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MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level

Hélène Chiapello, Annie Gendrault, Christophe Caron, Jérome Blum, Marie-Agnès Petit, Meriem El Karoui
2008 BMC Bioinformatics  
This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level.  ...  A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at  ...  Yang for communicating the coordinates of rearrangements detected in Shigella genomes. We thank Drs G. Aguileta, J. Garnier, J.F. Gibrat and A. Gruss for valuable comments on the manuscript.  ... 
doi:10.1186/1471-2105-9-498 pmid:19038022 pmcid:PMC2607288 fatcat:2bvtmtzddjford3harchixtjoy

Databases and software for the comparison of prokaryotic genomes

D. Field
2005 Microbiology  
The explosion in the number of complete genomes over the past decade has spawned a new and exciting discipline, that of comparative genomics.  ...  To exploit the full potential of this approach requires the development of novel algorithms, databases and software which are sophisticated enough to draw meaningful comparisons between complete genome  ...  Comparative genomic studies have also led to a growing appreciation of the mosaic nature of bacterial genomes and the unexpectedly high levels of genetic diversity found among bacterial isolates corresponding  ... 
doi:10.1099/mic.0.28006-0 pmid:16000703 fatcat:p5bgkzdv2zfaleuywsrftkgrry

Genome (re-)annotation and open-source annotation pipelines

Roland J. Siezen, Sacha A. F. T. Van Hijum
2010 Microbial Biotechnology  
Acknowledgements This project was carried out within the research programmes of the Kluyver Centre for Genomics of Industrial Fermentation and the Netherlands Bioinformatics Centre, which are part of the  ...  Netherlands Genomics Initiative/Netherlands Organization for Scientific Research.  ... BacMap/ Stothard et al. (2005) MOSAIC INRA, France Database dedicated to the comparative genomics of bacterial strains at the intra-species level http:  ... 
doi:10.1111/j.1751-7915.2010.00191.x pmid:21255336 pmcid:PMC3815804 fatcat:6qxapk4bsre5jfbjq4onjphcre

Nematodes: The Worm and Its Relatives

Mark Blaxter
2011 PLoS Biology  
The C. elegans genome, at 100 Mb, is small compared to that of humans (which is 30 times bigger), but appears to be about standard for nematodes (the other sequenced species genomes range from 50 Mb to  ...  Also includes comparative analyses of the genomes of other nematodes.  ... 
doi:10.1371/journal.pbio.1001050 pmid:21526226 pmcid:PMC3079589 fatcat:7bb4mjg3sjchlet6yonlnvayiy

A Robust Framework for Microbial Archaeology

Christina Warinner, Alexander Herbig, Allison Mann, James A. Fellows Yates, Clemens L. Weiß, Hernán A. Burbano, Ludovic Orlando, Johannes Krause
2017 Annual review of genomics and human genetics (Print)  
We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data.  ...  Finally, we outline standards and precautions to guide future research in the field.  ...  sequencing projects at various stages of completion registered in the Genomes Online Database (GOLD) as of March 2017 (125) .  ... 
doi:10.1146/annurev-genom-091416-035526 pmid:28460196 pmcid:PMC5581243 fatcat:l3id6vomknbc7fivsttppucwhe

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

Stephen J Bush, Dona Foster, David W Eyre, Emily L Clark, Nicola De Maio, Liam P Shaw, Nicole Stoesser, Tim E A Peto, Derrick W Crook, A Sarah Walker
2020 GigaScience  
Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set  ...  Conclusions The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity.  ...  Acknowledgements The authors would also like to thank the REHAB consortium, which currently includes (bracketed individuals in the main au-  ... 
doi:10.1093/gigascience/giaa007 pmid:32025702 pmcid:PMC7002876 fatcat:33cwq2aln5butdhhu2qybxjsdi

Genomic diversity affects the accuracy of bacterial SNP calling pipelines [article]

Stephen J Bush, Dona Foster, David W. Eyre, Emily L. Clark, Nicola De Maio, Liam P. Shaw, Nicole Stoesser, Timothy E. A. Peto, Derrick W. Crook, A. Sarah Walker
2019 biorxiv/medrxiv   pre-print
Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set  ...  Results: We evaluated the performance of 41 SNP calling pipelines, aligning reads to genomes of the same or a divergent strain.  ...  Acknowledgements The authors would also like to thank the REHAB consortium, which currently includes (bracketed individuals in the main au-  ... 
doi:10.1101/653774 fatcat:qkmibmufjrgtvnagptftntgv34

Assessment of genomic changes in a CRISPR/Cas9 Phaeodactylum tricornutum mutant through whole genome resequencing

Monia Teresa Russo, Riccardo Aiese Cigliano, Walter Sanseverino, Maria Immacolata Ferrante
2018 PeerJ  
Since there are no reports on off-target occurrence at the genome level in microalgae, we performed whole-genome Illumina sequencing and found a number of different unspecific changes in both the wild  ...  Transforming P. tricornutum by bacterial conjugation, we have performed CRISPR/Cas9-based mutagenesis delivering the nuclease as an episome; this allowed for avoiding unwanted perturbations due to random  ...  The pPtPuc3_diaCas9_sgRNA and the pTA-Mob plasmids were kind gifts of M. Nymark and R. Lale, respectively. Whole-genome Illumina sequencing was performed by Biodiversa s.r.l.  ... 
doi:10.7717/peerj.5507 pmid:30310734 pmcid:PMC6174884 fatcat:w6pb6l6bxzdg5gwnc7m3mxltje

A window into lysogeny: revealing temperate phage biology with transcriptomics

Siân V. Owen, Rocío Canals, Nicolas Wenner, Disa L. Hammarlöf, Carsten Kröger, Jay C. D. Hinton
2020 Microbial Genomics  
Prophages are integrated phage elements that are a pervasive feature of bacterial genomes.  ...  Here, we use bacterial RNA-seq data to examine the transcriptional landscapes of five Salmonella prophages.  ...  Acknowledgements We are grateful to present and former members of the Hinton laboratory, particularly to Alex Predeus for assistance with data submission, and Heather Allison for helpful discussions.  ... 
doi:10.1099/mgen.0.000330 pmid:32022660 pmcid:PMC7067206 fatcat:tal4e2va45fynnq5v5woqaw6de

Analysis of the type II-A CRISPR-Cas system of Streptococcus agalactiae reveals distinctive features according to genetic lineages

Clément Lier, Elodie Baticle, Philippe Horvath, Eve Haguenoer, Anne-Sophie Valentin, Philippe Glaser, Laurent Mereghetti, Philippe Lanotte
2015 Frontiers in Genetics  
An analysis of sequenced strains representing the overall species diversity revealed a mosaic organization, with a core genome containing all the ubiquitous genes, and a dispensable genome consisting of  ...  The investigation of intra-species polymorphism at CRISPR loci represents a molecular tool highly promising for the genotyping of many bacteria and the understanding of their evolution.  ... 
doi:10.3389/fgene.2015.00214 pmid:26124774 pmcid:PMC4466440 fatcat:y25sdzxhuveh5hyj4qgajzsibm

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

Dmitry A. Rodionov, Aleksandr A. Arzamasov, Matvei S. Khoroshkin, Stanislav N. Iablokov, Semen A. Leyn, Scott N. Peterson, Pavel S. Novichkov, Andrei L. Osterman
2019 Frontiers in Microbiology  
A cross-species comparison was applied to assess the extent of conservation of vitamin phenotypes at distinct taxonomic levels (from strains to families).  ...  in the diet for many other bacterial species (auxotrophs) as well as for the mammalian host.  ...  ACKNOWLEDGMENTS We thank Robert Olson from the SEED/RAST development team at Argonne National Lab for dedicated support of the mcSEEDbased genomic analyses. We are grateful to PhenoBiome Inc.  ... 
doi:10.3389/fmicb.2019.01316 pmid:31275260 pmcid:PMC6593275 fatcat:kl7wvnot6bebhhbfpb5vxt4eti

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

Dieter M Tourlousse, Koji Narita, Takamasa Miura, Mitsuo Sakamoto, Akiko Ohashi, Keita Shiina, Masami Matsuda, Daisuke Miura, Mamiko Shimamura, Yoshifumi Ohyama, Atsushi Yamazoe, Yoshihito Uchino (+23 others)
2021 Microbiome  
We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge).  ...  Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human  ...  Availability of data and materials Genome sequences generated in this study are available in the DDBJ/EMBL/ GenBank database (see Table S1 for accession numbers).  ... 
doi:10.1186/s40168-021-01048-3 pmid:33910647 fatcat:xvs64fv62neklhzgll5hlf6mzm

Intraspecific Diversity of Fission Yeast Mitochondrial Genomes

2019 Genome Biology and Evolution  
In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated.  ...  Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp  ...  Acknowledgments We thank Wen Hu for generating the Illumina sequencing library of DY15505. We thank Yang Liu and Wei Jiang for contributing to the mitogenome analysis at the early stage of this work.  ... 
doi:10.1093/gbe/evz165 pmid:31364709 pmcid:PMC6736045 fatcat:yk2bucwaszdmxkjyou6brydjri

Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases

Yves Quentin, Patricia Siguier, Mick Chandler, Gwennaele Fichant
2018 BMC Genomics  
Similar secondary structures, Repeated Extragenic Palindromes (REP), are present in many bacterial genomes.  ...  Our goal is to characterize the diversity of these proteins collectively referred as the TnpA Y1 family.  ...  Availability of data and materials The sequence data as well as the phylogeny data, including alignments, used and/or analyzed during the current study are available in the TreeBASE repository, http://  ... 
doi:10.1186/s12864-018-4836-1 pmid:29914351 pmcid:PMC6006769 fatcat:3l65u4sxojfhnnrgq4o22m2zqm

The INRAE Centre for Vegetable Germplasm: Geographically and Phenotypically Diverse Collections and Their Use in Genetics and Plant Breeding

Jérémy Salinier, Véronique Lefebvre, Didier Besombes, Hélène Burck, Mathilde Causse, Marie-Christine Daunay, Catherine Dogimont, Juliette Goussopoulos, Christophe Gros, Brigitte Maisonneuve, Louis McLeod, Fatiha Tobal (+1 others)
2022 Plants  
have been screened for resistance to plant pathogens, including viruses, fungi, oomycetes and insects; and the tomato collection has been at the heart of genome-wide association studies for fruit quality  ...  Each collection has its own merits and highlights, which are discussed in this review: the aubergine collection is a rich source of crop wild relatives of Solanum; the pepper, melon and lettuce collections  ...  Acknowledgments: The authors would like to thank all those who have participated in the buildingup, conservation, maintenance and characterisation of these collections over the years and those who have  ... 
doi:10.3390/plants11030347 pmid:35161327 pmcid:PMC8838894 fatcat:ykglgfn7nfde5p6qykgdyzokju
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