Biology subjects

Duong, T. A.

Publications and source records attributed to Duong, T. A..

3 recordsLinked to original sources

bioRxiv2025

Chromosome-level genome assemblies for the latent pine pathogen, Diplodia sapinea, reveal two rapidly evolving accessory chromosomes

Diplodia sapinea (Dothideomycetes) is a latent fungal pathogen with a global distribution that predominantly infects Pinus species. The impact of the fungus is increasing due to climate-driven range expansion and thus wide-scale disease outbreaks. With the aim of developing high quality genome resources, we generated chromosome-level genome assemblies for three D. sapinea isolates and low-coverage Illumina genome data for six additional isolates. By comparing these genome assemblies, we identified 14 core chromosomes and two accessory chromosomes (ACs) in the pathogen. The ACs encode 80 and 155 proteins, respectively, while 11374 - 11609 genes were identified in the core chromosomes. Both ACs had lower gene density and higher proportions of transposable elements compared to the core chromosomes. Sequence analysis indicated that genes on the ACs are rapidly evolving, suggesting they serve as evolutionary hotspots in the species. Sequence homology analyses suggested that the ACs were likely acquired horizontally, probably from a species in the Dothideomycetes. We designed PCR-based assays to aid in the detection of the ACs and applied these on a set of 37 isolates from 14 countries. One of the ACs was detected in 33 isolates from 13 countries, while the other AC was absent in all isolates tested. Pathogenicity trials on Pinus patula seedlings showed no correlation between the presence of ACs and isolate aggressiveness. The high-quality genomes provided here offer important resources for future research on this globally important pathogen, including the biological roles of the ACs.

genomics↗

bioRxiv2025

A haplotype-resolved reference genome for Eucalyptus grandis

E. grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials and biorefinery products. The current v2.0 genome reference for the species (Bartholome et al., 2015; Myburg et al., 2014) served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The two haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70 to 90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8% to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4% and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pan-genome variation in the species. Paper summaryWe assembled a haplotype-phased genome for Eucalyptus grandis that will serve as reference for the most widely planted hardwood crop globally. It includes more than 430 new gene models with long introns and has 6% higher annotation completeness. The phased assembly provides a more accurate look at genome variation at DNA and transcript level and will better support future studies of genome structure and function. The improved assembly contains more tandem duplicate genes compared to the previous unphased reference. Finally, major genomic rearrangements between the two phased genomes provide a preview of pangenome and structural variation in E. grandis.

genomics↗

bioRxiv2022

Haplotype mining panel for genetic dissection and breeding in Eucalyptus

To improve our understanding of genetic mechanisms underlying complex traits in plants, a comprehensive analysis of gene variants is required. Eucalyptus is an important forest plantation genus that is highly outbred. Trait dissection and molecular breeding in eucalypts currently relies on biallelic SNP markers. These markers fail to capture the large amount of haplotype diversity in these species and thus multi-allelic markers are required. We aimed to develop a gene-based haplotype mining panel for Eucalyptus species. We generated 17 999 oligonucleotide probe sets for targeted sequencing of selected regions of 6 293 genes implicated in growth and wood properties, pest and disease resistance and abiotic stress responses. We identified and phased 195 834 SNPs using a read-based phasing approach to reveal SNP-based haplotypes. A total of 8 915 target regions (at 4 637 gene loci) passed tests for Mendelian inheritance. We evaluated the haplotype panel in four Eucalyptus species (E. grandis, E. urophylla, E. dunnii and E. nitens) to determine its ability to capture diversity across eucalypt species. This revealed an average of 3.13 to 4.52 haplotypes per target region in each species and 33.36% of the identified haplotypes were shared by at least two species. This haplotype mining panel will enable the analysis of haplotype diversity within and between species and provide multi-allelic markers that can be used for genome-wide association studies and gene-based breeding approaches. Significance StatementWe developed a haplotype sequencing panel for Eucalyptus targeting 8915 regions at 4637 gene loci associated with growth and wood properties, pest and disease resistance and abiotic stress response providing a genome-wide, multi-allelic, gene centric genotyping resource for eucalypts. We tested the panel in four Eucalyptus species (E. grandis, E. dunnii, E. nitens and E. urophylla) and found an average of 3.65 haplotypes per target region per species, and 9.98 across all four species.

genetics↗