Displaying publications 1 - 20 of 175 in total

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  1. Fulltext Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing
    Mat-Hussin NH, Siew SW, Maghpor MN, Gan HM, Ahmad HF
    MethodsX, 2024 Jun;12:102636.
    PMID: 38439930 DOI: 10.1016/j.mex.2024.102636
    The exposure of the air microbiome in indoor air posed a detrimental health effect to the building occupants compared to the outdoor air. Indoor air in hospitals has been identified as a reservoir for various pathogenic microbes. The conventional culture-dependent method has been widely used to access the microbial community in the air. However, it has limited capability in enumerating the complex air microbiome communities, as some of the air microbiomes are uncultivable, slow-growers, and require specific media for cultivation. Here, we utilized a culture-independent method via amplicon sequencing to target the V3 region of 16S rRNA from the pool of total genomic DNA extracted from the dust samples taken from hospital interiors. This method will help occupational health practitioners, researchers, and health authorities to efficiently and comprehensively monitor the presence of harmful air microbiome thus take appropriate action in controlling and minimizing the health risks to the hospital occupants. Key features;•Culture-independent methods offer fast, comprehensive, and unbias profiles of pathogenic and non-pathogenic bacteria from the air microbiomes.•Unlike the culture-dependent method, amplicon sequencing allows bacteria identification to the lowest taxonomy levels.
  2. Fulltext Whole-genome sequencing of four culturable endophytic bacteria from German hardneck garlic cloves (Allium sativum L.)
    Kumar G, Gan HM, Wengert P, Penix T, Parthasarathy A, Hudson AO, et al.
    Microbiol Resour Announc, 2024 Apr 11;13(4):e0122523.
    PMID: 38470029 DOI: 10.1128/mra.01225-23
    We present the whole-genome sequence of four bacterial endophytes associated with German hardneck garlic cloves (Allium sativum L.). Among them, Agrobacterium fabrum and Pantoea agglomerans are associated with plant protection, while Rahnella perminowiae and Stenotrophomonas lactitubi are pathogens. These data will facilitate the identification of genes to improve garlic.
  3. Fulltext Nanopore sequencing for identification and characterization of antimicrobial-resistant Escherichia coli and Salmonella spp. from tilapia and shrimp sold at wet markets in Dhaka, Bangladesh
    Rheman S, Hossain S, Sarker MS, Akter F, Khor L, Gan HM, et al.
    Front Microbiol, 2024;15:1329620.
    PMID: 38516018 DOI: 10.3389/fmicb.2024.1329620
    Wet markets in low-and middle-income countries are often reported to have inadequate sanitation resulting in fecal contamination of sold produce. Consumption of contaminated wet market-sourced foods has been linked to individual illness and disease outbreaks. This pilot study, conducted in two major wet markets in Dhaka city, Bangladesh during a 4-month period in 2021 aimed to assess the occurrence and characteristics of Escherichia coli and non-typhoidal Salmonella spp. (NTS) from tilapia (Oreochromis niloticus) and shrimp (Penaeus monodon). Fifty-four individuals of each species were collected. The identity of the bacterial isolates was confirmed by PCR and their susceptibility toward 15 antimicrobials was tested by disk diffusion. The whole genome of 15 E. coli and nine Salmonella spp. were sequenced using Oxford Nanopore Technology. E. coli was present in 60-74% of tilapia muscle tissue and 41-44% of shrimp muscle tissue. Salmonella spp. was found in skin (29%) and gills (26%) of tilapia, and occasionally in muscle and intestinal samples of shrimp. The E. coli had several Multilocus sequence typing and serotypes and limited antimicrobial resistance (AMR) determinants, such as point mutations on glpT and pmrB. One E. coli (BD17) from tilapia carried resistance genes for beta-lactams, quinolones, and tetracycline. All the E. coli belonged to commensal phylogroups B1 and A and showed no Shiga-toxin and other virulence genes, confirming their commensal non-pathogenic status. Among the Salmonella isolates, five belonged to Kentucky serovar and had similar AMR genes and phenotypic resistance patterns. Three strains of this serovar were ST198, often associated with human disease, carried the same resistance genes, and were genetically related to strains from the region. The two undetermined sequence types of S. Kentucky were distantly related and positioned in a separate phylogenetic clade. Two Brunei serovar isolates, one Augustenborg isolate, and one Hartford isolate showed different resistance profiles. This study revealed high fecal contamination levels in tilapia and shrimp sold at two main wet markets in Dhaka. Together with the occurrence of Salmonella spp., including S. Kentucky ST198, a well-known human pathogen, these results stress the need to improve hygienic practices and sanitation standards at markets to improve food safety and protect consumer health.
  4. Fulltext A multiplexed RT-PCR assay for nanopore whole genome sequencing of Tilapia lake virus (TiLV)
    Delamare-Deboutteville J, Meemetta W, Pimsannil K, Sangpo P, Gan HM, Mohan CV, et al.
    Sci Rep, 2023 Nov 20;13(1):20276.
    PMID: 37985860 DOI: 10.1038/s41598-023-47425-w
    Tilapia lake virus (TiLV) is a highly contagious viral pathogen that affects tilapia, a globally significant and affordable source of fish protein. To prevent the introduction and spread of TiLV and its impact, there is an urgent need for increased surveillance, improved biosecurity measures, and continuous development of effective diagnostic and rapid sequencing methods. In this study, we have developed a multiplexed RT-PCR assay that can amplify all ten complete genomic segments of TiLV from various sources of isolation. The amplicons generated using this approach were immediately subjected to real-time sequencing on the Nanopore system. By using this approach, we have recovered and assembled 10 TiLV genomes from total RNA extracted from naturally TiLV-infected tilapia fish, concentrated tilapia rearing water, and cell culture. Our phylogenetic analysis, consisting of more than 36 TiLV genomes from both newly sequenced and publicly available TiLV genomes, provides new insights into the high genetic diversity of TiLV. This work is an essential steppingstone towards integrating rapid and real-time Nanopore-based amplicon sequencing into routine genomic surveillance of TiLV, as well as future vaccine development.
  5. Endophytic bacteria associated with wild-type banana seed (Musa balbisiana): whole genome sequencing
    Kumar G, Gan HM, Popielarz H, Steele J, Parthasarathy A, Hudson AO, et al.
    Microbiol Resour Announc, 2023 Nov 03.
    PMID: 37921458 DOI: 10.1128/MRA.00650-23
    We present the whole-genome sequences of five endophytic bacteria isolated from Musa balbisiana seeds. These strains represent five different genera: Bacillus, Brachybacterium, Enterobacter, Enterococcus, and Pantoea. Among these, three genera (Bacillus, Pantoea, and Enterobacter) were previously recognized for their antagonistic effects against Fusarium wilt, a highly destructive disease that affects banana plants.
  6. Whole-Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides
    Kho CJY, Lau MML, Chung HH, Chew IYY, Gan HM
    Curr Microbiol, 2023 Jun 25;80(8):255.
    PMID: 37356021 DOI: 10.1007/s00284-023-03354-5
    Unlike environmental P. koreensis isolated from soil, which has been studied extensively for its role in promoting plant growth, pathogenic P. koreensis isolated from fish has been rarely reported. Therefore, we investigated and isolated the possible pathogen that is responsible for the diseased state of Tor tambroides. Herein, we reported the morphological and biochemical characteristics, as well as whole-genome sequences of a newly identified P. koreensis strain. We assembled a high-quality draft genome of P. koreensis CM-01 with a contig N50 value of 233,601 bp and 99.5% BUSCO completeness. The genome assembly of P. koreensis CM-01 is consists of 6,171,880 bp with a G+C content of 60.5%. Annotation of the genome identified 5538 protein-coding genes, 3 rRNA genes, 54 tRNAs, and no plasmids were found. Besides these, 39 interspersed repeat and 141 tandem repeat sequences, 6 prophages, 51 genomic islands, 94 insertion sequences, 4 clustered regularly interspaced short palindromic repeats, 5 antibiotic-resistant genes, and 150 virulence genes were also predicted in the P. koreensis CM-01 genome. Culture-based approach showed that CM-01 strain exhibited resistance against ampicillin, aztreonam, clindamycin, and cefoxitin with a calculated multiple antibiotic resistance (MAR) index value of 0.4. In addition, the assembled CM-01 genome was successfully annotated against the Cluster of Orthologous Groups of proteins database, Gene Ontology database, and Kyoto Encyclopedia of Genes and Genome pathway database. A comparative analysis of CM-01 with three representative strains of P. koreensis revealed that 92% of orthologous clusters were conserved among these four genomes, and only the CM-01 strain possesses unique elements related to pathogenicity and virulence. This study provides fundamental phenotypic and genomic information for the newly identified P. koreensis strain.
  7. Fulltext Whole-Genome Sequence of Endophytic Bacteria Associated with Poison Ivy Vine (Toxicodendron radicans)
    Gan HM, Penix TS, Wengert PC, Wong NH, Hudson AO, Kumar G, et al.
    Microbiol Resour Announc, 2023 Apr 18;12(4):e0123222.
    PMID: 36920211 DOI: 10.1128/mra.01232-22
    Here, we report the genome assemblies of 11 endophytic bacteria, isolated from poison ivy vine (Toxicodendron radicans). Five species belonging to the genus Pseudomonas, two species of Curtobacterium, one strain of Pantoea agglomerans, and one species from the Bacillus, Cellulomonas, and Enterobacter genera were isolated from the interior tissue of poison ivy.
  8. Fulltext Complete chloroplast genome data of Shorea macrophylla (Engkabang): Structural features, comparative and phylogenetic analysis
    Chew IYY, Chung HH, Lim LWK, Lau MML, Gan HM, Wee BS, et al.
    Data Brief, 2023 Apr;47:109029.
    PMID: 36936629 DOI: 10.1016/j.dib.2023.109029
    Shorea macrophylla belongs to the Shorea genus under the Dipterocarpaceae family. It is a woody tree that grows in the rainforest in Southeast Asia. The complete chloroplast (cp) genome sequence of S. macrophylla is reported here. The genomic size of S. macrophylla is 150,778 bp and it possesses a circular structure with conserved constitute regions of large single copy (LSC, 83,681 bp) and small single copy (SSC, 19,813 bp) regions, as well as a pair of inverted repeats with a length of 23,642 bp. It has 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The genome exhibits a similar GC content, gene order, structure, and codon usage when compared to previously reported chloroplast genomes from other plant species. The chloroplast genome of S. macrophylla contained 262 SSRs, the most prevalent of which was A/T, followed by AAT/ATT. Furthermore, the sequences contain 43 long repeat sequences, practically most of them are forward or palindrome type long repeats. The genome structure of S. macrophylla was compared to the genomic structures of closely related species from the same family, and eight mutational hotspots were discovered. The phylogenetic analysis demonstrated a close relationship between Shorea and Parashorea species, indicating that Shorea is not monophyletic. The complete chloroplast genome sequence analysis of S. macrophylla reported in this paper will contribute to further studies in molecular identification, genetic diversity, and phylogenetic research.
  9. Fulltext The complete mitochondrial genomes of Pangasius nasutus and P. conchophilus (Siluriformes: Pangasiidae)
    Abdul Halim SAA, Esa Y, Gan HM, Zainudin AA, Mohd Nor SA
    Mitochondrial DNA B Resour, 2023;8(1):38-41.
    PMID: 36620317 DOI: 10.1080/23802359.2022.2158694
    The catfish, Pangasius nasutus and P. conchophilus, are often misidentified between each other due to their similar morphology. Thus, the current study was conducted to differentiate them based on a molecular approach. The complete mitochondrial genomes of P. nasutus and P. conchophilus obtained from the Pahang River (Peninsular Malaysia) were sequenced, assembled, and annotated using next-generation sequencing (NGS). A 16,465 bp and 16,470 bp length mitogenome sequence of P. nasutus and P. conchophilus, respectively, was generated, each containing 13 protein genes, 22 tRNAs, and two rRNAs, typical of most vertebrates. This is the first report of the complete mitochondrial genome sequences of P. nasutus and P. conchophilus. These data are a valuable genetic resource for future studies of these two commercially important species.
  10. Fulltext Characterization of the complete mitochondrial genome of the critically endangered Southern River Terrapin, Batagur affinis affinis (Reptilia: Geoemydidae)
    Mohd Salleh MH, Esa Y, Gan HM
    Mitochondrial DNA B Resour, 2023;8(7):719-722.
    PMID: 37426572 DOI: 10.1080/23802359.2023.2222851
    In this study, we report the nearly complete mitochondrial sequence of Batagur affinis affinis. The assembled mitogenome consists of 13 PCGs, 22 tRNA genes, two rRNAs and one near-complete D-loop region. Of the annotated genes, the ND6 subunit gene and eight tRNA genes were encoded on the L-strand, while the remaining genes were dispersed on the H-strand. Except for CO1, which has a GTG start codon, all protein-coding genes begin with ATG. The mitogenome has been deposited in NCBI GenBank under the accession number OQ409915. Phylogenetic tree analysis based on publicly available mitogenomes indicate the sister grouping of B. affinis affinis with B. kachuga.
  11. Fulltext Genome sequence dataset of Bacillus altitudinis strain ST14 isolated from Tunggak River in Gebeng Industrial Park, Kuantan, Pahang
    Aziz AA, Zulbahri AS, Sharif MF, Mohamad MAN, Gan HM, Azizan NH
    Data Brief, 2022 Dec;45:108718.
    PMID: 36624876 DOI: 10.1016/j.dib.2022.108718
    Bacillus sp. has been reported to be involved in the biodegradation of various hydrocarbon pollutants which can potentially be useful in cleaning up hydrocarbon pollutants. Here we report the draft genome of Bacillus altitudinis strain ST14 isolated from Tunggak river, Gebeng, Kuantan, an area in close proximity to industrial activities. Genome sequencing was conducted using Illumina NovaSEQ 6000 technology. Structural genes in the genome were described, including rRNAs, tRNAs, and ncRNAs. Bacillus altitudinis strain ST14 was sequenced with a length of 3,801,811 bp containing 3,891 coding sequences (CDS). Functional gene annotation reported the presence of six enzymes involved in the degradation of aromatic compounds often found in hydrocarbon pollutants.
  12. A new set of microsatellite markers for Phoxinus lumaireul senso lato, Phoxinus marsilii and Phoxinus krkae for population and molecular taxonomic studies
    Vucić M, Jelić M, Klobučar G, Jelić D, Gan HM, Austin C, et al.
    J Fish Biol, 2022 Nov;101(5):1225-1234.
    PMID: 36054289 DOI: 10.1111/jfb.15194
    Minnows of the genus Phoxinus are common and an often highly abundant fish species in Palearctic freshwater habitats. Phoxinus species have a complex evolutionary history, phylogenetic relationships are not well understood and there are a number of unresolved taxonomic problems. There are currently 23 different mitochondrial genetic lineages identified in the genus Phoxinus, 13 of which are recognized as valid species. The taxonomic status of these lineages requires resolution, including the degree to which they can interbreed. Suitable nuclear molecular markers for studies of population divergence and interbreeding between morphotypes and mitochondrial lineages are lacking for Phoxinus species. Therefore, the authors developed a set of microsatellite markers using genomic information from Phoxinus lumaireul and tested their suitability for this and two related species, Phoxinus krkae and Phoxinus marsilii. Out of 16 microsatellite candidate loci isolated, 12 were found to be in Hardy-Weinberg equilibrium when tested on two P. lumaireul senso lato populations. Seven loci amplified across the three species, enabling the study of intraspecific genetic diversity and population structure within P. marsilii and P. krkae. The markers were able to clearly resolve differences among the three tested species, including the recently described P. krkae, and are therefore suitable for the detection of introgression and hybridization among populations consisting of mixtures of two or more of P. lumaireul s. l., P. marsilii and P. krkae.
  13. Fulltext Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda)
    Taheri S, Teo CH, Heslop-Harrison JS, Schwarzacher T, Tan YS, Wee WY, et al.
    Int J Mol Sci, 2022 Jun 30;23(13).
    PMID: 35806276 DOI: 10.3390/ijms23137269
    Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is assembled as 27,491 contigs with an N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has a 72% repeat content, with class I TEs occupying ~67% of the assembled genome. Fluorescence in situ hybridization of the 18 chromosome pairs at the metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. An SSR analysis identified 238,441 gSSRs and 4604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in the leaf to 53% CpG, 18% CHG and 25% CHH in the embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in the watery callus. B rotunda has a relatively large genome with a high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers.
  14. Fulltext Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater
    Robledo-Ruiz DA, Gan HM, Kaur P, Dudchenko O, Weisz D, Khan R, et al.
    Gigascience, 2022 Mar 29;11.
    PMID: 35348671 DOI: 10.1093/gigascience/giac025
    BACKGROUND: The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required.

    RESULTS: We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene.

    CONCLUSIONS: The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.

  15. Fulltext First high-quality genome assembly data of sago palm (Metroxylon sagu Rottboll)
    Lim LWK, Lau MML, Chung HH, Hussain H, Gan HM
    Data Brief, 2022 Feb;40:107800.
    PMID: 35059482 DOI: 10.1016/j.dib.2022.107800
    The sago palm (Metroxylon sagu Rottboll) is a tropical halophytic starch-producing, economically important crop palm mainly located in Southeast Asian countries. Recently, a genome survey was conducted on this palm using the Illumina sequencing platform, with a very low (21.5%) BUSCO genome completeness score, and most of them (∼78%) are either fragmented or missing. Thus, in this study, the sago palm genome completeness was further improved with the utilization of the Nanopore sequencing platform that produced longer reads. A hybrid genome assembly was conducted, and the outcome was a much complete sago palm genome with BUSCO completeness achieved at as high as 97.9%, with only ∼2% of them either fragmented or missing. The estimated genome size of the sago palm is 509,812,790 bp in this study. A sum of 33,242 protein-coding genes was revealed from the sago palm genome and around 96.39% of them had been functionally annotated. An investigation on the carbohydrate metabolism KEGG pathways also unearthed that starch synthesis was one of the major sago palm activities. The genome data obtained from this work is indispensable for future molecular evolutionary and genome-wide association studies on the economically important sago palm.
  16. Labile sex chromosomes in the Australian freshwater fish family Percichthyidae
    Pavlova A, Harrisson KA, Turakulov R, Lee YP, Ingram BA, Gilligan D, et al.
    Mol Ecol Resour, 2021 Dec 04.
    PMID: 34863023 DOI: 10.1111/1755-0998.13569
    Sex-specific ecology has management implications, but rapid sex-chromosome turnover in fishes hinders sex-marker development for monomorphic species. We used annotated genomes and reduced-representation sequencing data for two Australian percichthyids, Macquarie perch Macquaria australasica and golden perch M. ambigua, and whole genome resequencing for 50 Macquarie perch of each sex, to identify sex-linked loci and develop an affordable sexing assay. In silico pool-seq tests of 1,492,004 Macquarie perch SNPs revealed that a 275-kb scaffold was enriched for gametologous loci. Within this scaffold, 22 loci were sex-linked in a predominantly XY system, with females being homozygous for the X-linked allele at all 22, and males having the Y-linked allele at >7. Seven XY-gametologous loci (all males, but no females, are heterozygous or homozygous for the male-specific allele) were within a 146-bp region. A PCR-RFLP sexing assay targeting one Y-linked SNP, tested in 66 known-sex Macquarie perch and two of each sex of three confamilial species, plus amplicon sequencing of 400 bp encompassing the 146-bp region, revealed that the few sex-linked positions differ between species and between Macquarie perch populations. This indicates sex-chromosome lability in Percichthyidae, supported by nonhomologous scaffolds containing sex-linked loci for Macquarie- and golden perches. The present resources facilitate genomic research in Percichthyidae, including formulation of hypotheses about candidate genes of interest such as transcription factor SOX1b that occurs in the 275-kb scaffold ~38 kb downstream of the 146-bp region containing seven XY-gametologous loci. Sex-linked markers will be useful for determining genetic sex in some populations and studying sex chromosome turnover.
  17. The first transcriptome sequencing and data analysis of the Javan mahseer (Tor tambra)
    Lau MML, Lim LWK, Chung HH, Gan HM
    Data Brief, 2021 Dec;39:107481.
    PMID: 34712757 DOI: 10.1016/j.dib.2021.107481
    The Javan mahseer (Tor tambra) is one of the most valuable freshwater fish found in Tor species. To date, other than mitogenomic data (BioProject: PRJNA422829), genomic and transcriptomic resources for this species are still lacking which is crucial to understand the molecular mechanisms associated with important traits such as growth, immune response, reproduction and sex determination. For the first time, we sequenced the transcriptome from a whole juvenile fish using Illumina NovaSEQ6000 generating raw paired-end reads. De novo transcriptome assembly generated a draft transcriptome (BUSCO5 completeness of 91.2% [Actinopterygii_odb10 database]) consisting of 259,403 putative transcripts with a total and N50 length of 333,881,215 bp and 2283 bp, respectively. A total count of 77,503 non-redundant protein coding sequences were predicted from the transcripts and used for functional annotation. We mapped the predicted proteins to 304 known KEGG pathways with signal transduction cluster having the highest representation followed by immune system and endocrine system. In addition, transcripts exhibiting significant similarity to previously published growth-and immune-related genes were identified which will facilitate future molecular breeding of Tor tambra.
  18. Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing
    Delamare-Deboutteville J, Taengphu S, Gan HM, Kayansamruaj P, Debnath PP, Barnes A, et al.
    J Fish Dis, 2021 Oct;44(10):1491-1502.
    PMID: 34101853 DOI: 10.1111/jfd.13467
    Infectious diseases represent one of the major challenges to sustainable aquaculture production. Rapid, accurate diagnosis and genotyping of emerging pathogens during early-suspected disease cases is critical to facilitate timely response to deploy adequate control measures and prevent or reduce spread. Currently, most laboratories use PCR to amplify partial pathogen genomic regions, occasionally combined with sequencing of PCR amplicon(s) using conventional Sanger sequencing services for confirmatory diagnosis. The main limitation of this approach is the lengthy turnaround time. Here, we report an innovative approach using a previously developed specific PCR assay for pathogen diagnosis combined with a new Oxford Nanopore Technologies (ONT)-based amplicon sequencing method for pathogen genotyping. Using fish clinical samples, we applied this approach for the rapid confirmation of PCR amplicon sequences identity and genotyping of tilapia lake virus (TiLV), a disease-causing virus affecting tilapia aquaculture globally. The consensus sequences obtained after polishing exhibit strikingly high identity to references derived by Illumina and Sanger methods (99.83%-100%). This study suggests that ONT-based amplicon sequencing is a promising platform to deploy in regional aquatic animal health diagnostic laboratories in low- and medium-income countries, for fast identification and genotyping of emerging infectious pathogens from field samples within a single day.
  19. Fulltext Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia
    Zainulabid UA, Kamarudin N, Zulkifly AH, Gan HM, Tay DD, Siew SW, et al.
    Microbiol Resour Announc, 2021 Aug 05;10(31):e0065721.
    PMID: 34351228 DOI: 10.1128/MRA.00657-21
    Here, we report the nearly complete genome sequences of nine severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the D614G mutation. These viruses were detected from various infected individuals with different levels of severity from Pahang, Malaysia. In addition, this study described the presence of lineage B.1.351 as a type of variant of concern (VOC) and lineages B.1.466.2 and B.1.524 as local variants.
  20. Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers
    Lim LWK, Chung HH, Lau MML, Aziz F, Gan HM
    Gene, 2021 Jul 30;791:145708.
    PMID: 33984441 DOI: 10.1016/j.gene.2021.145708
    The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.
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