Nam V. Hoang

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• Doctor of Philosophy
• PostDoc Position at Wageningen University & Research

Cambium drives the lateral growth of stems and roots, contributing to diverse plant growth forms. The root crop is one of the outstanding examples 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 during root gr...

Background and Aims The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 million years ago), differential lineage diversification and genomic changes contributed to an array of divergence in morphol...

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 pseudo-molecules with a total length of 740 Mb...

Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sug...

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 f...

Oryza is a remarkable genus comprising 27 species and 11 genome types, with ~3.4-fold genome size variation, that possesses a virtually untapped reservoir of genes that can be used for crop improvement and neodomestication. Here we present 11 chromosome-level assemblies (nine tetraploid, two diploid) in the context of ~15 million years of evolution...

Background and Aims The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 million years ago), differential lineage diversification and genomic changes contributed to an array of divergence in morphol...

Oryza is remarkable genus - with two domesticated (i.e. Asian and African rice) and 25 diploid and tetraploid wild species, 11 extant genome types, and a ∼3.4-fold genome size variation - that possesses a virtually untapped reservoir of genes that can be used for crop improvement. Here we unveil and interrogate 11 new chromosome-level assemblies of...

The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 million years ago), different lineages and species underwent differential chromosomal rearrangements (diploidization) leading to diverse patterns...

In this study, we found a single quantitative trait locus for photosystem II efficiency (ΦPSII) in the Arabidopsis Ler-0 x Col-0 recombinant inbred line population. This locus on chromosome 5 is caused by genetic variation in a cluster of tandemly repeated SQUALENE EPOXIDASE-LIKE (SQE-like) genes, with unknown function. We show the QTL is caused by...

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’/‘G2...

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‐...

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 pseudo-molecules with a total length of 740 Mb...

Background 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...

Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C 4 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...

Background: 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. I...

The major carbon source and sink organs (roots, leaves and internodes) of sugarcane (Saccharum spp. hybrids) have different roles and consequently different apportioning of carbon into the major components of these organs. This study performed RNA-seq on two leaves, three internodes (of differing maturity) and roots in two similar commercial sugarc...

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 salinit...

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, trad...

Laser capture microdissection (LCM) coupled with transcriptome profiling is a powerful technique that allows for tissue-specific gene expression analysis in a complex system. One major challenge in using this technique is to obtain RNA without compromising its integrity. Here, we present a protocol optimized for radish root tissue sections using St...

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...

The plasticity of plant development relies on its ability to balance growth and stress resistance. To do this, plants have established highly coordinated gene regulatory networks (GRNs) of the transcription factors and signaling components involved in developmental processes and stress responses. In root crops, yields of storage roots are mainly de...

Cambium drives lateral growth of stems and roots, contributing to diverse plant growth forms. Root crop is one outstanding example 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 pat...

Low-temperature (LT) stress is known to restrain sugarcane productivity in sub-tropical India significantly. Many researchers have prioritized their work towards developing climateresilient sugarcane varieties through the incorporation of genome of stress-tolerant sugarcane related wild-type species in the pre-breeding program. However, the lack of...

Normalization of cDNA is widely used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Recently, long-read technology has been emerging as a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly similar transcripts and transcrip...

Background Sugarcane accumulates very high levels of sucrose in the culm. Elucidation of the molecular mechanisms that allows such high sucrose synthesis and accumulation (up to 650 mM) is made difficult by the complexity of the highly polyploid genome. Here we report the use of RNA Seq data to characterize the sucrose synthase (SuSy) genes express...

cDNA normalization is used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Long-read technology has become a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly similar transcripts and transcript-spliced isoforms. We analyze...

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 c...

Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of...

Sugarcane biomass has been used for sugar, bioenergy and biomaterial production. The majority of the sugarcane biomass comes from the culm, which makes it important to understand the genetic control of biomass production in this part of the plant. A meta-transcriptome of the culm was obtained in an earlier study by using about one billion paired-en...

Abstract Background Sugarcane is a major crop of the tropics cultivated mainly for its high sucrose content. The crop is genetically less explored due to its complex polyploid genome. Sucrose synthesis and accumulation are complex processes influenced by physiological, biochemical and genetic factors, and the growth environment. The recent focus on...

About 64% of the total aboveground biomass in sugarcane production is from the culm, of which ~90% is present in fiber and sugars. Understanding the transcriptome in the sugarcane culm, and the transcripts that are associated with the accumulation of the sugar and fiber components would facilitate the modification of biomass composition for enhance...

Differentially expressed transcripts that were annotated as photosynthesis. Log2FC was used, red color denotes the up-regulated in the bottom internodal tissues while blue color denotes the down-regulated in the bottom internodal tissue. Each heatmap is representative of one of the identified differentially expressed transcripts. (XLSX)

MapMan annotation of the DE transcripts between the top and bottom internodal tissues. (a) All genotypes, (b) Low fiber genotypes and (c) High fiber genotypes. Classification based on the MapMan annotation. PS denotes photosynthesis while CHO denotes carbohydrates. Red color indicates up-regulation while blue color indicates down-regulation in the...

MapMan annotation of the DE transcripts between the low and high fiber genotypes. (a) All tissues from all genotypes, (b) Bottom tissues from low and high fiber genotypes, (c) Top tissues from low and high fiber genotypes. The classification was based on the MapMan annotation. PS denotes photosynthesis while CHO denotes carbohydrates. Blue color in...

Percentage of transcripts annotated against MapMan functional bins of all comparisons in this study. (XLSX)

List of identified transcripts that involved in the accumulation fiber and sugar between the top and bottom tissues of sugarcane plant. (XLSX)

List of genes and primer sequences used in qPCR analysis. (XLSX)

qPCR results and correlation analysis with the RNA-Seq data. (XLSX)

Lignocellulosic biomass from sugarcane (Saccharum spp. hybrids) could potentially be a major feedstock for second-generation biofuel production. Consequently, selecting sugarcane varieties with favorable biomass characteristics, typically less enzymatic recalcitrance and better saccharification yield without sugar-yield penalty, will be important i...

Sugarcane (Saccharum spp. hybrids) is a leading industrial crop in tropical and subtropical regions worldwide. More recently, sugarcane has been selected as a key feedstock for biofuels due to its rapid growth, high fiber content and favorable energy input/output ratio. Breeding sugarcane varieties with biomass for efficient conversion to biofuels...

Analysis of the sugarcane transcriptome is complicated by the highly polyploid genome. Assembly of transcripts from short reads is especially difficult for long transcripts from closely related genes. Our objective was to establish a reference transcriptome for the key tissues of sugarcane. We used PacBio isoform sequencing (Iso-Seq) of RNA from le...

The sugarcane chloroplast genome sequence and heteroplasmy in sugarcane chloroplast was re-investigated using next generation sequencing. NGS data from total DNA of sugarcane (Saccharum spp. hybrids) cultivar Q155 was used for chloroplast genome assembly, employing a combined approach of de novo assembly and reference-based mapping. It was found th...

Background The chloroplast genome of plants has been frequently sequenced using chloroplast DNA derived by techniques involving chloroplast isolation and or by PCR amplification using primer sequences targeted to amplify the chloroplast genome. Using these approaches, chloroplast heteroplasmy, described as variations in the chloroplast sequence wit...

Sugarcane (Saccharum spp. hybrids) has great potential as a major feedstock for biofuel production worldwide. It is considered among the best options for producing biofuels today due to an exceptional biomass production capacity, high carbohydrate (sugar + fiber) content, and a favorable energy input/output ratio. To maximize the conversion of suga...

Sugarcane (Saccharum hybrid ssp.) is a leading industrial crop globally with significant use for sugar, energy and biofuel production. An available genome sequence will help to dissect and identify the genes underpining important agronomic traits in sugarcane such as biomass yield, sugar content, fiber content and disease resistance. However, sugar...