ORCID Profile
0000-0003-0782-2835
Current Organisation
Wageningen University & Research
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Publisher: Cold Spring Harbor Laboratory
Date: 13-11-2019
DOI: 10.1101/839464
Abstract: Cambium drives lateral growth of stems and roots, contributing to erse plant growth forms. Root crop is one outstanding ex le of the cambium-driven growth. To understand its molecular basis, we used radish to generate a compendium of root tissue- and stage-specific transcriptomes from two contrasting inbred lines in root growth. Expression patterns of key cambium regulators and hormone signaling components were validated. Clustering and GO enrichment analyses of radish datasets followed by comparative analysis against the newly established Arabidopsis early cambium data revealed evolutionary conserved stress-response transcription factors that might intimately control the cambium. Indeed, in vivo network made of selected stress-response and cambium regulators indicated ERF-1 as a potential key checkpoint of cambial activities, explaining how the cambium-driven growth is altered in response to environmental changes. Together, this study provides rich information about dynamic gene expression changes along the cambium-driven root growth with future engineering schemes for crop yields.
Publisher: Elsevier BV
Date: 03-2018
Publisher: Elsevier BV
Date: 12-2020
Publisher: Springer Science and Business Media LLC
Date: 02-08-2018
DOI: 10.1038/S41598-018-30033-4
Abstract: Sugarcane ( Saccharum spp. hybrids) is a potential lignocellulosic feedstock for biofuel production due to its exceptional biomass accumulation ability, high convertible carbohydrate content and a favorable energy input/output ratio. Genetic modification of biofuel traits to improve biomass conversion requires an understanding of the regulation of carbohydrate and lignin biosynthesis. RNA-Seq was used to investigate the transcripts differentially expressed between the immature and mature tissues of the sugarcane genotypes varying in fiber content. Most of the differentially expressed transcripts were found to be down-regulated during stem maturation, highlighting their roles in active secondary cell-wall development in the younger tissues of both high and low fiber genotypes. Several cellulose synthase genes (including CesA2, CesA4, CesA7 and COBRA-like protein), lignin biosynthesis-related genes (ρ-coumarate 3-hydroxylase, ferulate 5-hydroxylase, cinnamyl alcohol dehydrogenase and gentiobiase) and transcription regulators for the secondary cell-wall synthesis (including LIM, MYB, PLATZ, IAA24, C2H2 and C2C2 DOF zinc finger gene families) were exclusively differentially expressed between immature and mature tissues of high fiber genotypes. These findings reveal target genes for subsequent research on the regulation of cellulose and lignin metabolism.
Publisher: Elsevier BV
Date: 03-2020
Publisher: Cold Spring Harbor Laboratory
Date: 10-07-2022
DOI: 10.1101/2022.07.09.499295
Abstract: Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to Arabidopsis. Here, we present a high-quality genome sequence of G. gynandra , anchored onto 17 main super- scaffolds with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. We revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event ( Gg-α ), then an addition of a third genome ( Th-α, +1x) took place in T. hassleriana but not in G. gynandra . Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3 T. hassleriana , and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra . Collectively, this study enhances our understanding of the impact of gene duplication and gene retention on the evolution of C4 photosynthesis in Cleomaceae.
Publisher: Frontiers Media SA
Date: 17-06-2020
Publisher: Wiley
Date: 28-11-2014
DOI: 10.1111/PBI.12300
Abstract: The productivity of plants as biofuel or biomaterial crops is established by both the yield of plant biomass per unit area of land and the efficiency of conversion of the biomass to biofuel. Higher yielding biofuel crops with increased conversion efficiencies allow production on a smaller land footprint minimizing competition with agriculture for food production and bio ersity conservation. Plants have traditionally been domesticated for food, fibre and feed applications. However, utilization for biofuels may require the breeding of novel phenotypes, or new species entirely. Genomics approaches support genetic selection strategies to deliver significant genetic improvement of plants as sources of biomass for biofuel manufacture. Genetic modification of plants provides a further range of options for improving the composition of biomass and for plant modifications to assist the fabrication of biofuels. The relative carbohydrate and lignin content influences the deconstruction of plant cell walls to biofuels. Key options for facilitating the deconstruction leading to higher monomeric sugar release from plants include increasing cellulose content, reducing cellulose crystallinity, and/or altering the amount or composition of noncellulosic polysaccharides or lignin. Modification of chemical linkages within and between these biomass components may improve the ease of deconstruction. Expression of enzymes in the plant may provide a cost-effective option for biochemical conversion to biofuel.
Publisher: Elsevier BV
Date: 08-2020
Publisher: Frontiers Media SA
Date: 14-05-2018
Publisher: Springer Science and Business Media LLC
Date: 18-07-2023
DOI: 10.1038/S41598-023-38571-2
Abstract: In grafted apple, rootstock-derived signals influence scion cold tolerance by initiating physiological changes to survive over the winter. To understand the underlying molecular interactions between scion and rootstock responsive to cold, we developed transcriptomics and metabolomics data in the stems of two scion/rootstock combinations, ‘Gala’/‘G202’ (cold resistant rootstock) and ‘Gala’/‘M9’ (cold susceptible rootstock). Outer layers of scion and rootstock stem, including vascular tissues, were collected from the field-grown grafted apple during the winter. The clustering of differentially expressed genes (DEGs) and gene ontology enrichment indicated distinct expression dynamics in the two graft combinations, which supports the dependency of scion cold tolerance on the rootstock genotypes. We identified 544 potentially mobile mRNAs of DEGs showing highly-correlated seasonal dynamics between scion and rootstock. The mobility of a subset of 544 mRNAs was validated by translocated genome-wide variants and the measurements of selected RNA mobility in tobacco and Arabidopsis . We detected orthologous genes of potentially mobile mRNAs in Arabidopsis thaliana , which belong to cold regulatory networks with RNA mobility. Together, our study provides a comprehensive insight into gene interactions and signal exchange between scion and rootstock responsive to cold. This will serve for future research to enhance cold tolerance of grafted tree crops.
Publisher: Elsevier
Date: 2021
Publisher: Elsevier BV
Date: 2022
Publisher: Springer Science and Business Media LLC
Date: 30-11-2017
Publisher: Unpublished
Date: 2016
Publisher: Frontiers Media SA
Date: 17-11-2015
Publisher: Unpublished
Date: 2016
Publisher: Figshare
Date: 2019
Publisher: Elsevier
Date: 2021
Publisher: Springer Science and Business Media LLC
Date: 22-05-2017
Publisher: Frontiers Media SA
Date: 23-07-2019
Publisher: Wiley
Date: 2022
DOI: 10.1111/PPL.13645
Abstract: Saccharum spontaneum, a wild relative of sugarcane, is highly tolerant to drought and salinity. The exploitation of germplasm resources for salinity tolerance is a major thrust area in India. In this study, we utilized suppression subtractive hybridization (SSH) followed by sequencing for the identification of upregulated transcripts during salinity stress in S. spontaneum clones coming from different geographical regions of India. Our sequencing of the SSH library revealed that 95% of the transformants contained inserts of size 200-1500 bp. We have identified 314 differentially expressed transcripts in the salinity-treated s les after subtraction, which were subsequently validated by quantitative real-time polymerase chain reaction. Functional annotation and pathway analysis revealed that the upregulated transcripts were a result of protein modifications, stress, and hormone signaling along with cell wall development and lignification. The prominently upregulated transcripts included UDP glucose dehydrogenase, cellulose synthase, ribulose, cellulose synthase COBRA, leucine-rich protein, NAC domain protein, pectin esterase, ABA-responsive element binding factor 1, and heat stress protein. Our results is a step forward the understanding of the molecular response of S. spontaneum under salinity stress, which will lead to the identification of genes and transcription factors as novel targets for salinity tolerance in sugarcane.
Publisher: Springer Science and Business Media LLC
Date: 13-01-2023
DOI: 10.1186/S12864-023-09124-8
Abstract: The importance of uridine 5′-diphosphate glucose (UDP-G) synthesis and degradation on carbon (C) partitioning has been indicated in several studies of plant systems, whereby the kinetic properties and abundance of involved enzymes had a significant effect upon the volume of C moving into the hemicellulose, cellulose and sucrose pools. In this study, the expression of 136 genes belonging to 32 gene families related to UDP-G metabolism was studied in 3 major sugarcane organs (including leaf, internode and root) at 6 different developmental stages in 2 commercial genotypes. Analysis of the genes associated with UDP-G metabolism in leaves indicated low expression of sucrose synthase , but relatively high expression of invertase genes, specifically cell-wall invertase 4 and neutral acid invertase 1–1 and 3 genes. Further, organs that are primarily responsible for sucrose synthesis or bioaccumulation, i.e., in source organs (mature leaves) and storage sink organs (mature internodes), had very low expression of sucrose, cellulose and hemicellulose synthesis genes, specifically sucrose synthase 1 and 2 , UDP-G dehydrogenase 5 and several cellulose synthase subunit genes. Gene expression was mostly very low in both leaf and mature internode s les however, leaves did have a comparatively heightened invertase and sucrose phosphate synthase expression. Major differences were observed in the transcription of several genes between immature sink organs (roots and immature internodes). Gene transcription favoured utilisation of UDP-G toward insoluble and respiratory pools in roots. Whereas, there was comparatively higher expression of sucrose synthetic genes, sucrose phosphate synthase 1 and 4 , and comparatively lower expression of many genes associated with C flow to insoluble and respiratory pools including myo-Inositol oxygenase , UDP-G dehydrogenase 4 , vacuolar invertase 1 , and several cell-wall invertase s in immature internodes. This study represents the first effort to quantify the expression of gene families associated with UDP-G metabolism in sugarcane. Transcriptional analysis displayed the likelihood that C partitioning in sugarcane is closely related to the transcription of genes associated with the UDP-G metabolism. The data presented may provide an accurate genetic reference for future efforts in altering UDP-G metabolism and in turn C partitioning in sugarcane.
Publisher: Wiley
Date: 11-07-2023
DOI: 10.1111/PCE.14662
Abstract: Research on C4 and C3‐C4 photosynthesis has attracted significant attention because the understanding of the genetic underpinnings of these traits will support the introduction of its characteristics into commercially relevant crop species. We used a panel of 19 taxa of 18 Brassiceae species with different photosynthesis characteristics (C3 and C3‐C4) with the following objectives: (i) create draft genome assemblies and annotations, (ii) quantify orthology levels using synteny maps between all pairs of taxa, (iii) describe the phylogenetic relatedness across all the species, and (iv) track the evolution of C3‐C4 intermediate photosynthesis in the Brassiceae tribe. Our results indicate that the draft de novo genome assemblies are of high quality and cover at least 90% of the gene space. Therewith we more than doubled the s ling depth of genomes of the Brassiceae tribe that comprises commercially important as well as biologically interesting species. The gene annotation generated high‐quality gene models, and for most genes extensive upstream sequences are available for all taxa, yielding potential to explore variants in regulatory sequences. The genome‐based phylogenetic tree of the Brassiceae contained two main clades and indicated that the C3‐C4 intermediate photosynthesis has evolved five times independently. Furthermore, our study provides the first genomic support of the hypothesis that Diplotaxis muralis is a natural hybrid of D. tenuifolia and D. viminea . Altogether, the de novo genome assemblies and the annotations reported in this study are a valuable resource for research on the evolution of C3‐C4 intermediate photosynthesis.
Publisher: Wiley
Date: 16-11-2021
DOI: 10.1111/TPJ.15561
Abstract: Radish, Raphanus sativus L., is an important root crop that is cultivated worldwide. Owing to its evolutionary proximity to Arabidopsis thaliana , radish can be used as a model root crop in research on the molecular basis of agronomic traits. Pithiness is a significant defect that reduces the production of radish with commercial value however, traditional breeding to eliminate this trait has thus far been unsuccessful. Here, we performed transcriptomics and genotype‐by‐sequencing (GBS)‐based quantitative trait locus (QTL) analyses of radish inbred lines to understand the molecular basis of pithiness in radish roots. The transcriptome data indicated that pithiness likely stems from the response to oxidative stress, leading to cell death of the xylem parenchyma during the root‐thickening process. Subsequently, we narrowed down a list of candidates responsible for pithiness near a major QTL and found polymorphisms in a radish homologue of Arabidopsis ANAC013 (RsNAC013), an endoplasmic reticulum bound NAC transcription factor that is targeted to the nucleus to mediate the mitochondrial retrograde signal. We analysed the effects of polymorphisms in RsNAC013 using Arabidopsis transgenic lines overexpressing RsNAC013 alleles as well as in radish inbred lines bearing these alleles. This analysis indicated that non‐synonymous variations within the coding sequence result in different levels of RsNAC013 activities, thereby providing a genetic condition for root pithiness. The elevated oxidative stress or hypoxia that activates RsNAC013 for mitochondrial signalling enhances this process. Collectively, this study serves as an exemplary case of translational research taking advantage of the extensive information available from a model organism.
Publisher: Elsevier BV
Date: 08-2015
Publisher: Oxford University Press (OUP)
Date: 24-01-2023
Abstract: Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1×) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae.
Publisher: Cold Spring Harbor Laboratory
Date: 21-09-2023
Publisher: Public Library of Science (PLoS)
Date: 17-08-2017
Publisher: Springer Science and Business Media LLC
Date: 25-04-2019
Publisher: Springer Science and Business Media LLC
Date: 25-11-2017
Publisher: Springer Science and Business Media LLC
Date: 12-2020
DOI: 10.1186/S13068-020-01837-2
Abstract: The composition of biomass determines its suitability for different applications within a biorefinery system. The proportion of the major biomass fractions (sugar, cellulose, hemicellulose and lignin) may vary in different sugarcane genotypes and growth environments and different parts of the plant. This study investigated the composition of mature and immature internodes, roots and mature leaves of sugarcane. Internodes were found to have a significantly larger alcohol-soluble component than leaves and roots. The primary difference between the immature and mature internodes was the ratio of soluble sugars. In mature tissues, sucrose content was significantly higher, whereas in immature internodal tissues there was lower sucrose and heightened concentrations of reducing sugars. Carbon (C) partitioning in leaf tissues was characterised by low levels of soluble components and high “other” and cell wall fractions. Root tissue had low ratios of soluble fractions relative to their cell wall contents, indicating a lack of storage of soluble carbon. There was no significant difference in the ratio of the major cell wall fractions between the major organ types. Characterisation of in idual non-cellulosic monomers indicated leaf and root tissues had significantly higher arabinose and galactose fractions. Significantly larger proportions of syringyl lignin compounds and the hydroxycinnamic compound, p- coumaric acid were observed in mature internodal tissues compared to the other tissue types. Tissue-specific differences in composition were shown to greatly affect the recalcitrance of the cell wall to enzymatic saccharification. Overall, this study displayed clear evidence of the differential partitioning of C throughout the sugarcane plant in specific organs. These organ-specific differences have major implications in their utility as a bioproduct feedstock. For ex le, the inclusion of trash (leaves) with the culms (internodes) may alter processing efficiency.
No related grants have been discovered for Nam V Hoang.