Comparative Sequence of Human and Mouse BAC Clones from the mnd2 Region of Chromosome 2p13

The mnd2 mutation on mouse chromosome 6 produces a progressive neuromuscular disorder. To determine the gene content of the 400-kb mnd2 nonrecombinant region, we sequenced 108 kb of mouse genomic DNA and 92 kb of human genomic sequence from the corresponding region of chromosome 2p13.3. Three genes with the indicated sizes and intergenic distances were identified:D6Mm5e (⩾81 kb)–787 bp–DOK (2 kb)–845 bp–LOR2 (⩾6 kb). D6Mm5e is expressed in many tissues at very low abundance and the predicted 526-residue protein contains no known functional domains. DOK encodes the p62dok rasGAP binding protein involved in signal transduction. LOR2 encodes a novel lysyl oxidase-related protein of 757 amino acid residues. We describe a simple search protocol for identification of conserved internal exons in genomic sequence. Evolutionary conservation proved to be a useful criterion for distinguishing between authentic exons and artifactual products obtained by exon amplification, RT–PCR, and 5′ RACE. Conserved noncoding sequence elements longer than 80 bp with ⩾75% nucleotide sequence identity comprise ∼1% of the genomic sequence in this region. Comparative analysis of this human and mouse genomic DNA sequence was an efficient method for gene identification and is independent of developmental stage or quantitative level of gene expression.[The sequence data described in this paper have been submitted to the GenBank data library under the following accession numbers: AC003061, mouse BAC clone 245c12; AC003065, human BAC clone h173(E10); AF053368, mouse Lor2 cDNA; AF084363, 108-kb contig from mouse BAC 245c12; AF084364, mouse D6Mm5ecDNA.]

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Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.054171-0 ◽

2014 ◽

Vol 64 (Pt_2) ◽

pp. 316-324 ◽

Cited By ~ 258

Author(s):

Jongsik Chun ◽

Fred A. Rainey

Keyword(s):

Genomic Sequence ◽

Sequence Data ◽

Original Research ◽

Rrna Gene ◽

New Taxon ◽

Genome Sequences ◽

Microbial World ◽

Content Type ◽

Link Type ◽

Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

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BrADseq for DNA v1

10.17504/protocols.io.bsx9nfr6 ◽

2021 ◽

Author(s):

S. Thomas Kelly ◽

tsuneo.hakoyama not provided ◽

Kie Kumaishi ◽

Haruka Okuda-Yabukami ◽

Sachi Kato ◽

...

Keyword(s):

Genomic Dna ◽

Genomic Sequence ◽

Sequence Data ◽

Gc Content ◽

Handling Time ◽

Cost Effective ◽

Dna Amount ◽

Dna Libraries ◽

Genomic Regions ◽

Next Generation Sequencing Ngs

The amount of input DNA available to prepare next-generation sequencing (NGS) libraries is often limited, which can lead to GC content bias and enrichment of specific genomic regions with currently available protocols. In this study, we used breath capture technology to incorporate sequencing adapters into DNA to develop a novel cost-effective protocol for the preparation of genomic DNA libraries. We performed a benchmarking experiment comparing our protocol with common commercially available kits for genomic DNA library preparation with input DNA amount in the range of 1 to 50 ng. Our protocol can generate high-quality genomic sequence data with a marked improvement in coverage breadth and low GC bias, in contrast to standard protocols. Further, our protocol reduces sample handling time and reagent costs, and requires comparatively fewer enzymatic steps relative to other protocols, making it suitable for a range of genomics applications.

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Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results

10.1101/191783 ◽

2017 ◽

Author(s):

Gil Alterovitz ◽

Dennis Dean ◽

Carole Goble ◽

Michael R. Crusoe ◽

Stian Soiland-Reyes ◽

...

Keyword(s):

Precision Medicine ◽

High Throughput Sequencing ◽

Genomic Sequence ◽

Sequence Data ◽

Data Provenance ◽

Provenance Analysis ◽

Link Type ◽

Sequencing Studies ◽

Standardized Reporting ◽

Personalized Approach

AbstractA personalized approach based on a patient’s or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to FAIR guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet lab procedures to computational methods. The BioCompute framework (https://osf.io/zm97b/) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCO) offer that standard, and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development”. By communication of high-throughput sequencing studies using a BCO, regulatory agencies (e.g., FDA), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next generation sequencing workflow exchange, reporting, and regulatory reviews.

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Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.048983-0 ◽

2013 ◽

Vol 63 (Pt_7) ◽

pp. 2727-2741 ◽

Cited By ~ 28

Author(s):

James J. Davis ◽

Fangfang Xia ◽

Ross A. Overbeek ◽

Gary J. Olsen

Keyword(s):

Ribosomal Proteins ◽

Genomic Sequence ◽

Sequence Data ◽

Taxonomic Revision ◽

Trna Synthetase ◽

Microbial Evolution ◽

23S Rrna ◽

Content Type ◽

Link Type ◽

Metabolic Functions

The tree of life is paramount for achieving an integrated understanding of microbial evolution and the relationships between physiology, genealogy and genomics. It provides the framework for interpreting environmental sequence data, whether applied to microbial ecology or to human health. However, there remain many instances where there is ambiguity in our understanding of the phylogeny of major lineages, and/or confounding nomenclature. Here we apply recent genomic sequence data to examine the evolutionary history of members of the classes Mollicutes (phylum Tenericutes ) and Erysipelotrichia (phylum Firmicutes ). Consistent with previous analyses, we find evidence of a specific relationship between them in molecular phylogenies and signatures of the 16S rRNA, 23S rRNA, ribosomal proteins and aminoacyl-tRNA synthetase proteins. Furthermore, by mapping functions over the phylogenetic tree we find that the erysipelotrichia lineages are involved in various stages of genomic reduction, having lost (often repeatedly) a variety of metabolic functions and the ability to form endospores. Although molecular phylogeny has driven numerous taxonomic revisions, we find it puzzling that the most recent taxonomic revision of the phyla Firmicutes and Tenericutes has further separated them into distinct phyla, rather than reflecting their common roots.

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rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data

Microbial Genomics ◽

10.1099/mgen.0.000583 ◽

2021 ◽

Vol 7 (6) ◽

Author(s):

Ivan Sserwadda ◽

Gerald Mboowa

Keyword(s):

Low Income ◽

Type Species ◽

Genomic Sequence ◽

Sequence Data ◽

Whole Genome Sequence ◽

Whole Genome ◽

Analysis Pipeline ◽

Content Type ◽

Link Type ◽

Microbial Analysis

The recent re-emergence of multidrug-resistant pathogens has exacerbated their threat to worldwide public health. The evolution of the genomics era has led to the generation of huge volumes of sequencing data at an unprecedented rate due to the ever-reducing costs of whole-genome sequencing (WGS). We have developed the Rapid Microbial Analysis Pipeline (rMAP), a user-friendly pipeline capable of profiling the resistomes of ESKAPE pathogens ( Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa and Enterobacter species) using WGS data generated from Illumina’s sequencing platforms. rMAP is designed for individuals with little bioinformatics expertise, and automates the steps required for WGS analysis directly from the raw genomic sequence data, including adapter and low-quality sequence read trimming, de novo genome assembly, genome annotation, single-nucleotide polymorphism (SNP) variant calling, phylogenetic inference by maximum likelihood, antimicrobial resistance (AMR) profiling, plasmid profiling, virulence factor determination, multi-locus sequence typing (MLST), pangenome analysis and insertion sequence characterization (IS). Once the analysis is finished, rMAP generates an interactive web-like html report. rMAP installation is very simple, it can be run using very simple commands. It represents a rapid and easy way to perform comprehensive bacterial WGS analysis using a personal laptop in low-income settings where high-performance computing infrastructure is limited.

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Genome rearrangements and megaplasmid loss in the filamentous bacteriumKitasatospora viridifaciensare associated with protoplast formation and regeneration

10.1101/629089 ◽

2019 ◽

Author(s):

Karina Ramijan ◽

Zheren Zhang ◽

Gilles P. van Wezel ◽

D. Claessen

Keyword(s):

Genomic Sequence ◽

Sequence Data ◽

Morphological Diversity ◽

Protoplast Formation ◽

Genetic Changes ◽

Sequence Elements ◽

The Right ◽

Accession Code ◽

Insertion Sequence Elements ◽

Replicative Transposition

AbstractFilamentous Actinobacteria are multicellular bacteria with linear replicons.Kitasatospora viridifaciensDSM 40239 contains a linear 7.8 Mb chromosome and an autonomously replicating plasmid KVP1 of 1.7 Mb. Here we show that lysozyme-induced protoplast formation of the multinucleated mycelium ofK. viridifaciensdrives morphological diversity. Characterization and sequencing of an individual revertant colony that had lost the ability to differentiate revealed that the strain had not only lost most of KVP1 but also carried lesions in the right arm of the chromosome. Strikingly, the lesion sites were preceded by insertion sequence elements, suggesting that the rearrangements may have been caused by replicative transposition and homologous recombination between both replicons. These data indicate that protoplast formation is a stressful process that can lead to profound genetic changes.RepositoriesGenomic sequence data for strain B3.1 has been deposited in the NCBI SRA database under accession code SAMN11514356.

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Gene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis

Genome Research ◽

10.1101/gr.159800 ◽

2000 ◽

Vol 10 (12) ◽

pp. 2030-2043

Author(s):

Justen Andrews ◽

Gerard G. Bouffard ◽

Chris Cheadle ◽

Jining Lü ◽

Kevin G. Becker ◽

...

Keyword(s):

Microarray Analysis ◽

Genomic Sequence ◽

Sequence Data ◽

Expression Profiles ◽

Transcript Abundance ◽

Cdna Libraries ◽

Link Type ◽

Microarray Expression ◽

Expressed Sequence ◽

Data Library

Identification and annotation of all the genes in the sequencedDrosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophilatestis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis matchDrosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601.[The sequence data described in this paper have been submitted to the dbEST data library under accession nos.AI944400–AI947263 and BE661985–BE662262.][The microarray data described in this paper have been submitted to the GEO data library under accession nos. GPLS, GSM3–GSM10.]

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Characterization of Clustered MHC-Linked Olfactory Receptor Genes in Human and Mouse

Genome Research ◽

10.1101/gr.160301 ◽

2001 ◽

Vol 11 (4) ◽

pp. 519-530 ◽

Cited By ~ 2

Author(s):

Ruth M. Younger ◽

Claire Amadou ◽

Graeme Bethel ◽

Anke Ehlers ◽

Kirsten Fischer Lindahl ◽

...

Keyword(s):

Olfactory Receptor ◽

Mate Selection ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Long Distance ◽

Functional Studies ◽

Link Type ◽

Genomic Environment ◽

Human And Mouse

Olfactory receptor (OR) loci frequently cluster and are present on most human chromosomes. They are members of the seven transmembrane receptor (7-TM) superfamily and, as such, are part of one of the largest mammalian multigene families, with an estimated copy number of up to 1000 ORs per haploid genome. As their name implies, ORs are known to be involved in the perception of odors and possibly also in other, nonolfaction-related, functions. Here, we report the characterization of ORs that are part of the MHC-linked OR clusters in human and mouse (partial sequence only). These clusters are of particular interest because of their possible involvement in olfaction-driven mate selection. In total, we describe 50 novel OR loci (36 human, 14 murine), making the human MHC-linked cluster the largest sequenced OR cluster in any organism so far. Comparative and phylogenetic analyses confirm the cluster to be MHC-linked but divergent in both species and allow the identification of at least one ortholog that will be useful for future regulatory and functional studies. Quantitative feature analysis shows clear evidence of duplications of blocks of OR genes and reveals the entire cluster to have a genomic environment that is very different from its neighboring regions. Based on in silico transcript analysis, we also present evidence of extensive long-distance splicing in the 5′-untranslated regions and, for the first time, of alternative splicing within the single coding exon of ORs. Taken together with our previous finding that ORs are also polymorphic, the presented data indicate that the expression, function, and evolution of these interesting genes might be more complex than previously thought.[The sequence data described in this paper have been submitted to the EMBL nucleotide data library under accession nos.Z84475, Z98744, Z98745, AL021807, AL021808, AL022723, AL022727,AL031893, AL035402, AL035542, AL050328, AL050339, AL078630, AL096770,AL121944, AL133160, and AL133267.]

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A Sequence-Ready BAC Clone Contig of a 2.2-Mb Segment of Human Chromosome 1q24

Genome Research ◽

10.1101/gr.9.2.150 ◽

1999 ◽

Vol 9 (2) ◽

pp. 150-157 ◽

Cited By ~ 1

Author(s):

Douglas Vollrath ◽

Virna L. Jaramillo-Babb

Keyword(s):

Large Scale ◽

Sequence Data ◽

Artificial Chromosome ◽

Average Density ◽

Walking Distance ◽

Disease Genes ◽

Bac Clone ◽

Distance Information ◽

Link Type ◽

Duplication Events

Human chromosomal region 1q24 encodes two cloned disease genes and lies within large genetic inclusion intervals for several disease genes that have yet to be identified. We have constructed a single bacterial artificial chromosome (BAC) clone contig that spans over 2 Mb of 1q24 and consists of 78 clones connected by 100 STSs. The average density of mapped STSs is one of the highest described for a multimegabase region of the human genome. The contig was efficiently constructed by generating STSs from clone ends, followed by library walking. Distance information was added by determining the insert sizes of all clones, and expressed sequence tags (ESTs) and genes were incorporated to create a partial transcript map of the region, providing candidate genes for local disease loci. The gene order and content of the region provide insight into ancient duplication events that have occurred on proximal 1q. The stage is now set for further elucidation of this interesting region through large-scale sequencing.[The sequence data described in this paper have been submitted to GenBank under accession nos. G42259–G42312 and G42330–G42335.]

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Arenibacter arenosicollis sp. nov., isolated from a sand dune

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004709 ◽

2021 ◽

Author(s):

Sooyeon Park ◽

Seo Yeon Lee ◽

Jung-Sook Lee ◽

Wonyong Kim ◽

Jung-Hoon Yoon

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Genomic Sequence ◽

Sequence Data ◽

The Yellow Sea ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterial strain, designated BSSL-BM3T, was isolated from sand collected from a dune near the Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain BSSL-BM3T fell within the clade comprising the type strains of Arenibacter species. Strain BSSL-BM3T exhibited 16S rRNA gene sequence similarity values of 98.0–99.0 % to the type strains of Arenibacter catalasegens , Arenibacter hampyeongensis , Arenibacter echinorum , Arenibacter palladensis and Arenibacter troitsensis and of 94.2–96.7 % to the type strains of the other Arenibacter species. The averagenucleotide identity and digitalDNA–DNA hybridization values between strain BSSL-BM3T and the type strains of A. catalasegens , A. hampyeongensis , A. echinorum , A. palladensis and A. troitsensis were 82.2–88.8 % and 25.0–36.5 %, respectively. The DNA G+C content of strain BSSL-BM3T from genomic sequence data was 38.75 mol%. Strain BSSL-BM3T contained MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 1 G as the major fatty acids. The major polar lipids of strain BSSL-BM3T were phosphatidylethanolamine and two unidentified lipids. Distinguishing phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain BSSL-BM3T is separated from recognized Arenibacter species. On the basis of the data presented here, strain BSSL-BM3T is considered to represent a novel species of the genus Arenibacter , for which the name Arenibacter arenosicollis sp. nov. is proposed. The type strain is BSSL-BM3T (=KACC 21632T=NBRC 114502T).

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