Additional file 7: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Additional file 6: of A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes

Yonas Tekle (5984270)
Fiona Wood (3499862)

November 2018

Figure S6. Histogram of average distances within genome-matching and nonmatching single-copy eukaryo...

Additional file 7: of Phylogenetic, epidemiological and functional analyses of the Streptococcus bovis/Streptococcus equinus complex through an overarching MLST scheme

Christoph Jans (786001)
Tomas de Wouters (422290)
Bassirou Bonfoh (424496)
Christophe Lacroix (35954)
Dasel Kaindi (3533747)
Janine Anderegg (3533756)
Désirée Böck (3533750)
Sabrina Vitali (3533738)
Thomas Schmid (428873)
Julia Isenring (3533741)
Fabienne Kurt (3533744)
Wambui Kogi-Makau (3533753)
Leo Meile (35957)

June 2016

Title of data: SplitsTree visualization of the 10 MLST loci. Description of data: The trees were obt...

Additional file 6: of Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7

Vijay Sharma (651200)
Suryatej Akavaram (6441005)
Robert Schaut (6441008)
Darrell Bayles (3468284)

March 2019

Table S1. Bacterial strains with their corresponding accession numbers used in the study. (DOCX 29 k...

Additional file 3: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S3. Size of the pangenome at any given number of strains. At every step, 10 combinations of s...

Additional file 12: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Table S5 Genomes and gene loci used for bacteriocin- and streptolysin S synteny comparison (XLSX 5 k...

Additional file 1: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S1. Whole Genome Synteny Dotplot. Sequences of CRBO_1381 and UBOCC-A-315001 were compared aga...

Additional file 2: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S2. Variable regions in groups C and D genomes. MicroScope RGP-finder was used to identify sp...

Additional file 6: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S6. Schematic representation of the stop mutation disrupting the malolactic transcriptional r...

Additional file 4: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S4. Comparison of genomic regions overlapping a streptolysin operon. Pairwise BLAST hits show...

Additional file 5: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S5. Competence genes identified in the pangenome. Gene presence in blue, fragments in light b...

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains.

Lorentzen, Marc P.
Campbell-Sills, Hugo
Jorgensen, Tue S
Nielsen, Tue K
Coton, Monika
Coton, Emmanuel
Hansen, Lars
Lucas, Patrick

May 2019

International audienceOenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethan...

Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.

CAMPBELL-SILLS, Hugo
EL KHOURY, Mariette
FAVIER, Marion
ROMANO, Andrea
BIASIOLI, Franco
SPANO, Giuseppe
SHERMAN, David James
BOUCHEZ, Olivier
COTON, Emmanuel
COTON, Monika
OKADA, Sanae
TANAKA, Naoto
DOLS-LAFARGUE, Marguerite
LUCAS, Patrick M

May 2015

Oenococcus oeni is a lactic acid bacteria species encountered particularly in wine, where it achieve...

Additional file 7: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

Johanne Ahrenfeldt (3165513)
Carina Skaarup (3620504)
Henrik Hasman (519537)
Anders Pedersen (249829)
Frank Aarestrup (3514247)
Ole Lund (26628)

January 2017

a Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_017641 used as reference....

Additional file 5: Figure S5. of Carbohydrate metabolism in Oenococcus oeni: a genomic insight

Alice Cibrario (3399452)
Claire Peanne (3399449)
Marine Lailheugue (3399455)
Hugo Campbell-Sills (573476)
Marguerite Dols-Lafargue (573484)

December 2016

The distinct PTS cellobiose operons and their insertion sites on O. oeni chromosome. The blue arrows...

Additional file 8: of SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

Gabriella De Lorenzis (3242994)
Francesco Mercati (3265629)
Carlo Bergamini (6010136)
Maria Cardone (6178256)
Antonio Lupini (3639271)
Antonio Mauceri (5581739)
Angelo Caputo (6178259)
Loredana Abbate (3288243)
Maria Barbagallo (6178262)
Donato Antonacci (2246935)
Francesco Sunseri (3265626)
Lucio Brancadoro (2850842)

January 2019

Neiâs standard genetic distance (below the diagonal) and Fst index (above the diagonal) calculated...

Additional file 6: of A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes

Yonas Tekle (5984270)
Fiona Wood (3499862)

November 2018

Figure S6. Histogram of average distances within genome-matching and nonmatching single-copy eukaryo...

Additional file 7: of Phylogenetic, epidemiological and functional analyses of the Streptococcus bovis/Streptococcus equinus complex through an overarching MLST scheme

Christoph Jans (786001)
Tomas de Wouters (422290)
Bassirou Bonfoh (424496)
Christophe Lacroix (35954)
Dasel Kaindi (3533747)
Janine Anderegg (3533756)
Désirée Böck (3533750)
Sabrina Vitali (3533738)
Thomas Schmid (428873)
Julia Isenring (3533741)
Fabienne Kurt (3533744)
Wambui Kogi-Makau (3533753)
Leo Meile (35957)

June 2016

Title of data: SplitsTree visualization of the 10 MLST loci. Description of data: The trees were obt...

Additional file 6: of Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7

Vijay Sharma (651200)
Suryatej Akavaram (6441005)
Robert Schaut (6441008)
Darrell Bayles (3468284)

March 2019

Table S1. Bacterial strains with their corresponding accession numbers used in the study. (DOCX 29 k...

Additional file 3: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S3. Size of the pangenome at any given number of strains. At every step, 10 combinations of s...

Additional file 12: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Table S5 Genomes and gene loci used for bacteriocin- and streptolysin S synteny comparison (XLSX 5 k...

Additional file 1: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S1. Whole Genome Synteny Dotplot. Sequences of CRBO_1381 and UBOCC-A-315001 were compared aga...

Additional file 2: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S2. Variable regions in groups C and D genomes. MicroScope RGP-finder was used to identify sp...

Additional file 6: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S6. Schematic representation of the stop mutation disrupting the malolactic transcriptional r...

Additional file 4: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S4. Comparison of genomic regions overlapping a streptolysin operon. Pairwise BLAST hits show...

Additional file 5: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Marc Lorentzen (6660605)
Hugo Campbell-Sills (573476)
Tue Jorgensen (6660608)
Tue Nielsen (6660611)
Monika Coton (118374)
Emmanuel Coton (758107)
Lars Hansen (206874)
Patrick Lucas (1516321)

May 2019

Figure S5. Competence genes identified in the pangenome. Gene presence in blue, fragments in light b...

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains.

Lorentzen, Marc P.
Campbell-Sills, Hugo
Jorgensen, Tue S
Nielsen, Tue K
Coton, Monika
Coton, Emmanuel
Hansen, Lars
Lucas, Patrick

May 2019

International audienceOenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethan...

Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.

CAMPBELL-SILLS, Hugo
EL KHOURY, Mariette
FAVIER, Marion
ROMANO, Andrea
BIASIOLI, Franco
SPANO, Giuseppe
SHERMAN, David James
BOUCHEZ, Olivier
COTON, Emmanuel
COTON, Monika
OKADA, Sanae
TANAKA, Naoto
DOLS-LAFARGUE, Marguerite
LUCAS, Patrick M

May 2015

Oenococcus oeni is a lactic acid bacteria species encountered particularly in wine, where it achieve...

Additional file 7: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

Johanne Ahrenfeldt (3165513)
Carina Skaarup (3620504)
Henrik Hasman (519537)
Anders Pedersen (249829)
Frank Aarestrup (3514247)
Ole Lund (26628)

January 2017

a Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_017641 used as reference....

Additional file 5: Figure S5. of Carbohydrate metabolism in Oenococcus oeni: a genomic insight

Alice Cibrario (3399452)
Claire Peanne (3399449)
Marine Lailheugue (3399455)
Hugo Campbell-Sills (573476)
Marguerite Dols-Lafargue (573484)

December 2016

The distinct PTS cellobiose operons and their insertion sites on O. oeni chromosome. The blue arrows...

Additional file 8: of SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

Gabriella De Lorenzis (3242994)
Francesco Mercati (3265629)
Carlo Bergamini (6010136)
Maria Cardone (6178256)
Antonio Lupini (3639271)
Antonio Mauceri (5581739)
Angelo Caputo (6178259)
Loredana Abbate (3288243)
Maria Barbagallo (6178262)
Donato Antonacci (2246935)
Francesco Sunseri (3265626)
Lucio Brancadoro (2850842)

January 2019

Neiâs standard genetic distance (below the diagonal) and Fst index (above the diagonal) calculated...

Additional file 6: of A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes

Yonas Tekle (5984270)
Fiona Wood (3499862)

November 2018

Figure S6. Histogram of average distances within genome-matching and nonmatching single-copy eukaryo...

Additional file 7: of Phylogenetic, epidemiological and functional analyses of the Streptococcus bovis/Streptococcus equinus complex through an overarching MLST scheme

Christoph Jans (786001)
Tomas de Wouters (422290)
Bassirou Bonfoh (424496)
Christophe Lacroix (35954)
Dasel Kaindi (3533747)
Janine Anderegg (3533756)
Désirée Böck (3533750)
Sabrina Vitali (3533738)
Thomas Schmid (428873)
Julia Isenring (3533741)
Fabienne Kurt (3533744)
Wambui Kogi-Makau (3533753)
Leo Meile (35957)

June 2016

Title of data: SplitsTree visualization of the 10 MLST loci. Description of data: The trees were obt...

Additional file 6: of Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7

Vijay Sharma (651200)
Suryatej Akavaram (6441005)
Robert Schaut (6441008)
Darrell Bayles (3468284)

March 2019

Table S1. Bacterial strains with their corresponding accession numbers used in the study. (DOCX 29 k...

Additional file 7: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Abstract

Extracted data

Additional file 7: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Abstract

Extracted data

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