensional channels. In a mixture containing four olefins, the composite can selectively transport the substrates smaller than its pores to the platinum-nickel surface and catalyse their hydrogenation. This molecular sieve effect can be also applied to selectively produce imines, which are important intermediates in the reductive imination of nitroarene, by restraining further hydrogenation via cascade processes.
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http://dx.doi.org/10.1038/ncomms9248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595627PMC
September 2015
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