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Fulltext Design and characterization of a 52K SNP chip for goats

Tosser-Klopp G, Bardou P, Bouchez O, Cabau C, Crooijmans R, Dong Y, et al.

PLoS One, 2014;9(1):e86227.
PMID: 24465974 DOI: 10.1371/journal.pone.0086227

The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.

Matched MeSH terms: Genomics
Fulltext Molecular Detection of Legionella: Moving on From mip

Yong SF, Tan SH, Wee J, Tee JJ, Sansom FM, Newton HJ, et al.

Front Microbiol, 2010;1:123.
PMID: 21687766 DOI: 10.3389/fmicb.2010.00123

The detection of Legionella pneumophila in environmental and clinical samples is frequently performed by PCR amplification of the mip and/or 16S rRNA genes. Combined with DNA sequencing, these two genetic loci can be used to distinguish different species of Legionella and identify L. pneumophila. However, the recent Legionella genome sequences have opened up hundreds of possibilities for the development of new molecular targets for detection and diagnosis. Ongoing comparative genomics has the potential to fine tune the identification of Legionella species and serogroups by combining specific and general genetic targets. For example, the coincident detection of LPS biosynthesis genes and virulence genes may allow the differentiation of both pathogen and serogroup without the need for nucleotide sequencing. We tested this idea using data derived from a previous genomic subtractive hybridization we performed between L. pneumophila serogroup 1 and L. micdadei. Although not yet formally tested, these targets serve as an example of how comparative genomics has the potential to improve the scope and accuracy of Legionella molecular detection if embraced by laboratories undertaking Legionella surveillance.

Matched MeSH terms: Genomics
Fulltext Functional significance of GnRH and kisspeptin, and their cognate receptors in teleost reproduction

Gopurappilly R, Ogawa S, Parhar IS

Front Endocrinol (Lausanne), 2013;4:24.
PMID: 23482509 DOI: 10.3389/fendo.2013.00024

Guanine nucleotide binding protein (G-protein)-coupled receptors (GPCRs) are eukaryotic transmembrane proteins found in all living organisms. Their versatility and roles in several physiological processes make them the single largest family of drug targets. Comparative genomic studies using various model organisms have provided useful information about target receptors. The similarity of the genetic makeup of teleosts to that of humans and other vertebrates aligns with the study of GPCRs. Gonadotropin-releasing hormone (GnRH) represents a critical step in the reproductive process through its cognate GnRH receptors (GnRHRs). Kisspeptin (Kiss1) and its cognate GPCR, GPR54 (=kisspeptin receptor, Kiss-R), have recently been identified as a critical signaling system in the control of reproduction. The Kiss1/Kiss-R system regulates GnRH release, which is vital to pubertal development and vertebrate reproduction. This review highlights the physiological role of kisspeptin-Kiss-R signaling in the reproductive neuroendocrine axis in teleosts through the modulation of GnRH release. Moreover, we also review the recent developments in GnRHR and Kiss-R with respect to their structural variants, signaling mechanisms, ligand interactions, and functional significance. Finally, we discuss the recent progress in identifying many teleost GnRH-GnRHR and kisspeptin-Kiss-R systems and consider their physiological significance in the control of reproduction.

Matched MeSH terms: Genomics
Fulltext Economic evaluations of personalized medicine: existing challenges and current developments

Shabaruddin FH, Fleeman ND, Payne K

Pharmgenomics Pers Med, 2015;8:115-26.
PMID: 26309416 DOI: 10.2147/PGPM.S35063

Personalized medicine, with the aim of safely, effectively, and cost-effectively targeting treatment to a prespecified patient population, has always been a long-time goal within health care. It is often argued that personalizing treatment will inevitably improve clinical outcomes for patients and help achieve more effective use of health care resources. Demand is increasing for demonstrable evidence of clinical and cost-effectiveness to support the use of personalized medicine in health care. This paper begins with an overview of the existing challenges in conducting economic evaluations of genetics- and genomics-targeted technologies, as an example of personalized medicine. Our paper illustrates the complexity of the challenges faced by these technologies by highlighting the variations in the issues faced by diagnostic tests for somatic variations, generally referring to genetic variation in a tumor, and germline variations, generally referring to inherited genetic variation in enzymes involved in drug metabolic pathways. These tests are typically aimed at stratifying patient populations into subgroups on the basis of clinical effectiveness (response) or safety (avoidance of adverse events). The paper summarizes the data requirements for economic evaluations of genetics and genomics-based technologies while outlining that the main challenges relating to data requirements revolve around the availability and quality of existing data. We conclude by discussing current developments aimed to address the challenges of assessing the cost-effectiveness of genetics and genomics-based technologies, which revolve around two central issues that are interlinked: the need to adapt available evaluation methods and identifying who is responsible for generating evidence for these technologies.

Matched MeSH terms: Genomics
Novel mutations in SKIV2L and TTC37 genes in Malaysian children with trichohepatoenteric syndrome

Lee WS, Teo KM, Ng RT, Chong SY, Kee BP, Chua KH

Gene, 2016 Jul 15;586(1):1-6.
PMID: 27050310 DOI: 10.1016/j.gene.2016.03.049

Trichohepatoenteric syndrome (THES) is a rare autosomal recessive disorder that is classically associated with intractable diarrhea with an onset within the first few months of life. Herein, we investigated and reported novel mutations in two causal genes in 3 Malaysian cases. Genomic DNA was extracted from peripheral blood obtained from patients in two Malaysian Chinese families. The exons of SKIV2L and TTC37 genes were amplified and sequenced by bi-directional sequencing to identify the point mutations within the coding sequence. Three Chinese boys from two families with characteristic features and clinical course were diagnosed with THES. In family-1, two point mutations were identified in the SKIV2L gene (c.1891G>A and c.3187C>T). In family-2, a single-nucleotide duplication (c.3426dupA) was found in the TTC37 gene. These mutations cause the production of abnormal non-functional gene product leading to the clinical manifestations in the patients. We reported three point mutations, which have not been previously described in other patients with THES in SKIV2L and TTC37 genes, including one nonsense, one frameshift, and one missense mutations.

Matched MeSH terms: Genomics
Fulltext Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

Yap KP, Ho WS, Gan HM, Chai LC, Thong KL

Front Microbiol, 2016;7:270.
PMID: 26973639 DOI: 10.3389/fmicb.2016.00270

Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus sequence typing (MLST) is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2) co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC, and tviD that may explain the variations that differentiate between seemingly successful (widespread) and unsuccessful (poor dissemination) S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.

Matched MeSH terms: Genomics
Fulltext Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters

Khalili Samani N, Esa Y, Amin SM, Fatin Mohd Ikhsan N

PeerJ, 2016;4:e1930.
PMID: 27231645 DOI: 10.7717/peerj.1930

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P. canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395-0.771 and 0.033-0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (Ho ) value of 0.2168, which was lower than the standard heterozygosity in marine populations (Ho = 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.

Matched MeSH terms: Genomics
Fulltext An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily

Ong AL, Teh CK, Mayes S, Massawe F, Appleton DR, Kulaveerasingam H

Plants (Basel), 2020 Nov 03;9(11).
PMID: 33152992 DOI: 10.3390/plants9111476

Oil palm (Elaeis guineensis Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of E. guineensis that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by assigning an additional 1968 originally unplaced scaffolds that were available publicly into the physical genome. By integrating three ultra-dense linkage maps and using them to place genomic scaffolds, the 16 pseudomolecules were extended. As we show, the improved genome has enhanced the mapping resolution for genome-wide association studies (GWAS) and permitted further identification of candidate genes/protein-coding regions (CDSs) and any non-coding RNA that may be associated with them for further studies. We then employed the new physical map in a comparative genomics study against two other agriculturally and economically important palm species-date palm (Phoenix dactylifera L.) and coconut palm (Cocos nucifera L.)-confirming the high level of conserved synteny among these palm species. We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map. The improved genome of oil palm will enable molecular breeding approaches to expedite crop improvement, especially in the largest subfamily of Arecoideae, which consists of 107 species belonging to Arecaceae.

Matched MeSH terms: Genomics
Fulltext Diet Composition of the Wild Stump-Tailed Macaque (Macaca arctoides) in Perlis State Park, Peninsular Malaysia, Using a Chloroplast tRNL DNA Metabarcoding Approach: A Preliminary Study

Osman NA, Abdul-Latiff MAB, Mohd-Ridwan AR, Yaakop S, Nor SM, Md-Zain BM

Animals (Basel), 2020 Nov 26;10(12).
PMID: 33255964 DOI: 10.3390/ani10122215

Understanding dietary diversity is a fundamental task in the study of stump-tailed macaque, Macaca arctoides in its natural habitat. However, direct feeding observation and morphological identification using fecal samples are not effective and nearly impossible to obtain in natural habitats because this species is sensitive to human presence. As ecological methods are challenging and time-consuming, DNA metabarcoding offers a more powerful assessment of the diet. We used a chloroplast tRNL DNA metabarcoding approach to identify the diversity of plants consumed by free-ranging M. arctoides in the Malaysia-Thailand border region located in Perlis State Park, Peninsular Malaysia. DNA was extracted from three fecal samples, and chloroplast tRNL DNA was amplified and sequenced using the Illumina MiniSeq platform. Sequences were analyzed using the CLC Genomic Workbench software. A total of 145 plant species from 46 families were successfully identified as being consumed by M. arctoides. The most abundant species were yellow saraca, Saraca thaipingensis (11.70%), common fig, Ficus carica (9.33%), aramata, Clathrotropis brachypetala (5.90%), sea fig, Ficus superba (5.44%), and envireira, Malmea dielsiana (1.70%). However, Clathrotropis and Malmea are not considered Malaysian trees because of limited data available from Malaysian plant DNA. Our study is the first to identify plant taxa up to the species level consumed by stump-tailed macaques based on a DNA metabarcoding approach. This result provides an important understanding on diet of wild M. arctoides that only reside in Perlis State Park, Malaysia.

Matched MeSH terms: Genomics
Fulltext The whole genome sequence data analyses of a Mycobacterium tuberculosis strain SBH321 isolated in Sabah, Malaysia, belongs to Ural family of Lineage 4

Jani J, Mustapha ZA, Ling CK, Hui ASM, Teo R, Ahmed K

Data Brief, 2020 Dec;33:106388.
PMID: 33102655 DOI: 10.1016/j.dib.2020.106388

In 2019, 10 million new cases of tuberculosis have been reported worldwide. Our data reports genetic analyses of a Mycobacterium tuberculosis strain SBH321 isolated from a 31-year-old female with pulmonary tuberculosis. The genomic DNA of the strain was extracted from pure culture and subjected to sequencing using Illumina platform. M. tuberculosis strain SBH321 consists of 4,374,895 bp with G+C content of 65.59%. The comparative analysis by SNP-based phylogenetic analysis using maximum-likelihood method showed that our strain belonging to sublineage of the Ural family of Europe-America-Africa lineage (Lineage 4) and clustered with M. tuberculosis strain OFXR-4 from Taiwan. The whole genome sequence is deposited at DDBJ/ENA/GenBank under the accession WCJH00000000 (SRR10230353).

Matched MeSH terms: Genomics
Fulltext Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era

Neik TX, Amas J, Barbetti M, Edwards D, Batley J

Plants (Basel), 2020 Oct 10;9(10).
PMID: 33050509 DOI: 10.3390/plants9101336

Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.

Matched MeSH terms: Genomics
Fulltext Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers

Moura AE, Shreves K, Pilot M, Andrews KR, Moore DM, Kishida T, et al.

Mol Phylogenet Evol, 2020 05;146:106756.
PMID: 32028032 DOI: 10.1016/j.ympev.2020.106756

Phylogeographic inference has provided extensive insight into the relative roles of geographical isolation and ecological processes during evolutionary radiations. However, the importance of cross-lineage admixture in facilitating adaptive radiations is increasingly being recognised, and suggested as a main cause of phylogenetic uncertainty. In this study, we used a double digest RADseq protocol to provide a high resolution (~4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results suggest monophyly for the genus Tursiops, with the recently proposed T. australis species falling within the T. aduncus lineage. We also show the presence of extensive cross-lineage gene flow between pelagic and European coastal ecotypes of T. truncatus, as well as in the early stages of diversification between spotted (Stenella frontalis; Stenella attenuata), spinner (Stenella longirostris), striped (Stenella coeruleoalba), common (Delphinus delphis), and Fraser's (Lagenodelphis hosei) dolphins. Our study suggests that cross-lineage gene flow in this group has been more extensive and complex than previously thought. In the context of biogeography and local habitat dependence, these results improve our understanding of the evolutionary processes determining the history of this lineage.

Matched MeSH terms: Genomics
Fulltext Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly

Tan MH, Austin CM, Hammer MP, Lee YP, Croft LJ, Gan HM

Gigascience, 2018 03 01;7(3):1-6.
PMID: 29342277 DOI: 10.1093/gigascience/gix137

Background: Some of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity, and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes that warrant investigation. Leveraging on the advancement in Nanopore long read technology, we report the first hybrid assembly of the clown anemonefish (Amphiprion ocellaris) genome utilizing Illumina and Nanopore reads, further demonstrating the substantial impact of modest long read sequencing data sets on improving genome assembly statistics.
Results: We generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads, representing approximate genome coverage of 54× and 11×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 and 967 Mbp. The final assembled genome is contained in 6404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared with the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with an 18-fold increase in N50 length (401 kb) and increased the genome completeness by an additional 16%. A total of 27 240 high-quality protein-coding genes were predicted from the clown anemonefish, 26 211 (96%) of which were annotated functionally with information from either sequence homology or protein signature searches.
Conclusions: We present the first genome of any anemonefish and demonstrate the value of low coverage (∼11×) long Nanopore read sequencing in improving both genome assembly contiguity and completeness. The near-complete assembly of the A. ocellaris genome will be an invaluable molecular resource for supporting a range of genetic, genomic, and phylogenetic studies specifically for clownfish and more generally for other related fish species of the family Pomacentridae.

Matched MeSH terms: Genomics
Genomic characterization of endemic Salmonella enterica serovar Typhimurium and Salmonella enterica serovar I 4,[5],12:i:- isolated in Malaysia

Ngoi ST, Yap KP, Thong KL

Infect Genet Evol, 2018 08;62:109-121.
PMID: 29684710 DOI: 10.1016/j.meegid.2018.04.027

Salmonella enterica serovar Typhimurium (S. Typhimurium) and the monophasic variant Salmonella I 4,[5],12:i:- are two clinically-important non-typhoidal Salmonella serovars worldwide. However, the genomic information of these two organisms, especially the monophasic variant, is still lacking in Malaysia. The objective of the study was to compare the genomic features of a monophasic variant and two endemic S. Typhimurium strains isolated from humans. All three strains were subjected to whole genome sequencing followed by comparative genomic and phylogenetic analyses. Extensive genomic deletion in the fljAB operon (from STM2757 to iroB) is responsible for the monophasic phenotype of STM032/04. The two S. Typhimurium genomes (STM001/70 and STM057/05) were essentially identical, despite being isolated 35 years apart. All three strains were of sequence type ST19. Both S. Typhimurium genomes shared unique prophage regions not identified in the monophasic STM032/04 genome. Core genome phylogenetic analyses showed that the monophasic STM032/04 was closely-related to the S. Typhimurium LT2, forming a distinctive clade separated from the two endemic S. Typhimurium strains in Malaysia. The presence of serovar Typhimurium-specific mdh gene, conserved Gifsy and Fels-1 prophages, and the close genomic resemblance with S. Typhimurium LT2 suggested that the monophasic STM032/04 was originated from an LT2-like S. Typhimurium ancestor in Malaysia, following an evolutionary path different from the S. Typhimurium strains. In conclusion, the monophasic Salmonella I 4,[5],12:i:- and the S. Typhimurium strains isolated in Malaysia descended from different phylogenetic lineages. The high genomic resemblance between the two S. Typhimurium strains isolated for at least 35 years apart indicated their successful evolutionary lineage. The identification of multiple virulence and antimicrobial resistance determinants in the Salmonella I 4,[5],12:i:- and S. Typhimurium genomes explained the pathogenic nature of the organisms.

Matched MeSH terms: Genomics
Fulltext First genomic insights into carbapenem-resistant Klebsiella pneumoniae from Malaysia

Gan HM, Eng WWH, Dhanoa A

J Glob Antimicrob Resist, 2020 03;20:153-159.
PMID: 31325618 DOI: 10.1016/j.jgar.2019.07.008

OBJECTIVES: Despite the increasing reports of carbapenem-resistant Enterobacteriaceae in Malaysia, genomic resources for carbapenem-resistant clinical strains of Klebsiella pneumoniae (K. pneumoniae) remain unavailable. This study aimed to sequence the genomes of multiple carbapenem-resistant K. pneumoniae strains from Malaysia and to identify the genetic basis for their resistance.
METHODS: Illumina whole genome sequencing was performed on eight carbapenem-resistant K. pneumoniae isolated from a Malaysian hospital. Genetic diversity was inferred from the assembled genomes based on in silico multilocus sequence typing (MLST). In addition, plasmid-derived and chromosome-derived contigs were predicted using the machine learning approach. After genome annotation, genes associated with carbapenem resistance were identified based on similarity searched against the ResFinder database.
RESULTS: The eight K. pneumoniae isolates were grouped into six different sequence types, some of which were represented by a single isolate in the MLST database. Genomic potential for carbapenem-resistance was attributed to the presence of plasmid-localised blaNDM (blaNDM-1/blaNDM-5) or blaKPC (blaKPC-2/blaKPC-6) in these sequenced strains. The majority of these carbapenem resistance genes was flanked by repetitive (transposase or integrase) sequences, suggesting their potential mobility. This study also reported the first blaKPC-6-harbouring plasmid contig to be assembled for K. pneumoniae, and the second for the genus Klebsiella.
CONCLUSION: This study reported the first genomic resources for carbapenem-resistant K. pneumoniae from Malaysia. The high diversity of carbapenem resistance genes and sequence types uncovered from eight isolates from the same hospital is worrying and indicates an urgent need to improve the genomic surveillance of clinical K. pneumoniae in Malaysia.

Matched MeSH terms: Genomics
Analysis of raw meats and fats of pigs using polymerase chain reaction for Halal authentication

Aida AA, Che Man YB, Wong CM, Raha AR, Son R

Meat Sci, 2005 Jan;69(1):47-52.
PMID: 22062638 DOI: 10.1016/j.meatsci.2004.06.020

A method for species identification from pork and lard samples using polymerase chain reaction (PCR) analysis of a conserved region in the mitochondrial (mt) cytochrome b (cyt b) gene has been developed. Genomic DNA of pork and lard were extracted using Qiagen DNeasy(®) Tissue Kits and subjected to PCR amplification targeting the mt cyt b gene. The genomic DNA from lard was found to be of good quality and produced clear PCR products on the amplification of the mt cyt b gene of approximately 360 base pairs. To distinguish between species, the amplified PCR products were cut with restriction enzyme BsaJI resulting in porcine-specific restriction fragment length polymorphisms (RFLP). The cyt b PCR-RFLP species identification assay yielded excellent results for identification of pig species. It is a potentially reliable technique for detection of pig meat and fat from other animals for Halal authentication.

Matched MeSH terms: Genomics
Fulltext A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause

Boyle JH, Rastas PMA, Huang X, Garner AG, Vythilingam I, Armbruster PA

Insects, 2021 Feb 16;12(2).
PMID: 33669192 DOI: 10.3390/insects12020167

The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (~1.19-1.28 Gb by cytofluorometric estimates), comprised of ~68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our reassembled genome sequence, AalbF3, represents several improvements relative to AalbF2. First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as a reference for a bulk-segregant-based comparative genomics analysis that identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of A. albopictus.

Matched MeSH terms: Genomics
Fulltext A modified method for genomic DNA extraction from the fish intestinal microflora

Han Z, Sun J, Lv A, Sung Y, Sun X, Shi H, et al.

AMB Express, 2018 Apr 02;8(1):52.
PMID: 29610998 DOI: 10.1186/s13568-018-0578-3

A modified genomic DNA extraction method named the combination of lysozyme and ultrasonic lysis (CLU) method was used to analyze the fish intestinal microflora. In this method, the physical disruption and chemical lysis steps were combined, and some parameters in the key steps were adjusted. In addition, the results obtained by this method were compared with the results obtained by the Zirmil-beating cell disruption method and the QIAamp Fast DNA Stool Mini Kit. The OD260/OD280ratio and concentration of the DNA extracted using the CLU method were 2.02 and 282.8 µg/µL, respectively; when the incubation temperatures for lysozyme and RNase were adjusted to 37 °C, those values were 2.08 and 309.8 µg/µL, respectively. On the agarose gel, a major high-intensity, discrete band of more than 10 kb was found for the CLU method. However, the smearing intensity of degraded DNA was lower when the incubation temperatures were 60 °C for lysozyme and 30 °C for RNase than when incubation temperatures of 37 °C for lysozyme and 37 °C for RNase were used. The V3 variable region of the prokaryotic 16S rDNA was amplified, and an approximately 600-bp fragment was observed when the DNA extracted using the CLU method was used as a template. The CLU method is simple and cost effective, and it yields high-quality, unsheared, high-molecular-weight DNA, which is comparable to that obtained with a commercially available kit. The extracted DNA has potential for applications in critical molecular biology techniques.

Matched MeSH terms: Genomics
Reviewing the molecular mechanisms which increase endometrial cancer (EC) risk in women with polycystic ovarian syndrome (PCOS): time for paradigm shift?

Shafiee MN, Chapman C, Barrett D, Abu J, Atiomo W

Gynecol Oncol, 2013 Nov;131(2):489-92.
PMID: 23822891 DOI: 10.1016/j.ygyno.2013.06.032

Endometrial cancer (EC) is the commonest gynaecological cancer in North American and European women. Even though it has been shown that women with polycystic ovary syndrome (PCOS) have a three-fold increase in the risk of developing EC compared to women without PCOS, the precise molecular mechanisms which increase EC risk in women with PCOS remain unclear. Clinical strategies to prevent EC in PCOS are therefore not well researched and understood. Although raised estrogen levels, hyperinsulinaemia and, reduced apoptosis have been suggested as potential mechanisms, there is a lack of clarity about how these factors and other factors may interact to increase EC risk in PCOS. This article reviews the literature, on the potential molecular links between PCOS and EC but argues for a paradigm shift, to a systems biology-based approach in future research into the molecular links between PCOS and EC. The potential challenges of a systems biology-based approach are outlined but not considered insurmountable.

Matched MeSH terms: Genomics
Molecular phylogeny and ancestral biogeographic reconstruction of Platanthera subgenus Limnorchis (Orchidaceae) using target capture methods

Wettewa E, Wallace LE

Mol Phylogenet Evol, 2021 04;157:107070.
PMID: 33421614 DOI: 10.1016/j.ympev.2021.107070

Platanthera is one of the largest genera of temperate orchids in the Holarctic and exemplifies a lineage that has adaptively radiated into diverse habitats within North America, Asia, Europe, North Africa, Borneo, and Sarawak. Major centers of diversity in this genus are North America and eastern Asia. Despite its diversity, a thorough phylogenetic hypothesis for the genus is lacking because no studies have yet sampled taxa exhaustively or developed a robust molecular toolkit. While there is strong evidence that suggests monophyly of subgenus Limnorchis, most taxa in this group have not been included in a phylogenetic analysis. In this study, we developed a new toolkit for Platanthera consisting of genomic information from 617 low-copy nuclear loci. Using a targeted enrichment approach, we collected high-throughput sequence data in 23 accessions of nine of the 12 diploid species of subgenus Limnorchis and outgroup species across Platanthera. A maximum likelihood analysis resolved a strongly supported monophyletic clade for subgenus Limnorchis. Ancestral biogeographic reconstruction indicated that subgenus Limnorchis originated in western North America ca. 3-4.5 Mya from an ancestor that was widespread in western North America and eastern Asia and subsequently diversified in western North America, followed by dispersal of some species to eastern North America. Our results indicate complex biogeographic connections between Asia and North America, and therefore it suggests that Platanthera is a suitable system to test biogeographic hypotheses over time and space in the Holarctic. Our results are also expected to facilitate further study of diversification and biogeographic spread across Platanthera and lay the groundwork for understanding independent origins, biogeography, and morphological diversification of polyploid species within subgenus Limnorchis.

Matched MeSH terms: Genomics

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