Scalable metagenomic taxonomy classification using a reference genome database

AbstractMetagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen inclusion, data preparation, taxon labelling and accessibility, hindering their quality and comprehensiveness, and calling for the establishment of recommendations for reference genome database assembly. Here, we analyze existing fungal and bacterial databases and discuss guidelines for the development of a master reference database that promises to improve the quality and quantity of omics research.

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Two Approaches for a Genetic Analysis of Pompe Disease: A Literature Review of Patients with Pompe Disease and Analysis Based on Genomic Data from the General Population

Children ◽

10.3390/children8070601 ◽

2021 ◽

Vol 8 (7) ◽

pp. 601

Author(s):

Kyung-Sun Park

Keyword(s):

General Population ◽

Pompe Disease ◽

Genomic Data ◽

Japanese Patients ◽

Population Database ◽

Genome Database ◽

Genetic Database ◽

Pathogenic Variants ◽

Reference Genome Database ◽

Real Patients

In this study, two different approaches were applied in the analysis of the GAA gene. One was analyzed based on patients with Pompe disease, and the other was analyzed based on GAA genomic data from unaffected carriers in a general population genetic database. For this, GAA variants in Korean and Japanese patients reported in previous studies and in patients reported in the Pompe disease GAA variant database were analyzed as a model. In addition, GAA variants in the Korean Reference Genome Database (KRGDB), the Japanese Multi Omics Reference Panel (jMorp), and the Genome Aggregation Database (gnomAD) were analyzed. Overall, approximately 50% of the pathogenic or likely pathogenic variants (PLPVs) found in unaffected carriers were also found in real patients with Pompe disease (Koreans, 57.1%; Japanese, 46.2%). In addition, there was a moderate positive correlation (Spearman’s correlation coefficient of 0.45–0.69) between the proportion of certain PLPVs in patients and the minor allele frequency of their variants in a general population database. Based on the analysis of general population databases, the total carrier frequency for Pompe disease in Koreans and Japanese was estimated to be 1.7% and 0.7%, respectively, and the predicted genetic prevalence was 1:13,657 and 1:78,013, respectively.

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Pathogenic NOTCH3 Variants Are Frequent Among the Korean General Population

Neurology Genetics ◽

10.1212/nxg.0000000000000639 ◽

2021 ◽

Vol 7 (6) ◽

pp. e639

Author(s):

Chul-Hoo Kang ◽

Young Mee Kim ◽

Yang-Ji Kim ◽

Su-Jeong Hong ◽

Do Yoon Kim ◽

...

Keyword(s):

Cross Sectional Study ◽

Genome Project ◽

Jeju Island ◽

Cross Sectional ◽

Genome Database ◽

Pathogenic Variants ◽

Number Of Patients ◽

High Prevalence ◽

History Of ◽

Reference Genome Database

ObjectiveThis study aimed to determine the frequency of pathogenic NOTCH3 variants among Koreans.MethodsIn this cross-sectional study, we queried for pathogenic NOTCH3 variants in 2 Korean public genome databases: the Korean Reference Genome Database (KRGDB) and the Korean Genome Project (Korea1K). In addition, we screened the 3 most common pathogenic NOTCH3 variants (p.Arg75Pro, p.Arg544Cys, and p.Arg578Cys) for 1,000 individuals on Jeju Island, where the largest number of patients with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) have been reported in Korea.ResultsThe pathogenic NOTCH3 variant (p.Arg544Cys) was found in 0.12% of sequences in the KRGDB, and 3 pathogenic variants (p.Arg75Pro, p.Arg182Cys, and p.Arg544Cys) were present in 0.44% of the Korea1K database. Of the 1,000 individuals on Jeju Island, we found 2 cysteine-altering NOTCH3 variants (p.Arg544Cys variant in 9 and p.Arg578Cys in 1 individual) in 1.00% of the participants (95% confidence interval: 0.48%–1.83%). The presence of cysteine-altering NOTCH3 variants was significantly associated with a history of stroke (p < 0.001).DiscussionPathogenic NOTCH3 variants are frequently found in the general Korean population. Such a high prevalence of pathogenic variants could threaten the brain health of tens of thousands to hundreds of thousands of older adults in Korea.

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Bovine Genome Database: new annotation tools for a new reference genome

Nucleic Acids Research ◽

10.1093/nar/gkz944 ◽

2019 ◽

Cited By ~ 3

Author(s):

Md Shamimuzzaman ◽

Justin J Le Tourneau ◽

Deepak R Unni ◽

Colin M Diesh ◽

Deborah A Triant ◽

...

Keyword(s):

Genome Assembly ◽

Genome Annotation ◽

Reference Genome ◽

Gene Annotation ◽

Bovine Genome ◽

Data Retrieval ◽

Genome Database ◽

Ruminant Species ◽

Search Tool ◽

Efficient Data

Abstract The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.

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Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome

Animal Genetics ◽

10.1111/age.12962 ◽

2020 ◽

Vol 51 (5) ◽

pp. 675-682

Author(s):

D. A. Triant ◽

J. J. Le Tourneau ◽

C. M. Diesh ◽

D. R. Unni ◽

M. Shamimuzzaman ◽

...

Keyword(s):

Reference Genome ◽

Bovine Genome ◽

Genome Database ◽

Online Tools

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KRGDB: the large-scale variant database of 1722 Koreans based on whole genome sequencing

Database ◽

10.1093/database/baz146 ◽

2020 ◽

Vol 2020 ◽

Cited By ~ 1

Author(s):

Kwang Su Jung ◽

Kyung-Won Hong ◽

Hyun Youn Jo ◽

Jongpill Choi ◽

Hyo-Jeong Ban ◽

...

Keyword(s):

Large Scale ◽

Genome Wide Association Study ◽

Regulatory Elements ◽

Genome Database ◽

Genome Wide ◽

Variant Frequency ◽

Different Origins ◽

Java Server Page ◽

First Time ◽

Reference Genome Database

Abstract Since 2012, the Center for Genome Science of the Korea National Institute of Health (KNIH) has been sequencing complete genomes of 1722 Korean individuals. As a result, more than 32 million variant sites have been identified, and a large proportion of the variant sites have been detected for the first time. In this article, we describe the Korean Reference Genome Database (KRGDB) and its genome browser. The current version of our database contains both single nucleotide and short insertion/deletion variants. The DNA samples were obtained from four different origins and sequenced in different sequencing depths (10× coverage of 63 individuals, 20× coverage of 194 individuals, combined 10× and 20× coverage of 135 individuals, 30× coverage of 230 individuals and 30× coverage of 1100 individuals). The major features of the KRGDB are that it contains information on the Korean genomic variant frequency, frequency difference between the Korean and other populations and the variant functional annotation (such as regulatory elements in ENCODE regions and coding variant functions) of the variant sites. Additionally, we performed the genome-wide association study (GWAS) between Korean genome variant sites for the 30×230 individuals and three major common diseases (diabetes, hypertension and metabolic syndrome). The association results are displayed on our browser. The KRGDB uses the MySQL database and Apache-Tomcat web server adopted with Java Server Page (JSP) and is freely available at http://coda.nih.go.kr/coda/KRGDB/index.jsp. Availability: http://coda.nih.go.kr/coda/KRGDB/index.jsp

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New Data and Collaborations at the Saccharomyces Genome Database: Updated reference genome, alleles, and the Alliance of Genome Resources

10.1101/2021.09.16.460706 ◽

2021 ◽

Author(s):

Stacia R Engel ◽

Edith D Wong ◽

Robert S Nash ◽

Suzi Aleksander ◽

Micheal Alexander ◽

...

Keyword(s):

Reference Genome ◽

Model Organism ◽

Saccharomyces Genome Database ◽

Model Organisms ◽

Data Types ◽

Genome Database ◽

Product Function ◽

Chromosome Maps ◽

Genome Information ◽

Gene Product Function

Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.

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Computational analysis of the Plasmodiophora brassicae genome: mitochondrial sequence description and metabolic pathway database design

10.1101/335406 ◽

2018 ◽

Cited By ~ 1

Author(s):

S. Daval ◽

A. Belcour ◽

K. Gazengel ◽

L. Legrand ◽

J. Gouzy ◽

...

Keyword(s):

Metabolic Pathways ◽

Computational Analysis ◽

Reference Genome ◽

Plasmodiophora Brassicae ◽

Functional Study ◽

Spongospora Subterranea ◽

Pathway Database ◽

European Isolate ◽

Genome Database ◽

Brassicaceae Species

AbstractPlasmodiophora brassicae is an obligate biotrophic pathogenic protist responsible for clubroot, a root gall disease of Brassicaceae species. In addition to the reference genome of the P. brassicae European e3 isolate and the draft genomes of Canadian or Chinese isolates, we present the genome of eH, a second European isolate. Refinement of the annotation of the eH genome led to the identification of the mitochondrial genome sequence, which was found to be bigger than that of Spongospora subterranea, another plant parasitic Plasmodiophorid phylogenetically related to P. brassicae. New pathways were also predicted, such as those for the synthesis of spermidine, a polyamine up-regulated in clubbed regions of roots. A P. brassicae pathway genome database was created to facilitate the functional study of metabolic pathways in transcriptomics approaches. These available tools can help in our understanding of the regulation of P. brassicae metabolism during infection and in response to diverse constraints.

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Transcriptomics Analysis for the Detection of Novel Drought Tolerance Genes in Jojoba (Simmondsia Chinensis)

Proceedings ◽

10.3390/proceedings2019036135 ◽

2020 ◽

Vol 36 (1) ◽

pp. 135

Author(s):

Othman Al-Dossary ◽

Ardashir Kharabian ◽

Ibrahim Al-Mssallem ◽

Agnelo Furtado ◽

Robert Henry

Keyword(s):

Drought Tolerance ◽

Sonoran Desert ◽

Transcriptional Profiling ◽

Crop Improvement ◽

The United States ◽

Simmondsia Chinensis ◽

Genome Database ◽

Northwest Mexico ◽

Drought Tolerant ◽

Reference Genome Database

Jojoba (Simmondsia Chinensis) is a perennial stress tolerant desert shrub that has oil containing seeds and inhabits the Sonoran desert in the southwest of the United States and northwest Mexico. It has attracted a growing worldwide interest for multi-purpose uses. However, the most attractive characteristics of Jojoba are the richness of the oil content of the seed and the superior stress tolerance of the plant. Little has been done towards Jojoba genetic improvement. The exploration of jojoba genetic resources will define a molecular and biochemical fingerprint for jojoba and will aid sustainable crop commercialisation define. In this research, we aim to establish a reference genome database for Jojoba, which will help to facilitate crop improvement. Besides, the contribution to reveal the molecular background of its outstanding drought tolerance using transcriptional profiling during a water stress. RNA sequencing will be performed for samples collected under moderate and severe stress. The genetic database of jojoba will help to reveal the genetic mechanism of response and identify the genes responsible for the drought tolerant phenotype of this crop. Application of this knowledge will support the researchers, farmers, and the Jojoba industry.

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