Environmental DNA (eDNA) metabarcoding is a valuable tool for assessing aquatic biodiversity, but the high cost and complexity of DNA extraction pose challenges for widespread adoption, especially in developing countries. This study presents a cost-effective eDNA extraction method using a guanidine hydrochloride (GuHCl) buffer, proteinase-K digestion, and isopropanol precipitation to improve the detection of fish communities. Comparison with the Qiagen DNeasy Blood & Tissue Kit using MiFish universal primers showed that the GuHCl protocol detected more fish species in freshwater samples, with comparable performance in relative read abundance metrics. However, the GuHCl method exhibited higher PCR inhibition in brackish samples, likely due to salinity and natural inhibitors. The results suggest that the GuHCl-based method is a viable alternative, offering enhanced sensitivity for low-abundance species in freshwater samples and cost savings. This protocol facilitates large-scale eDNA metabarcoding for ecological studies and conservation management efforts.•The GuHCl protocol identified a greater diversity of fish species in freshwater samples than the Qiagen kit, but detected fewer species in brackish water samples.•Both extraction methods demonstrated robust positive correlations in metrics of relative read abundance.
Prior to this study, the mitogenomic characterization, genetic diversity, and phylogenetic placement of the Tinfoil Barb Barbonymus schwanefeldii remained largely unexplored, despite its notable ecological and economic importance. Hence, this study aimed to provide the first in-depth insight into the mitogenomic features of this species from its native range in Sumatra, Indonesia. The generated mitogenome is 16,578 bp in length and contains 37 genes along with a control region (CR). The genome also exhibited a 57.03% A + T bias and all protein-coding genes (PCGs) initiated with the ATG codon, except COI (GTG). The codon usage was dominated by arginine, leucine, and serine, whereas methionine and tryptophan were rare. The pairwise nonsynonymous-to-synonymous substitution ratios demonstrated strong purifying selection across all Barbonymus species. This pattern was further supported by complementary codon-based approaches, which showed that the 13 PCGs were predominantly subject to strong evolutionary constraints, with evidence of positive selection confined to a small number of sites in a limited subset of genes. Most transfer RNA genes of B. schwanefeldii maintained the canonical cloverleaf secondary structure, except tRNA-Ser1, which lacked the dihydrouridine stem. The comparative profiling of conserved sequence blocks within the CR among Barbonymus taxa highlighted variation in length and nucleotide composition, with tandem repeats exclusively detected in B. gonionotus. A mitogenome-wide assessment of B. schwanefeldii revealed considerable intra-specific genetic divergence (0%-3.932%) and notable haplotypic diversity across Southeast Asian islands and mainland populations. This population genetic structure likely reflects historical connectivity during the Pleistocene via ancient drainage systems of the Malacca Strait or North Sunda, followed by subsequent isolation after post-glacial eustatic sea-level rise. The phylogenetic inference robustly corroborated a sister-species relationship between B. schwanefeldii and Barbonymus altus within the clade 'Poropuntiinae'. Collectively, these findings elucidate the phylogeographic patterns and evolutionary history of this Southeast Asian endemic cyprinid fish within the Sundaland biodiversity hotspot.
In this surveillance study, we identified the genotypes, carbapenem resistance determinants, and structural variations of AbaR-type resistance islands among carbapenem-resistant Acinetobacter baumannii (CRAB) isolates from nine Asian locales. Clonal complex 92 (CC92), corresponding to global clone 2 (GC2), was the most prevalent in most Asian locales (83/108 isolates; 76.9%). CC108, or GC1, was a predominant clone in India. OXA-23 oxacillinase was detected in CRAB isolates from most Asian locales except Taiwan. blaOXA-24 was found in CRAB isolates from Taiwan. AbaR4-type resistance islands, which were divided into six subtypes, were identified in most CRAB isolates investigated. Five isolates from India, Malaysia, Singapore, and Hong Kong contained AbaR3-type resistance islands. Of these, three isolates harbored both AbaR3- and AbaR4-type resistance islands simultaneously. In this study, GC2 was revealed as a prevalent clone in most Asian locales, with the AbaR4-type resistance island predominant, with diverse variants. The significance of this study lies in identifying the spread of global clones of carbapenem-resistant A. baumannii in Asia.