Minh Thiet Vu

Khang Dan 18 (KD18) is an Oryza sativa L. subsp. indica rice cultivar widely cultivated in northern Vietnam and used as an experimental and breeding background in Vietnamese rice research. Although KD18 has previously been represented in low-depth population resequencing datasets, a contiguous and annotated cultivar-specific genome has not been available. Here, we report a chromosome-scale genome assembly of KD18 generated using Oxford Nanopore long-read and Illumina short-read sequencing. The 395.3-Mb assembly comprises 12 chromosome-scale pseudomolecules containing approximately 95% of the assembled sequence and 99.6% of the predicted protein-coding genes. The assembly showed 97.2% BUSCO completeness, an average Merqury quality value of 46 and a long terminal repeat assembly index of 13.21. A total of 56,546 protein-coding genes representing 71,237 transcripts were predicted, with 99% BUSCO and 98.68% OMArk completeness. These statistics are similar to those of other high-quality genome assemblies that were recently published for different Asian rice cultivars, therefore providing a cultivar-specific genomic resource for research involving KD18 and KD18-derived materials.

Cracking is a major cause of concrete deterioration because it allows water and aggressive ions to penetrate the material and accelerate structural damage. Microbially induced calcite precipitation (MICP) has emerged as a promising strategy for crack repair because selected bacteria can precipitate calcium carbonate and thereby seal damaged regions. In this study, we characterized strain ITBMC36, a calcite-precipitating bacterium isolated from a limestone-rich environment in Vietnam, and evaluated its potential for MICP-based crack repair. Strain ITBMC36 produced 26.73 ± 0.81 g/L of mineral precipitate in B4 medium. Mineral characterization showed that the precipitate consisted mainly of calcite, with minor amounts of vaterite and aragonite. Enzymatic assays showed urease activity of 35.71 ± 1.24 U/mL and carbonic anhydrase activity of 1.627 ± 0.010 U/mL. Hybrid genome sequencing generated a complete circular chromosome of 4,410,549 bp, and genome-based taxonomic analysis identified the isolate as Bacillus paralicheniformis. Genome mining revealed traits relevant to MICP and survival in cementitious environments, including a complete urea uptake and urease system, five putative carbonic anhydrase genes, exopolysaccharide and biofilm-associated loci, and multiple genes involved in stress response, pH homeostasis, and sporulation. In mortar specimens containing artificial microcracks (0.5 ± 0.1 mm), ITBMC36 promoted progressive crack closure, with visible mineral deposition by day 7 and near-complete sealing by day 35. Together, these results identify B. paralicheniformis ITBMC36 as a promising, locally sourced bacterium for MICP-based crack repair and provide a high-quality genome resource for future optimization of bio-based cementitious materials.

Animal mitogenomes are often portrayed as compact and conservative, and our hybrid Illumina–Oxford Nanopore Assembly of the southern giant hornet (Vespa soror) resolved a 22 046 bp circular mitogenome with the expected gene complement and conserved order. Phylogenetic analyses of the 13 protein-coding genes recovered V. soror in its expected position within Vespa, clustering with Vespa mandarinia. Against this canonical backdrop, we have identified two large repeat systems. The control region carried six long tandem repeats, mirroring expansions in the related hornets. More strikingly, the conserved trnY–trnI–trnM–trnQ block contained a head-to-tail array of three 209 bp cassettes, each encoding a functional trnM, yielding four trnM genes in total, which is unique among Vespa. Sequence context and DNA-mode folding indicate that each cassette was a chimaera derived from the ancestral trnI–trnM–trnQ block, with a trnQ-derived fragment forming a stable hairpin. We propose that a microhomology-mediated template switch, enabled by key 8 bp microhomology (ATTTTTAT) occurring at the trnY/trnQ boundaries, seeded the first block insertion, followed by slipped-strand mispairing that expanded the tandem array. Together, these results provide a mechanism-backed example of genic repeat formation in an animal mitogenome and underscore the value of long-read sequencing in revealing hidden mitochondrial architectures.

We report the complete genome of calcite-precipitating Cytobacillus kochii strain ITBMC_116, isolated from limestone karst in Vietnam. Hybrid Illumina–Nanopore sequencing yielded a 4.83-Mbp chromosome and an 87.4-kbp plasmid. This resource supports studies of microbially induced calcite precipitation and biomineralization-based biotechnologies.

Ludwigia peruviana (L.) H.Hara 1953, a member of the Onagraceae, exhibits diverse potential applications, yet genomic resources – particularly chloroplast (cp) genome data – remain limited. Here, we sequenced and characterized the complete cp genome of L. peruviana, which was 158,938 bp in length and encoded 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. Phylogenetic analyses indicate a close relationship between L. peruviana and Ludwigia hyssopifolia. These results provide a useful genetic resource for further phylogenetic and taxonomic investigations of Ludwigia and Onagraceae, contributing to a more comprehensive understanding of their relationships.

Background The family Bagridae, a diverse catfish group, is known for its taxonomic complexity, wherein evolutionary relationships are often obscured by morphological convergence. The Asian Bumblebee Catfish, Pseudomystus siamensis (Regan, 1913), endemic to the Mekong and Chao Phraya River basins, exemplifies this ambiguity. Its phylogenetic position has remained uncertain due to limited molecular data, hindering taxonomic clarity and conservation planning. Methods and results To resolve the phylogenetic placement of P. siamensis, we sequenced its complete mitogenome using Oxford Nanopore Technologies. The circular mitogenome is 16,525 bp long and contains the canonical 37 vertebrate genes. A maximum-likelihood phylogeny built from a concatenated dataset of 13 protein-coding genes across 40 bagrid species robustly placed P. siamensis as a distinct lineage sister to the large, paraphyletic East Asian assemblage comprising Tachysurus, Pseudobagrus, Leiocassis, and Pelteobagrus. To test the monophyly of Pseudomystus, we conducted a second analysis using the cytochrome b gene that included two congeners. This analysis recovered Pseudomystus species as a strongly supported monophyletic group. Conclusion This study provides the first mitogenomic-scale placement of P. siamensis, definitively refuting earlier hypotheses that allied it with Hemibagrus and Mystus. We also provide the first molecular evidence supporting the monophyly of Pseudomystus. Our findings reinforce the widespread paraphyly of several East Asian bagrid genera, highlighting an urgent need for formal taxonomic revision. The mitogenome presented here is a useful genomic resource for future systematic and conservation studies in Bagridae.

The genus Aquilaria (Thymelaeaceae) is renowned for producing agarwood, a highly valuable resinous product of significant economic and cultural value. Yet, many of its species, including the endemic Aquilaria banaense from Vietnam, face conservation challenges due to overexploitation. This study presents the first complete chloroplast (cp) genome of A. banaense to investigate its genome structure, evolutionary characteristics, and phylogenetic position. The cp genome of A . banaense was 174,810 bp, exhibiting a typical quadripartite structure with a large single‐copy (LSC) region (87,264 bp), a small single‐copy (SSC) region (3342 bp), and two inverted repeat (IR) regions (42,102 bp), encoding unique 79 protein‐coding genes, 30 tRNA genes, and four rRNA genes. Comparative analysis across Aquilaria species revealed conserved genomic features, including IR expansion into the SSC region, absence of clpP1 introns, alongside moderate nucleotide divergent regions (such as matK ‐ rps16 , petN‐trnT‐GGU , rps4‐ndhJ , and ndhF‐rpl32 ) and a distinct accD variant in A. banaense . Phylogenetic reconstruction using whole cp genomes of 13 Aquilaria species placed A. banaense sister to mainland Southeast Asian species like A. crassna and A. subintegra , clearly separated from insular Southeast Asian groups. The correlation between phylogenetic structure and geographic distribution suggests that historical biogeography and ecological factors have driven lineage divergence in Aquilaria . These findings highlight the genetic distinctiveness of A. banaense and provide valuable genetic resources for species identification and conservation planning for this vulnerable species.

The genus Pithecellobium Mart. (Caesalpinioideae, Fabaceae) plays vital ecological roles, including nitrogen fixation and habitat stabilization, and holds significant medicinal and economic values. However, its genetic diversity and evolutionary relationships remain poorly understood. This study presents the first complete chloroplast (cp.) genome of Pithecellobium dulce (Roxb.) Benth., a widely distributed tropical tree. The complete cp. genome was assembled de novo using NOVOPlasty and annotated with GeSeq and Geneious Prime. Repeat elements and codon usage analyses were analyzed using REPuter, Phobos, and Geneious Prime. Comparative genomic analyses included structural comparisons, IR expansion/contraction, and nucleotide divergence. Phylogenetic relationships were inferred from protein-coding genes using IQ-TREE and MrBayes, with divergence times estimated via BEAST2. The cp. genome of P. dulce was 179,483 bp long, exhibiting a typical quadripartite structure with a large single-copy (LSC) region of 91,513 bp, a small single-copy (SSC) region of 4,560 bp, and two inverted repeat regions (IRs) of 41,705 bp each. It encoded 142 genes, including 97 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis revealed a conserved genomic structure within the Pithecellobium subclade, with notable IR expansion into SSC and LSC regions. Phylogenetic analysis placed P. dulce within the Pithecellobium subclade, closely related to Ebenopsis ebano Britton & Rose and Havardia acatlensis (Benth.) Britton & Rose. Divergence time estimates suggest that Pithecellobium subclade diverged in the late Miocene (~ 29.96 Ma), with P. dulce and E. ebano separating around 16.79 Ma. This study provides an essential genomic resource for resolving phylogenetic relationships and advancing taxonomic research in Caesalpinioideae.