Biology subjects

Hung, T. H.

Publications and source records attributed to Hung, T. H..

7 recordsLinked to original sources

bioRxiv2025

Environmental and transcriptomic determinants of drought response in critically endangered Siamese rosewood

Rosewoods account for up to 40% of the global illegal wildlife trade, with Dalbergia cochinchinensis (Siamese rosewood) being the most heavily exploited species in Southeast Asia. Its survival is further threatened by intensifying drought linked to climate change and hydrological alteration. Here we combine greenhouse drought experiments across six provenances with full-length cDNA-seq to uncover how water-relations and carbon-use strategies vary within this species. Multivariate trait analysis resolves a two-dimensional isohydry space, in which a water-flux stringency axis (gs-E) is largely orthogonal to a carbon-economics axis (A-WUEi). Provenances differed strikingly, where two (KKH and DN) showed a rare E{downarrow}A{uparrow} response, achieving high WUEi and maintaining growth under drought. Contrary to expectation, precipitation of the wettest month, not the driest, predicted isohydry, indicating that wet-season conditions set a developmental and hydrological floor for later drought responses. We identified 76 drought-responsive genes and two genes associated with isohydry axes, SEOR1 and a poorly characterised Notch-like protein AT4G14746. We also detected provenance-specific isoform switches, where drought favoured a loss-of-function PRX52 isoform lacking its signal peptide in the anisohydric provenance THB, and gain-of-function isoforms of ANN3 and LTPG5 in NP. These results reveal previously hidden diversity in drought strategies, identify mechanism-related markers for screening, and provide a simple climatic lever for climate-adjusted provenancing. We reveal post-transcriptional regulation as a novel candidate substrate for local adaptation in a threatened tropical tree, directly linking ecophysiology, climate, and genomics for conservation and restoration.

ecology↗

bioRxiv2024

Genetic diversity and population structure of pedunculate oaks (Quercus robur) in Wytham Woods

O_LIGenetic diversity is fundamental for adaptation to changing environments. It is particularly important in forest trees because of their significant role in natures contribution to people. However, their genetic diversity has been significantly changed by human activities in the past centuries. C_LIO_LIThis paper investigates a focal site, the Wytham Woods, one of the most researched woodlands on Earth, and presents a population genetic study on pedunculate oaks (Quercus robur), a keystone species in the ecosystem. We characterised 210 trees with Genotyping by Sequencing (GbS) and quantified levels of genetic diversity across stands with different histories and management regimes. C_LIO_LIWe detected only a weak population structure within the 218,567 SNPs, such that most genetic variation occurred within but not among stands, which included semi-natural woodland areas and plantations aged between 200 to 50 years ago. We also observed little difference in observed and expected heterozygosity among stand types, but detected some inbreeding in the youngest plantation. We discovered 26,174 SNPs (11.98%) that were highly differentiated and under potential selection. C_LIO_LIWe suggest that the life history traits of oak contribute to its resistance against genetic erosion, which is also observed in beeches, spruces, and pines. Preference for oaks as a timber tree and the tendency to use local seed source might have resulted in the homogeneous population structure. However, tree-to-tree differences may harbour variation in putative adaptive loci. Our study contributes crucial baseline information on for conservation and management of human-modified woodlands, in addition to supporting long-term ecological studies on many other species, which depend on this keystone oak species. C_LI Societal Impact StatementOur study highlights the importance of monitoring and preserving genetic diversity in forest trees, particularly in keystone species like pedunculate oaks. Human activities, including land use changes and forestry practices, could influence their genetic diversity and potentially alter natures contribution to people. We demonstrate how understanding the genetic structure of oaks in stands ranging from semi-natural to plantations could (1) shed light on the natural history and the consequence of human activities in Wytham Woods, (2) support the many continuing, long-term ecological studies including adaptational potential in the oak population, and (3) be translated for other co-occurring species and other woodlands for effective genetic monitoring at large.

genomics↗

bioRxiv2024

Pre-implantation genome-wide methylation enables environmental adaptation in a social meso-carnivore

Many wild populations are increasingly stressed by rapid climatic change. While behavioural plasticity can enable limited tactical adaptive responses, standing genetic variation limits the species capacity to respond to climate change velocity. Epigenetic modification may provide a more rapid and plastic adaptive mechanism, but has been little studied in wild-living animals. Here we investigated CpG methylation during the pre-natal and early-life development of 95 European badger cubs between 2003 and 2011). During 10-months of delayed pre-implantation variability in precipitation between previous years February and April was the top determinant of methylation patterns among neonates, followed by mean temperature and temperature variability. Among the 4,641 significant weather-associated CpG sites, most occurred in the 47S rDNA region. Methylation of 47S rDNA was also associated with early-life weight, implying a mechanism that relays environmental stress to phenotypic stress. We also detected evidence for predictive adaptive response. Among the 1,641 CpG sites associated with early-life weight, pathways were associated with early-life growth, immune regulation, and to the development of aggression for competitive access to weather-limited food resources were over-represented. We conclude that a species epigenetics can have an important role in adaptive plasticity to environmental changes with important implications for biodiversity conservation and management.

genomics↗

bioRxiv2023

Conifers concentrate large numbers of NLR immune receptor genes on one chromosome

Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis) but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae and other gymnosperms were scanned for NLR genes using existing and customised pipelines. Discovered genes were mapped across chromosomes and linkage groups, and analysed phylogenetically for evolutionary history. Conifer genomes are characterised by dense clusters of NLR genes, highly localised on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and non-coniferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plants resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding. Plain language summaryNLR immune receptor genes are important in pest, disease and drought resistance of plants. In the giga-genomes of conifers, they concentrate on very small chromosomal regions. These regions act as important reservoirs for NLR diversity and can be used in breeding to improve the resilience of conifer trees.

genomics↗

bioRxiv2023

The invasive brown seaweed Rugulopteryx okamurae (Dictyotales, Ochrophyta) continues to expand: first record in Italy.

The brown seaweed Rugulopteryx okamurae (Dictyotales, Ochrophyta), native to the Pacific Ocean and widely distributed in Asia, has been recently recognized as an emblematic case of biological invasion by marine macroalgae in European waters. Since 2015 and from the Strait of Gibraltar, R. okamurae has rapidly spread towards Atlantic and Mediterranean coastal areas exhibiting an invasive behaviour with significant ecological and economic impacts. Here, we report by morphology and genetics the first observation of this species in Italy along the north-western coast of Sicily (Gulf of Palermo), as drifted material and an established population on Posidonia oceanica, representing its new eastern distribution limit in the Mediterranean Sea, previously established in Marseilles (France). Furthermore, we have performed with the current introduced distribution of the species a favorability distribution model for the Mediterranean, which shows most of the western Mediterranean, including the Balearic archipelago, Corsica and Sardinia, central Mediterranean, including Sicily, and the northern coast of Africa together with eastern Mediterranean basin, as highly favorable for R. okamurae. Arrival of the species into this new area is suggested by means of sea currents and maritime traffic, including fishing activities, hypothesis supported by some of the ranked variables that entered the favorability model, i.e, current velocity, and proximity of fishing ports. These results are a warning that the species can cover large sea distances favored by sea currents, thus also threatening the ecosystems and marine resources of the central and eastern Mediterranean, highly favorable regions for the species. We suggest coordinated actions at the European level regarding prevention, among which those that have the complicity of the fishing sector should be considered, both because it is a highly affected sector and because it potentially has a very important role in the dispersion of the species.

plant biology↗

bioRxiv2023

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene Betaglu-1 with large variations in white spruce but not Norway spruce

Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and {beta}glu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of {beta}glu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of {beta}glu-1 and Ugt5 genes. We observed very large copy numbers of {beta}glu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of {beta}glu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.

evolutionary biology↗

bioRxiv2023

Range-wide differential adaptation and genomic vulnerability in critically endangered Asian rosewoods

In the billion-dollar global illegal wildlife trade, rosewoods have been the worlds most trafficked wild product since 20051. Dalbergia cochinchinensis and D. oliveri are the most sought-after rosewoods in the Greater Mekong Subregion2. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic vulnerability to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance3. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on vulnerability hotspots in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change. Significant statementIn the billion-dollar global illegal wildlife trade, rosewoods have been the worlds most trafficked wild product since 2005, with Dalbergia cochinchinensis and D. oliveri being the most sought-after and endangered species in Southeast Asia. Emerging efforts for their restoration have lacked a suitable evidence base on adaptability and adaptive potential. We integrated range-wide genomic data and climate models to detect the differential adaptation between D. cochinchinensis and D. oliveri in relevance to temperature- and precipitation-related variables and projected their vulnerability until 2100. We highlighted the stronger local adaptation in the coastal edge of the species ranges suggesting conservation priority. We developed genomic resources including chromosome-level genome assemblies and a web-based application seedeR for genomic model-enabled assisted migration and restoration.

genomics↗