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Fulltext StaphyloBase: a specialized genomic resource for the staphylococcal research community

Heydari H, Mutha NV, Mahmud MI, Siow CC, Wee WY, Wong GJ, et al.

Database (Oxford), 2014;2014:bau010.
PMID: 24578355 DOI: 10.1093/database/bau010

With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses. Database URL: http://staphylococcus.um.edu.my/.

Matched MeSH terms: Genome, Bacterial/genetics
Fulltext CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips

Heydari H, Siow CC, Tan MF, Jakubovics NS, Wee WY, Mutha NV, et al.

PLoS One, 2014;9(1):e86318.
PMID: 24466021 DOI: 10.1371/journal.pone.0086318

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.

Matched MeSH terms: Genome, Bacterial/genetics*
Fulltext Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes

Gan HM, Schultz MB, Austin CM

BMC Evol. Biol., 2014;14:19.
PMID: 24484414 DOI: 10.1186/1471-2148-14-19

Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline.

Matched MeSH terms: Genome, Mitochondrial*
The mitogenome of Pangasius sutchi (Teleostei, Siluriformes: Pangasiidae)

Zhao H, Kong X, Zhou C

Mitochondrial DNA, 2014 Oct;25(5):342-4.
PMID: 23795847 DOI: 10.3109/19401736.2013.800492

The Pangasius sutchi is an important ornamental and economic fish in Southeast Asia e.g. Thailand, Malaysia and China. The complete mitochondrial genome sequence of P. sutchi has been sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and a non-coding control region with the total length of 16,522 bp. The gene order and composition are similar to most of other vertebrates. Just like most other vertebrates, the bias of G and C was found in different region/genes statistics results. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The mitogenome sequence of P. sutchi would contribute to better understand population genetics, evolution of this lineage.

Matched MeSH terms: Genome, Mitochondrial*
Genome-scale metabolic models as platforms for strain design and biological discovery

Mienda BS

J Biomol Struct Dyn, 2017 Jul;35(9):1863-1873.
PMID: 27251747 DOI: 10.1080/07391102.2016.1197153

Genome-scale metabolic models (GEMs) have been developed and used in guiding systems' metabolic engineering strategies for strain design and development. This strategy has been used in fermentative production of bio-based industrial chemicals and fuels from alternative carbon sources. However, computer-aided hypotheses building using established algorithms and software platforms for biological discovery can be integrated into the pipeline for strain design strategy to create superior strains of microorganisms for targeted biosynthetic goals. Here, I described an integrated workflow strategy using GEMs for strain design and biological discovery. Specific case studies of strain design and biological discovery using Escherichia coli genome-scale model are presented and discussed. The integrated workflow presented herein, when applied carefully would help guide future design strategies for high-performance microbial strains that have existing and forthcoming genome-scale metabolic models.

Matched MeSH terms: Genome, Bacterial/genetics*
Fulltext Complete Mitochondrial Genome of Three Bactrocera Fruit Flies of Subgenus Bactrocera (Diptera: Tephritidae) and Their Phylogenetic Implications

Yong HS, Song SL, Lim PE, Eamsobhana P, Suana IW

PLoS One, 2016;11(2):e0148201.
PMID: 26840430 DOI: 10.1371/journal.pone.0148201

Bactrocera latifrons is a serious pest of solanaceous fruits and Bactrocera umbrosa is a pest of Artocarpus fruits, while Bactrocera melastomatos infests the fruit of Melastomataceae. They are members of the subgenus Bactrocera. We report here the complete mitochondrial genome of these fruit flies determined by next-generation sequencing and their phylogeny with other taxa of the subgenus Bactrocera. The whole mitogenomes of these three species possessed 37 genes namely, 13 protein-coding genes (PCGs), 2 rRNA and 22 tRNA genes. The mitogenome of B. latifrons (15,977 bp) was longer than those of B. melastomatos (15,954 bp) and B. umbrosa (15,898 bp). This difference can be attributed to the size of the intergenic spacers (283 bp in B. latifrons, 261 bp in B. melastomatos, and 211 bp in B. umbrosa). Most of the PCGs in the three species have an identical start codon, except for atp8 (adenosine triphosphate synthase protein 8), which had an ATG instead of GTG in B. umbrosa, whilst the nad3 (NADH dehydrogenase subunit 3) and nad6 (NADH dehydrogenase subunit 6) genes were characterized by an ATC instead of ATT in B. melastomatos. The three species had identical stop codon for the respective PCGs. In B. latifrons and B. melastomatos, the TΨC (thymidine-pseudouridine-cytidine)-loop was absent in trnF (phenylalanine) and DHU (dihydrouracil)-loop was absent in trnS1 (serine S1). In B. umbrosa, trnN (asparagine), trnC (cysteine) and trnF lacked the TψC-loop, while trnS1 lacked the DHU-stem. Molecular phylogeny based on 13 PCGs was in general concordant with 15 mitochondrial genes (13 PCGs and 2 rRNA genes), with B. latifrons and B. umbrosa forming a sister group basal to the other species of the subgenus Bactrocera which was monophyletic. The whole mitogenomes will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the many species of Bactrocera genus in particular, and tephritid fruit flies in general.

Matched MeSH terms: Genome, Mitochondrial*
Fulltext Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi

Assefa S, Lim C, Preston MD, Duffy CW, Nair MB, Adroub SA, et al.

Proc Natl Acad Sci U S A, 2015 Oct 20;112(42):13027-32.
PMID: 26438871 DOI: 10.1073/pnas.1509534112

Malaria cases caused by the zoonotic parasite Plasmodium knowlesi are being increasingly reported throughout Southeast Asia and in travelers returning from the region. To test for evidence of signatures of selection or unusual population structure in this parasite, we surveyed genome sequence diversity in 48 clinical isolates recently sampled from Malaysian Borneo and in five lines maintained in laboratory rhesus macaques after isolation in the 1960s from Peninsular Malaysia and the Philippines. Overall genomewide nucleotide diversity (π = 6.03 × 10(-3)) was much higher than has been seen in worldwide samples of either of the major endemic malaria parasite species Plasmodium falciparum and Plasmodium vivax. A remarkable substructure is revealed within P. knowlesi, consisting of two major sympatric clusters of the clinical isolates and a third cluster comprising the laboratory isolates. There was deep differentiation between the two clusters of clinical isolates [mean genomewide fixation index (FST) = 0.21, with 9,293 SNPs having fixed differences of FST = 1.0]. This differentiation showed marked heterogeneity across the genome, with mean FST values of different chromosomes ranging from 0.08 to 0.34 and with further significant variation across regions within several chromosomes. Analysis of the largest cluster (cluster 1, 38 isolates) indicated long-term population growth, with negatively skewed allele frequency distributions (genomewide average Tajima's D = -1.35). Against this background there was evidence of balancing selection on particular genes, including the circumsporozoite protein (csp) gene, which had the top Tajima's D value (1.57), and scans of haplotype homozygosity implicate several genomic regions as being under recent positive selection.

Matched MeSH terms: Genome, Protozoan*
Fulltext Development of ListeriaBase and comparative analysis of Listeria monocytogenes

Tan MF, Siow CC, Dutta A, Mutha NV, Wee WY, Heydari H, et al.

BMC Genomics, 2015;16:755.
PMID: 26444974 DOI: 10.1186/s12864-015-1959-5

Listeria consists of both pathogenic and non-pathogenic species. Reports of similarities between the genomic content between some pathogenic and non-pathogenic species necessitates the investigation of these species at the genomic level to understand the evolution of virulence-associated genes. With Listeria genome data growing exponentially, comparative genomic analysis may give better insights into evolution, genetics and phylogeny of Listeria spp., leading to better management of the diseases caused by them.

Matched MeSH terms: Genome, Bacterial*
Fulltext Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

Redwan RM, Saidin A, Kumar SV

BMC Plant Biol, 2015;15:196.
PMID: 26264372 DOI: 10.1186/s12870-015-0587-1

Pineapple (Ananas comosus var. comosus) is known as the king of fruits for its crown and is the third most important tropical fruit after banana and citrus. The plant, which is indigenous to South America, is the most important species in the Bromeliaceae family and is largely traded for fresh fruit consumption. Here, we report the complete chloroplast sequence of the MD-2 pineapple that was sequenced using the PacBio sequencing technology.

Matched MeSH terms: Genome, Chloroplast*
Fulltext Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies

Hoh BP, Deng L, Julia-Ashazila MJ, Zuraihan Z, Nur-Hasnah M, Nur-Shafawati AR, et al.

Hum Genomics, 2015 Jul 22;9:16.
PMID: 26194999 DOI: 10.1186/s40246-015-0039-x

Fine scale population structure of Malays - the major population in Malaysia, has not been well studied. This may have important implications for both evolutionary and medical studies. Here, we investigated the population sub-structure of Malay involving 431 samples collected from all states from peninsular Malaysia and Singapore. We identified two major clusters of individuals corresponding to the north and south peninsular Malaysia. On an even finer scale, the genetic coordinates of the geographical Malay populations are in correlation with the latitudes (R(2) = 0.3925; P = 0.029). This finding is further supported by the pairwise FST of Malay sub-populations, of which the north and south regions showed the highest differentiation (FST [North-south] = 0.0011). The collective findings therefore suggest that population sub-structure of Malays are more heterogenous than previously expected even within a small geographical region, possibly due to factors like different genetic origins, geographical isolation, could result in spurious association as demonstrated in our analysis. We suggest that cautions should be taken during the stage of study design or interpreting the association signals in disease mapping studies which are expected to be conducted in Malay population in the near future.

Matched MeSH terms: Genome-Wide Association Study*
Fulltext Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics

Jia G, Ping J, Shu X, Yang Y, Cai Q, Kweon SS, et al.

Am J Hum Genet, 2022 Dec 01;109(12):2185-2195.
PMID: 36356581 DOI: 10.1016/j.ajhg.2022.10.011

By combining data from 160,500 individuals with breast cancer and 226,196 controls of Asian and European ancestry, we conducted genome- and transcriptome-wide association studies of breast cancer. We identified 222 genetic risk loci and 137 genes that were associated with breast cancer risk at a p

Matched MeSH terms: Genome-Wide Association Study*
Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry

Mueller SH, Lai AG, Valkovskaya M, Michailidou K, Bolla MK, Wang Q, et al.

Genome Med, 2023 Jan 26;15(1):7.
PMID: 36703164 DOI: 10.1186/s13073-022-01152-5

BACKGROUND: Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.
METHODS: We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.
RESULTS: In European ancestry samples, 14 genes were significantly associated (q

Matched MeSH terms: Genome-Wide Association Study/methods
Fulltext Assessing the causal role of epigenetic clocks in the development of multiple cancers: a Mendelian randomization study

Morales Berstein F, McCartney DL, Lu AT, Tsilidis KK, Bouras E, Haycock P, et al.

Elife, 2022 Mar 29;11.
PMID: 35346416 DOI: 10.7554/eLife.75374

BACKGROUND: Epigenetic clocks have been associated with cancer risk in several observational studies. Nevertheless, it is unclear whether they play a causal role in cancer risk or if they act as a non-causal biomarker.
METHODS: We conducted a two-sample Mendelian randomization (MR) study to examine the genetically predicted effects of epigenetic age acceleration as measured by HannumAge (nine single-nucleotide polymorphisms (SNPs)), Horvath Intrinsic Age (24 SNPs), PhenoAge (11 SNPs), and GrimAge (4 SNPs) on multiple cancers (i.e. breast, prostate, colorectal, ovarian and lung cancer). We obtained genome-wide association data for biological ageing from a meta-analysis (N = 34,710), and for cancer from the UK Biobank (N cases = 2671-13,879; N controls = 173,493-372,016), FinnGen (N cases = 719-8401; N controls = 74,685-174,006) and several international cancer genetic consortia (N cases = 11,348-122,977; N controls = 15,861-105,974). Main analyses were performed using multiplicative random effects inverse variance weighted (IVW) MR. Individual study estimates were pooled using fixed effect meta-analysis. Sensitivity analyses included MR-Egger, weighted median, weighted mode and Causal Analysis using Summary Effect Estimates (CAUSE) methods, which are robust to some of the assumptions of the IVW approach.
RESULTS: Meta-analysed IVW MR findings suggested that higher GrimAge acceleration increased the risk of colorectal cancer (OR = 1.12 per year increase in GrimAge acceleration, 95% CI 1.04-1.20, p = 0.002). The direction of the genetically predicted effects was consistent across main and sensitivity MR analyses. Among subtypes, the genetically predicted effect of GrimAge acceleration was greater for colon cancer (IVW OR = 1.15, 95% CI 1.09-1.21, p = 0.006), than rectal cancer (IVW OR = 1.05, 95% CI 0.97-1.13, p = 0.24). Results were less consistent for associations between other epigenetic clocks and cancers.
CONCLUSIONS: GrimAge acceleration may increase the risk of colorectal cancer. Findings for other clocks and cancers were inconsistent. Further work is required to investigate the potential mechanisms underlying the results.
FUNDING: FMB was supported by a Wellcome Trust PhD studentship in Molecular, Genetic and Lifecourse Epidemiology (224982/Z/22/Z which is part of grant 218495/Z/19/Z). KKT was supported by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme) and by the Hellenic Republic's Operational Programme 'Competitiveness, Entrepreneurship & Innovation' (OΠΣ 5047228). PH was supported by Cancer Research UK (C18281/A29019). RMM was supported by the NIHR Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol and by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme). RMM is a National Institute for Health Research Senior Investigator (NIHR202411). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. GDS and CLR were supported by the Medical Research Council (MC_UU_00011/1 and MC_UU_00011/5, respectively) and by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme). REM was supported by an Alzheimer's Society project grant (AS-PG-19b-010) and NIH grant (U01 AG-18-018, PI: Steve Horvath). RCR is a de Pass Vice Chancellor's Research Fellow at the University of Bristol.

Matched MeSH terms: Genome-Wide Association Study/methods
Fulltext Genome-wide association analysis provides insights into the molecular etiology of dilated cardiomyopathy

Zheng SL, Henry A, Cannie D, Lee M, Miller D, McGurk KA, et al.

Nat Genet, 2024 Dec;56(12):2646-2658.
PMID: 39572783 DOI: 10.1038/s41588-024-01952-y

Dilated cardiomyopathy (DCM) is a leading cause of heart failure and cardiac transplantation. We report a genome-wide association study and multi-trait analysis of DCM (14,256 cases) and three left ventricular traits (36,203 UK Biobank participants). We identified 80 genomic risk loci and prioritized 62 putative effector genes, including several with rare variant DCM associations (MAP3K7, NEDD4L and SSPN). Using single-nucleus transcriptomics, we identify cellular states, biological pathways, and intracellular communications that drive pathogenesis. We demonstrate that polygenic scores predict DCM in the general population and modify penetrance in carriers of rare DCM variants. Our findings may inform the design of genetic testing strategies that incorporate polygenic background. They also provide insights into the molecular etiology of DCM that may facilitate the development of targeted therapeutics.

Matched MeSH terms: Genome-Wide Association Study*
Fulltext Pandemic one health clones of Escherichia coli and Klebsiella pneumoniae producing CTX-M-14, CTX-M-27, CTX-M-55 and CTX-M-65 ESβLs among companion animals in northern Ecuador

Gonzales-Zubiate FA, Tambor JHM, Valencia-Bacca J, Villota-Burbano MF, Cardenas-Arias A, Esposito F, et al.

Front Cell Infect Microbiol, 2023;13:1259764.
PMID: 39840255 DOI: 10.3389/fcimb.2023.1259764

From a One Health perspective, dogs and cats have begun to be recognized as important reservoirs for clinically significant multidrug-resistant bacterial pathogens. In this study, we investigated the occurrence and genomic features of ESβL producing Enterobacterales isolated from dogs, in the province of Imbabura, Ecuador. We identified four isolates expressing ESβLs from healthy and diseased animals. In this regard, two Escherichia coli strains producing CTX-M-55-like or CTX-M-65 ESβLs belonged to the international ST10 and ST162, whereas two Klebsiella pneumoniae producing CTX-M-14 or CTX-M-27 belonged to ST35 and ST661. Phylogenomic analysis clustered (95-105 SNP differences) CTX-M-55/ST10 E. coli from companion animal with food and human E. coli strains of ST10 isolated in 2016, in Australia and Cambodia, respectively; whereas CTX-M-27-positive K. pneumoniae ST661 was clustered (201-216 SNP differences) with human strains identified in Italy, in 2013 and 2017, respectively. In summary, we report the presence and genomic data of global human-associated clones of CTX-M-producing E. coli and K. pneumoniae in dogs, in Ecuador. The implementation of a national epidemiological surveillance program is necessary to establish future strategies to control the dissemination of antibiotic-resistant priority pathogens using a One Health approach.

Matched MeSH terms: Genome, Bacterial/genetics
A description of Joostella sp. strain CR20 with potential biotechnological applications

Zakaria MR, Vodovnik M, Zorec M, Liew KJ, Tokiman L, Chong CS

Antonie Van Leeuwenhoek, 2024 Nov 29;118(1):38.
PMID: 39613983 DOI: 10.1007/s10482-024-02045-w

The underexplored halophilic genus Joostella within the Flavobacteriaceae family consists of only two species, both of which have received little attention for their potential biotechnological applications. In this study, we report the isolation and characterisation of a novel halophilic bacterium, strain CR20, using a genomic approach to investigate its biotechnological potential. Analysis of the 16S rRNA gene revealed that strain CR20 shares 97.5% and 96.2% sequence similarity with Joostella marina DSM 19592 T and Joostella atrarenae M1-2 T, respectively. Strain CR20 exhibited average nucleotide identity and digital DNA-DNA hybridisation values of 76.8-79.1% and 20.8-22.8%, respectively, with Joostella spp., which fall below the species delineation thresholds. Additionally, strain CR20 demonstrated average amino acid identity and percentage of conserved proteins values of 81.3-84.0% and 71.7-75.3%, respectively, with Joostella spp., above the genus delineation thresholds. Meanwhile, the average amino acid identity and percentage of conserved proteins values of strain CR20 against Galbibacter spp. are 73.9-80.0% and 61.3-72.3%, respectively, also above the genus delineation thresholds. These findings indicated strain CR20 has a close relationship with both genera. Chemotaxonomic analysis of strain CR20 identified predominant fatty acids, including iso-C17:0 3OH (25.3%), iso-C15:0 (14%), and C16:1 ω6c/C16:1 ω7c (12.2%). The assembled genome comprises 62 contigs, with a size of approximately 3,168,727 bp and a G + C content of 35.1%. Among 2,804 predicted genes, 2,559 were classified into 25 COG functional groups. A total of 68 genes with potential industrial applications were identified, including 1 β-mannanase, 2 β-xylosidases, 1 polysaccharide deacetylase, 4 other hemicellulases, 6 β-glucosidases, 25 proteases, and 29 phosphate-solubilising enzymes. Hydrolytic assays confirmed that strain CR20 produces these enzymes extracellularly. These findings highlight strain CR20 has potential for industrial applications.

Matched MeSH terms: Genome, Bacterial*
Fulltext Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Bein B, Chrysostomakis I, Arantes LS, Brown T, Gerheim C, Schell T, et al.

Genome Biol, 2025 Feb 10;26(1):25.
PMID: 39930463 DOI: 10.1186/s13059-025-03487-9

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assemble the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.

Matched MeSH terms: Genome*; Genomics/methods
Fulltext The Interaction Between Cognitive Abilities and White Matter Hyperintensity Phenotypes: A Novel Perspective on Bidirectional Causality

Ren X, Li T, Li F, Liu S

Brain Behav, 2025 Feb;15(2):e70313.
PMID: 39925008 DOI: 10.1002/brb3.70313

PURPOSE: This study utilizes bidirectional Mendelian randomization (MR) to examine the causal relationships between white matter hyperintensity (WMH) phenotypes-namely, WMH volume, fractional anisotropy (FA), and mean diffusivity (MD)-and cognitive abilities, including cognitive performance, intelligence, and overall cognitive function.
METHODS: This study leverages genetic variation data from genome-wide association study (GWAS) datasets and employs a bidirectional two-sample MR analysis. The analysis incorporates MR Egger, weighted median, weighted mode, and inverse variance weighted (IVW) methods to assess the bidirectional causal relationship between cognitive abilities and WMH volume, FA, and MD.
RESULTS: This study employed MR to explore the causal relationships between WMH volume, FA, MD, and cognitive outcomes. Most MR methods yielded nonsignificant p values (>0.05) and wide confidence intervals. Heterogeneity tests indicated no significant heterogeneity or pleiotropy between WMH volume and cognitive performance or intelligence. However, significant heterogeneity was found between WMH volume and cognitive function, FA with cognitive performance and intelligence, and MD with cognitive performance and intelligence. Reverse analysis also revealed no significant causal relationships.
CONCLUSIONS: This study suggests that the bidirectional causal effects between cognitive abilities and WMH volume, FA, and MD are minimal or nonsignificant and highlights data heterogeneity as a concern.

Matched MeSH terms: Genome-Wide Association Study*
Whole genome analysis revealed the role of blaOXA-23 and blaOXA-66 genes in carbapenem resistance of Acinetobacter baumannii strains

Mat Ghani N, Hong KW, Liew YJM, Lau YY, Yong HS, Tee KK, et al.

Pathog Glob Health, 2025;119(1-2):10-21.
PMID: 39699991 DOI: 10.1080/20477724.2024.2442194

Acinetobacter baumannii is a multidrug-resistant bacterium that has emerged as a significant nosocomial pathogen globally and renowned for its ability to acquire antimicrobial resistance (AMR) genes. However, understanding of its resistance mechanisms to certain drug classes remains limited. This study focused on four bacterial strains (AB863, AB889, AB930, and AB960) exhibiting carbapenem resistance. They demonstrated high minimum inhibitory concentration (MIC) (128 mg/L) to meropenem and were categorized as extensively drug-resistant strains. Subsequently, they were identified as A. baumannii through 16S rRNA gene sequence analysis and species-specific PCR targeting the blaOXA51-like gene. Three strains were sequenced for their genomes to study the genetic determinants and functional relevance of carbapenem resistance. The draft genome length of the strains ranged from 3.8 to 4.0 Mbp. A total of 16 antibiotic resistance genes including the genes blaOXA-23 and blaOXA-66 which mediate carbapenem resistance were identified in the genomes. A comprehensive multilocus sequence typing analysis involving 95 A. baumannii strains from different Asian countries assigned the four strains to sequence type 2 (ST2), the most predominant ST circulating in Asia. Comparative genome analysis also revealed blaOXA-66 as the most dominant variant of blaOXA-51-like gene and also a widespread distribution of blaOXA-23 gene. In addition, various mobile genetic elements associated with AMR genes and three efflux pumps families were detected in the genomes of the strains. Transformation of blaOXA-23 and blaOXA-66 genes resulted in meropenem resistance in the transformant which exhibited a MIC of 2 mg/L, thus confirming direct involvement of both genes in carbapenem resistance.

Matched MeSH terms: Genome, Bacterial*
Fulltext Genome-wide association study of long COVID

Lammi V, Nakanishi T, Jones SE, Andrews SJ, Karjalainen J, Cortés B, et al.

Nat Genet, 2025 Jun;57(6):1402-1417.
PMID: 40399555 DOI: 10.1038/s41588-025-02100-w

Infections can lead to persistent symptoms and diseases such as shingles after varicella zoster or rheumatic fever after streptococcal infections. Similarly, severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infection can result in long coronavirus disease (COVID), typically manifesting as fatigue, pulmonary symptoms and cognitive dysfunction. The biological mechanisms behind long COVID remain unclear. We performed a genome-wide association study for long COVID including up to 6,450 long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We discovered an association of FOXP4 with long COVID, independent of its previously identified association with severe COVID-19. The signal was replicated in 9,500 long COVID cases and 798,835 population controls. Given the transcription factor FOXP4's role in lung physiology and pathology, our findings highlight the importance of lung function in the pathophysiology of long COVID.

Matched MeSH terms: Genome-Wide Association Study*

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