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Expansion and systematics redefinition of the most threatened freshwater mussel family, the Margaritiferidae

Lopes-Lima M, Bolotov IN, Do VT, Aldridge DC, Fonseca MM, Gan HM, et al.

Mol Phylogenet Evol, 2018 10;127:98-118.
PMID: 29729933 DOI: 10.1016/j.ympev.2018.04.041

Two Unionida (freshwater mussel) families are present in the Northern Hemisphere; the Margaritiferidae, representing the most threatened of unionid families, and the Unionidae, which include several genera of unresolved taxonomic placement. The recent reassignment of the poorly studied Lamprotula rochechouartii from the Unionidae to the Margaritiferidae motivated a new search for other potential species of margaritiferids from members of Gibbosula and Lamprotula. Based on molecular and morphological analyses conducted on newly collected specimens from Vietnam, we here assign Gibbosula crassa to the Margaritiferidae. Additionally, we reanalyzed all diagnostic characteristics of the Margaritiferidae and examined museum specimens of Lamprotula and Gibbosula. As a result, two additional species are also moved to the Margaritiferidae, i.e. Gibbosula confragosa and Gibbosula polysticta. We performed a robust five marker phylogeny with all available margaritiferid species and discuss the taxonomy within the family. The present phylogeny reveals the division of Margaritiferidae into four ancient clades with distinct morphological, biogeographical and ecological characteristics that justify the division of the Margaritiferidae into two subfamilies (Gibbosulinae and Margaritiferinae) and four genera (Gibbosula, Cumberlandia, Margaritifera, and Pseudunio). The systematics of the Margaritiferidae family is re-defined as well as their distribution, potential origin and main biogeographic patterns.

Matched MeSH terms: Genome, Mitochondrial
Fulltext Epigenome-wide association study of adiposity and future risk of obesity-related diseases

Campanella G, Gunter MJ, Polidoro S, Krogh V, Palli D, Panico S, et al.

Int J Obes (Lond), 2018 Dec;42(12):2022-2035.
PMID: 29713043 DOI: 10.1038/s41366-018-0064-7

BACKGROUND: Obesity is an established risk factor for several common chronic diseases such as breast and colorectal cancer, metabolic and cardiovascular diseases; however, the biological basis for these relationships is not fully understood. To explore the association of obesity with these conditions, we investigated peripheral blood leucocyte (PBL) DNA methylation markers for adiposity and their contribution to risk of incident breast and colorectal cancer and myocardial infarction.
METHODS: DNA methylation profiles (Illumina Infinium® HumanMethylation450 BeadChip) from 1941 individuals from four population-based European cohorts were analysed in relation to body mass index, waist circumference, waist-hip and waist-height ratio within a meta-analytical framework. In a subset of these individuals, data on genome-wide gene expression level, biomarkers of glucose and lipid metabolism were also available. Validation of methylation markers associated with all adiposity measures was performed in 358 individuals. Finally, we investigated the association of obesity-related methylation marks with breast, colorectal cancer and myocardial infarction within relevant subsets of the discovery population.
RESULTS: We identified 40 CpG loci with methylation levels associated with at least one adiposity measure. Of these, one CpG locus (cg06500161) in ABCG1 was associated with all four adiposity measures (P = 9.07×10-8 to 3.27×10-18) and lower transcriptional activity of the full-length isoform of ABCG1 (P = 6.00×10-7), higher triglyceride levels (P = 5.37×10-9) and higher triglycerides-to-HDL cholesterol ratio (P = 1.03×10-10). Of the 40 informative and obesity-related CpG loci, two (in IL2RB and FGF18) were significantly associated with colorectal cancer (inversely, P

Matched MeSH terms: Genome-Wide Association Study
Fulltext Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food

Lim SY, Yap KP, Thong KL

Gut Pathog, 2016;8:65.
PMID: 27999619 DOI: 10.1186/s13099-016-0147-8

BACKGROUND: Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia.
RESULTS: The genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively. Our virulence profiling indicated a total of 31 virulence genes shared by both analysed strains. These shared genes included those that encode for internalins and L. monocytogenes pathogenicity island 1 (LIPI-1). Both the Malaysian L. monocytogenes strains also harboured several genes associated with stress tolerance to counter the adverse conditions. Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolone, tetracycline, and penicillin, and macrolides were identified in the genomes of both strains.
CONCLUSIONS: Whole genome sequencing and comparative genomics analyses revealed two virulent L. monocytogenes strains isolated from ready-to-eat foods in Malaysia. The identification of strains with pathogenic, persistent, and antibiotic resistant potentials from minimally processed food warrant close attention from both healthcare and food industry.

Matched MeSH terms: Genome Size
Fulltext Hypertension genes among orang asli in peninsular Malaysia and ethno-medicinal plant

Sholehah, A. R., Ramle, A., Mohd Tajuddin, A., Wan Rohani, W. T., Jamilah, M. S., Razifah, M.

Asian Journal of Medicine and Biomedicine, 2018;2(1):0-0.
MyJurnal

The prevalence and incidence rate of hypertension among Orang Asli had been increasing due to
modernization and assimilation of outside practices such as intake of high cholesterol food, alcohol, and
smoking. Orang Asli utilize their herbs or plants to treat some illness due to the factor of logistics and the
knowledge on these nature resources since decades ago that is carried out from their ancestors. In this review
paper, hypertension genes of Orang Asli in Peninsular Malaysia and the utilization of ethno-medicinal plants
in reducing the clinical manifestation in hypertension were deliberated. There are quite a number of related
hypertensive genes particularly in renin-angiotensin-aldosterone system (RAAS) playing a pivotal role in
pathogenesis of hypertension. A genome-wide association studies showed potential candidate genes in
hypertension among Orang Asli in Peninsular Malaysia. However there is yet molecular study on these genes
among Orang Asli with their unique genetic profile. Noteworthy information on mechanism of ethnomedicine in treating hypertension are scarce, even the efficacy of modern medicine in treating hypertension
on Orang Asli are rare. Therefore, study on efficacy of ethno-medicine plant by Orang Asli and the
regulation effect on hypertension genes are needed to be further explored and elucidated.

Matched MeSH terms: Genome-Wide Association Study
Reconstruction of the transcriptional regulatory network in arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway

Khalidah-Syahirah Ashari, Zeti-Azura Mohamed-Hussein, Muhammad-Redha Abdullah-Zawawi, Sarahani Harun

Sains Malaysiana, 2018;47:2993-3002.

Aliphatic glucosinolate is an important secondary metabolite responsible in plant defense mechanism and carcinogenic
activity. It plays a crucial role in plant adaptation towards changes in the environment such as salinity and drought.
However, in many plant genomes, there are thousands of genes encoding proteins still with putative functions and
incomplete annotations. Therefore, the genome of Arabidopsis thaliana was selected to be investigated further to identify
any putative genes that are potentially involved in the aliphatic glucosinolate biosynthesis pathway, most of its gene are
with incomplete annotation. Known genes for aliphatic glucosinolates were retrieved from KEGG and AraCyc databases.
Three co-expression databases i.e., ATTED-II, GeneMANIA and STRING were used to perform the co-expression network
analysis. The integrated co-expression network was then being clustered, annotated and visualized using Cytoscape plugin,
MCODE and ClueGO. Then, the regulatory network of A. thaliana from AtRegNet was mapped onto the co-expression
network to build the transcriptional regulatory network. This study showed that a total of 506 genes were co-expressed
with the 61 aliphatic glucosinolate biosynthesis genes. Five transcription factors have been predicted to be involved
in the biosynthetic pathway of aliphatic glucosinolate, namely SEPALLATA 3 (SEP3), PHYTOCHROME INTERACTING FACTOR
3-like 5 (AtbHLH15/PIL5), ELONGATED HYPOCOTYL 5 (HY5), AGAMOUS-like 15 (AGL15) and GLABRA 3 (GL3). Meanwhile,
three other genes with high potential to be involved in the aliphatic glucosinolates biosynthetic pathway were identified,
i.e., methylthioalkylmalate-like synthase 4 (MAML-4) and aspartate aminotransferase (ASP1 and ASP4). These findings
can be used to complete the aliphatic glucosinolate biosynthetic pathway in A. thaliana and to update the information
on the glucosinolate-related pathways in public metabolic databases.

Matched MeSH terms: Genome, Plant
Mitogenome of gymnothorax minor and phylogenetic relationship with its congeners and related genera (anguilliformes: muraenidae)

Sze-Looi Song, Kar-Hoe Loh, Phaik-Eem Lim, Amy Yee-Hui Then, Hoi-Sen Yong, Praphathip Eamsobhana

Sains Malaysiana, 2018;47:2519-2531.

Gymnothorax minor is a moray eel of the family Muraenidae found in the Western Pacific Ocean. We report here
its complete mitogenome as determined by Illumina next-generation sequencing and the phylogenetic relationship
with its congeners and other taxa of the family Muraenidae. The whole mitogenome of G. minor had a total length
of 16,574 bp, comprising 37 genes - 13 protein-coding genes (PCGs), two ribosomal ribonucleic acid (rRNA) and 22
transfer ribonucleic acid (tRNA) genes - and a control region. Excepting cox1 with GTG, the other 12 PCGs had ATG
start codon. Seven of its PCGs had incomplete stop codon - five (nad2; cox1; cox2; nad3 and nad4) with T and two
(atp6 and cox3) with TA. Molecular phylogeny based on 13 PCGs was concordant with 15 mitochondrial genes (13 PCGs
and 2 rRNA genes). The subfamily Muraeninae as well as the subfamily Uropterygiinae were monophyletic. However,
the genus Gymnothorax was paraphyletic, with G. minor forming a sister group with Rhinomuraena quaesita in the
lineage containing also G. kidako and G. formosus forming a sister group with Enchelynassa canina. The phylogenetic
relationship of the genus Gymnothorax and related taxa of the family Muraenidae, based on the mitochondrial cob
gene, was in general similar to that based on 15 mt-genes. The mitogenome is useful for future studies on phylogenetics
and systematics of eels of the family Muraenidae and other taxa of the order Anguilliformes.

Matched MeSH terms: Genome, Mitochondrial
Using GWAS top hits to inform priors in Bayesian fine-mapping association studies

Walters K, Cox A, Yaacob H

Genet Epidemiol, 2019 Sep;43(6):675-689.
PMID: 31286571 DOI: 10.1002/gepi.22212

The default causal single-nucleotide polymorphism (SNP) effect size prior in Bayesian fine-mapping studies is usually the Normal distribution. This choice is often based on computational convenience, rather than evidence that it is the most suitable prior distribution. The choice of prior is important because previous studies have shown considerable sensitivity of causal SNP Bayes factors to the form of the prior. In some well-studied diseases there are now considerable numbers of genome-wide association study (GWAS) top hits along with estimates of the number of yet-to-be-discovered causal SNPs. We show how the effect sizes of the top hits and estimates of the number of yet-to-be-discovered causal SNPs can be used to choose between the Laplace and Normal priors, to estimate the prior parameters and to quantify the uncertainty in this estimation. The methodology can readily be applied to other priors. We show that the top hits available from breast cancer GWAS provide overwhelming support for the Laplace over the Normal prior, which has important consequences for variant prioritisation. This work in this paper enables practitioners to derive more objective priors than are currently being used and could lead to prioritisation of different variants.

Matched MeSH terms: Genome-Wide Association Study
Fulltext Whole genome sequencing data and analysis of a rifampicin-resistant Mycobacterium tuberculosis strain SBH162 from Sabah, Malaysia

Jani J, Mustapha ZA, Jamal NB, Stanis CS, Ling CK, Avoi R, et al.

Data Brief, 2019 Oct;26:104445.
PMID: 31534995 DOI: 10.1016/j.dib.2019.104445

A Mycobacterium tuberculosis strain SBH162 was isolated from a 49-year-old male with pulmonary tuberculosis. GeneXpert MDR/RIF identified the strain as rifampicin-resistant M. tuberculosis. The whole genome sequencing was performed using Illumina HiSeq 4000 system to further investigate and verify the mutation sites of the strain through genetic analyses namely variant calling using bioinformatics tools. The de novo assembly of genome generated 100 contigs with N50 of 156,381bp. The whole genome size was 4,343,911 bp with G + C content of 65.58% and consisted of 4,306 predicted genes. The mutation site, S450L, for rifampicin resistance was detected in the rpoB gene. Based on the phylogenetic analysis using the Maximum Likelihood method, the strain was identified as belonging to the Europe America Africa lineage (Lineage 4). The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number SMOE00000000.

Matched MeSH terms: Genome Size
Fulltext Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback in Theobroma cacao

Ali SS, Asman A, Shao J, Firmansyah AP, Susilo AW, Rosmana A, et al.

Fungal Biol Biotechnol, 2019;6:14.
PMID: 31583107 DOI: 10.1186/s40694-019-0077-6

Background: Ceratobasidium theobromae, a member of the Ceratobasidiaceae family, is the causal agent of vascular-streak dieback (VSD) of cacao, a major threat to the chocolate industry in the South-East Asia. The fastidious pathogen is very hard to isolate and maintain in pure culture, which is a major bottleneck in the study of its genetic diversity and genome.
Result: This study describes for the first time, a 33.90 Mbp de novo assembled genome of a putative C. theobromae isolate from cacao. Ab initio gene prediction identified 9264 protein-coding genes, of which 800 are unique to C. theobromae when compared to Rhizoctonia spp., a closely related group. Transcriptome analysis using RNA isolated from 4 independent VSD symptomatic cacao stems identified 3550 transcriptionally active genes when compared to the assembled C. theobromae genome while transcripts for only 4 C. theobromae genes were detected in 2 asymptomatic stems. De novo assembly of the non-cacao associated reads from the VSD symptomatic stems uniformly produced genes with high identity to predicted genes in the C. theobromae genome as compared to Rhizoctonia spp. or genes found in Genbank. Further analysis of the predicted C. theobromae transcriptome was carried out identifying CAZy gene classes, KEGG-pathway associated genes, and 138 putative effector proteins.
Conclusion: These findings put forth, for the first time, a predicted genome for the fastidious basidiomycete C. theobromae causing VSD on cacao providing a model for testing and comparison in the future. The C. theobromae genome predicts a pathogenesis model involving secreted effector proteins to suppress plant defense mechanisms and plant cell wall degrading enzymes.

Matched MeSH terms: Genome
Fulltext Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

Cross-Disorder Group of the Psychiatric Genomics Consortium. Electronic address: plee0@mgh.harvard.edu, Cross-Disorder Group of the Psychiatric Genomics Consortium

Cell, 2019 Dec 12;179(7):1469-1482.e11.
PMID: 31835028 DOI: 10.1016/j.cell.2019.11.020

Genetic influences on psychiatric disorders transcend diagnostic boundaries, suggesting substantial pleiotropy of contributing loci. However, the nature and mechanisms of these pleiotropic effects remain unclear. We performed analyses of 232,964 cases and 494,162 controls from genome-wide studies of anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, and Tourette syndrome. Genetic correlation analyses revealed a meaningful structure within the eight disorders, identifying three groups of inter-related disorders. Meta-analysis across these eight disorders detected 109 loci associated with at least two psychiatric disorders, including 23 loci with pleiotropic effects on four or more disorders and 11 loci with antagonistic effects on multiple disorders. The pleiotropic loci are located within genes that show heightened expression in the brain throughout the lifespan, beginning prenatally in the second trimester, and play prominent roles in neurodevelopmental processes. These findings have important implications for psychiatric nosology, drug development, and risk prediction.

Matched MeSH terms: Genome-Wide Association Study
Genetic polymorphisms of HbE/beta thalassemia related to clinical presentation: implications for clinical diversity

Azman NF, Abdullah WZ, Hanafi S, Diana R, Bahar R, Johan MF, et al.

Ann Hematol, 2020 Apr;99(4):729-735.
PMID: 32078010 DOI: 10.1007/s00277-020-03927-5

HbE/Beta thalassemia (HbE/β-thalassemia) is one of the common genetic disorders in South East Asia. It is heterogeneous in its clinical presentation and molecular defects. There are genetic modifiers which have been reported to influence the disease severity of this disorder. The aim of this study was to determine the genetic polymorphisms which were responsible for the disease clinical diversity. A case-control study was conducted among Malay transfusion-dependent HbE/β-thalassemia patients. Patients who were confirmed HbE/β-thalassemia were recruited and genotyping study was performed on these subjects. Ninety-eight patients were selected and divided into moderate and severe groups based on clinical parameters using Sripichai scoring system (based on hemoglobin level, spleen size, growth development, the age of first transfusion and age of disease presentation). Forty-three (44.9%) and 55 (56.1%) patients were found to have moderate and severe clinical presentation, respectively. Genotyping analysis was performed using Affymetrix 6.0 microarray platform. The SNPs were filtered using PLINK and Manhattan plot by R software. From the GWAS results, 20 most significant SNPs were selected based on disease severity when compared between moderate and severe groups. The significant SNPs found in this study were mostly related to thalassemia complications such as rs7372408, associated with KCNMB2-AS1 and SNPs associated with disease severity. These findings could be used as genetic predictors in managing patients with HbE/β-thalassemia and served as platform for future study.

Matched MeSH terms: Genome-Wide Association Study
Fulltext Pathogenic Mitochondria DNA Mutations: Current Detection Tools and Interventions

Mustafa MF, Fakurazi S, Abdullah MA, Maniam S

Genes (Basel), 2020 02 12;11(2).
PMID: 32059522 DOI: 10.3390/genes11020192

Mitochondria are best known for their role in energy production, and they are the only mammalian organelles that contain their own genomes. The mitochondrial genome mutation rate is reported to be 10-17 times higher compared to nuclear genomes as a result of oxidative damage caused by reactive oxygen species during oxidative phosphorylation. Pathogenic mitochondrial DNA mutations result in mitochondrial DNA disorders, which are among the most common inherited human diseases. Interventions of mitochondrial DNA disorders involve either the transfer of viable isolated mitochondria to recipient cells or genetically modifying the mitochondrial genome to improve therapeutic outcome. This review outlines the common mitochondrial DNA disorders and the key advances in the past decade necessary to improve the current knowledge on mitochondrial disease intervention. Although it is now 31 years since the first description of patients with pathogenic mitochondrial DNA was reported, the treatment for mitochondrial disease is often inadequate and mostly palliative. Advancements in diagnostic technology improved the molecular diagnosis of previously unresolved cases, and they provide new insight into the pathogenesis and genetic changes in mitochondrial DNA diseases.

Matched MeSH terms: Genome, Mitochondrial
Fulltext A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer

Zhong J, Jermusyk A, Wu L, Hoskins JW, Collins I, Mocci E, et al.

J Natl Cancer Inst, 2020 Oct 01;112(10):1003-1012.
PMID: 31917448 DOI: 10.1093/jnci/djz246

BACKGROUND: Although 20 pancreatic cancer susceptibility loci have been identified through genome-wide association studies in individuals of European ancestry, much of its heritability remains unexplained and the genes responsible largely unknown.
METHODS: To discover novel pancreatic cancer risk loci and possible causal genes, we performed a pancreatic cancer transcriptome-wide association study in Europeans using three approaches: FUSION, MetaXcan, and Summary-MulTiXcan. We integrated genome-wide association studies summary statistics from 9040 pancreatic cancer cases and 12 496 controls, with gene expression prediction models built using transcriptome data from histologically normal pancreatic tissue samples (NCI Laboratory of Translational Genomics [n = 95] and Genotype-Tissue Expression v7 [n = 174] datasets) and data from 48 different tissues (Genotype-Tissue Expression v7, n = 74-421 samples).
RESULTS: We identified 25 genes whose genetically predicted expression was statistically significantly associated with pancreatic cancer risk (false discovery rate < .05), including 14 candidate genes at 11 novel loci (1p36.12: CELA3B; 9q31.1: SMC2, SMC2-AS1; 10q23.31: RP11-80H5.9; 12q13.13: SMUG1; 14q32.33: BTBD6; 15q23: HEXA; 15q26.1: RCCD1; 17q12: PNMT, CDK12, PGAP3; 17q22: SUPT4H1; 18q11.22: RP11-888D10.3; and 19p13.11: PGPEP1) and 11 at six known risk loci (5p15.33: TERT, CLPTM1L, ZDHHC11B; 7p14.1: INHBA; 9q34.2: ABO; 13q12.2: PDX1; 13q22.1: KLF5; and 16q23.1: WDR59, CFDP1, BCAR1, TMEM170A). The association for 12 of these genes (CELA3B, SMC2, and PNMT at novel risk loci and TERT, CLPTM1L, INHBA, ABO, PDX1, KLF5, WDR59, CFDP1, and BCAR1 at known loci) remained statistically significant after Bonferroni correction.
CONCLUSIONS: By integrating gene expression and genotype data, we identified novel pancreatic cancer risk loci and candidate functional genes that warrant further investigation.

Matched MeSH terms: Genome-Wide Association Study
Fulltext The de novo transcriptome of workers head of the higher group termite Globitermes sulphureus Haviland (Blattodea: Termitidae)

Hussin NA, Najimudin N, Ab Majid AH

Heliyon, 2019 Dec;5(12):e02969.
PMID: 31872129 DOI: 10.1016/j.heliyon.2019.e02969

The subterranean termite Globitermus sulphureus is an important Southeast Asian pest with limited genomic resources that causes damages to agriculture crops and building structures. Therefore, the main goal of this study was to survey the G. sulphureus transcriptome composition. Here, we performed de novo transcriptome for G. sulphureus workers' heads using Illumina HiSeq paired-end sequencing technology. A total of 88, 639, 408 clean reads were collected and assembled into 243, 057 transcripts and 193, 344 putative genes. The transcripts were annotated with the Trinotate pipeline. In total, 27, 061 transcripts were successfully annotated using BLASTX against the SwissProt database and 17, 816 genes were assigned to 47, 598 GO terms. We classified 14, 223 transcripts into COG classification, resulting in 25 groups of functional annotations. Next, a total of 12, 194 genes were matched in the KEGG pathway and 392 metabolic pathways were predicted based on the annotation. Moreover, we detected two endogenous cellulases in the sequences. The RT-qPCR analysis showed that there were significant differences in the expression levels of two genes β-glucosidase and endo-β-1,4-glucanase between worker and soldier heads of G. sulphureus. This is the first study to characterize the complete head transcriptome of a higher termite G. sulphureus using a high-throughput sequencing. Our study may provide an overview and comprehensive molecular resource for comparative studies of the transcriptomics and genomics of termites.

Matched MeSH terms: Genome
Fulltext Whole genome sequencing data of a clinical Enterococcus gallinarum strain EGR748 from Sabah, Malaysia

Mastor NN, Subbiah VK, Bakar WNWA, Begum K, Alam MJ, Hoque MZ

Data Brief, 2020 Dec;33:106370.
PMID: 33102652 DOI: 10.1016/j.dib.2020.106370

Enterococcus gallinarum is a gram positive facultatively anaerobic bacteria that is typically found in mammalian intestinal tracts. It is generally not considered pathogenic to humans and is rarely reported. Here, we present the draft genome sequence data of Enterococcus gallinarum strain EGR748 isolated from a human clinical sample, and sequenced using the Illumina HiSeq 4000 system. The estimated whole genome size of the strain was 3,730,000 bp with a G + C content of 40.43%. The de novo assembly of the genome generated 55 contigs with an N50 of 208,509 bp. In addition, the Maximum Likelihood phylogenetic analysis based on the 16S rRNA sequence data accurately clustered EGR748 with other E. gallinarum strains. The data may be useful to demonstrate the capacity of this enterococcal species becoming the causal agents of nosocomial blood-stream infections. The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number JAABOR000000000.

Matched MeSH terms: Genome Size
Cross-Cancer Genome-Wide Association Study of Endometrial Cancer and Epithelial Ovarian Cancer Identifies Genetic Risk Regions Associated with Risk of Both Cancers

Glubb DM, Thompson DJ, Aben KKH, Alsulimani A, Amant F, Annibali D, et al.

Cancer Epidemiol Biomarkers Prev, 2021 Jan;30(1):217-228.
PMID: 33144283 DOI: 10.1158/1055-9965.EPI-20-0739

BACKGROUND: Accumulating evidence suggests a relationship between endometrial cancer and ovarian cancer. Independent genome-wide association studies (GWAS) for endometrial cancer and ovarian cancer have identified 16 and 27 risk regions, respectively, four of which overlap between the two cancers. We aimed to identify joint endometrial and ovarian cancer risk loci by performing a meta-analysis of GWAS summary statistics from these two cancers.
METHODS: Using LDScore regression, we explored the genetic correlation between endometrial cancer and ovarian cancer. To identify loci associated with the risk of both cancers, we implemented a pipeline of statistical genetic analyses (i.e., inverse-variance meta-analysis, colocalization, and M-values) and performed analyses stratified by subtype. Candidate target genes were then prioritized using functional genomic data.
RESULTS: Genetic correlation analysis revealed significant genetic correlation between the two cancers (rG = 0.43, P = 2.66 × 10-5). We found seven loci associated with risk for both cancers (P Bonferroni < 2.4 × 10-9). In addition, four novel subgenome-wide regions at 7p22.2, 7q22.1, 9p12, and 11q13.3 were identified (P < 5 × 10-7). Promoter-associated HiChIP chromatin loops from immortalized endometrium and ovarian cell lines and expression quantitative trait loci data highlighted candidate target genes for further investigation.
CONCLUSIONS: Using cross-cancer GWAS meta-analysis, we have identified several joint endometrial and ovarian cancer risk loci and candidate target genes for future functional analysis.
IMPACT: Our research highlights the shared genetic relationship between endometrial cancer and ovarian cancer. Further studies in larger sample sets are required to confirm our findings.

Matched MeSH terms: Genome-Wide Association Study
Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist

Patel RP, Förster DW, Kitchener AC, Rayan MD, Mohamed SW, Werner L, et al.

R Soc Open Sci, 2016 Oct;3(10):160350.
PMID: 27853549

Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based on morphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 Ma and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to Peninsular Malaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis.

Matched MeSH terms: Genome, Mitochondrial
Fulltext Draft genome sequencing data of a pathogenic Pantoea stewartii subspecies stewartii strain SQT1 causing bronzing disease of jackfruit in Malaysia

Ibrahim R, Ismail-Suhaimy NW, Shu-Qing T, Ismail SI, Ina-Salwany MY, Yusof MT, et al.

Data Brief, 2020 Jun;30:105634.
PMID: 32395592 DOI: 10.1016/j.dib.2020.105634

A Gram-negative bacterium, Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii) has been recognized as the causative agent for jackfruit bronzing disease in Malaysia. Here, we report the whole genome sequencing dataset of P. stewartii subsp. stewartii strain SQT1 isolated from local infected jackfruit. The paired-end libraries with an insert size of 350 bp was subjected to the Illumina Hiseq 4000, generating a genome size of 4,783,993 bp with a G+C content of 53.7%. A total protein of 4,671 was identified including virulence factors, resistance factors and secretion systems. Pantoea stewartii subsp. stewartii strain DC283 (NCBI accession no. CP017581.1) was used as a reference genome, where the query hit 72% coverage and average sequencing depth of 68. In total, 28,717 nucleotide polymorphisms, 520 small insertion/deletions and 142 structure variants were identified. The complete genome was deposited at the European Nucleotide Archive under the sample accession number ERP119356 and study accession number PRJEB36196.

Matched MeSH terms: Genome Size
Fulltext Population Genomic Structure and Recent Evolution of Plasmodium knowlesi, Peninsular Malaysia

Hocking SE, Divis PCS, Kadir KA, Singh B, Conway DJ

Emerg Infect Dis, 2020 08;26(8):1749-1758.
PMID: 32687018 DOI: 10.3201/eid2608.190864

Most malaria in Malaysia is caused by Plasmodium knowlesi parasites through zoonotic infection from macaque reservoir hosts. We obtained genome sequences from 28 clinical infections in Peninsular Malaysia to clarify the emerging parasite population structure and test for evidence of recent adaptation. The parasites all belonged to a major genetic population of P. knowlesi (cluster 3) with high genomewide divergence from populations occurring in Borneo (clusters 1 and 2). We also observed unexpected local genetic subdivision; most parasites belonged to 2 subpopulations sharing a high level of diversity except at particular genomic regions, the largest being a region of chromosome 12, which showed evidence of recent directional selection. Surprisingly, we observed a third subpopulation comprising P. knowlesi infections that were almost identical to each other throughout much of the genome, indicating separately maintained transmission and recent genetic isolation. Each subpopulation could evolve and present a broader health challenge in Asia.

Matched MeSH terms: Genome
Fulltext Dataset of complete genome assembly and analysis of mycobacterium tuberculosis strain SIT745/EAI1-MYS

Abdullah M, Suraiya S, Mohamad S, Harun A

Data Brief, 2020 Aug;31:105949.
PMID: 32671154 DOI: 10.1016/j.dib.2020.105949

In this dataset, we report the genome assembly and data analysis of Mycobacterium tuberculosis strain SIT745/EAI1-MYS. Previously, this strain was isolated from a Malaysian patient with extra-pulmonary tuberculosis, and identification of this strain is done by spoligotype patterns with fifteen known Shared International Type (SITs). Further analysis showed that this strain has a remarkable phylogeographical specificity for Malaysia. Based on the National Center for Biotechnology Information (NCBI) nucleotide database information, the complete genome consists of 150 contigs with various sequence lengths and was not assembled. In this assembly, the aforementioned contigs along with reference sequence from Mycobacterium tuberculosis strain H37Rv and Mycobacterium bovis strain AF2122/97 was used for gap closures, were assembled into a single circular chromosome length of approximately 4.42 Mega bases (Mb) with an average GC content of 65.6%. The single circular chromosome was shown to contain 4,009 protein-coding sequences, 3 ribosomal RNAs, 45 transfer RNAs, and 12 superclasses distributed with 277 subsystems which constitute nearly 1900 genes, respectively. The genome information will provide fundamental knowledge of this organism as well as insight for understanding genomic and proteomic profiling, phylogenetic relationship.

Matched MeSH terms: Genome

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