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Gaps in the genome of isolate 70-15 filled with sequences from the field isolates P131 and/or Y34.

Minfeng Xue (145493)
Jun Yang (2084)
Zhigang Li (145495)
Songnian Hu (6480)
Nan Yao (145498)
Ralph A. Dean (143492)
Wensheng Zhao (145502)
Mi Shen (145505)
Haiwang Zhang (145510)
Chao Li (145513)
Liyuan Liu (145516)
Lei Cao (134409)
Xiaowen Xu (145518)
Yunfei Xing (145521)
Tom Hsiang (145524)
Ziding Zhang (145526)
Jin-Rong Xu (119406)
You-Liang Peng (145527)

Publication date

August 2012

DOI

10.1371/journal.pgen.1002869.t002

Abstract

<p>Gaps in the genome of isolate 70-15 filled with sequences from the field isolates P131 and/or Y34.</p

Extracted data

Related items

General features of draft genomes of incipient isolates.

Winnie Ridderberg (435656)
Signe Maria Nielsen (789060)
Niels Nørskov-Lauritsen (789061)

August 2015

<p>*Number of coding sequences as determined by RAST.</p><p>General features of draft genomes of inc...

Phylogenetic relationships between Madagascan CV-A13 field strains and other CV-A13 isolates for which sequences are available in GenBank, based on 3′ one-third of the VP1 region (∼300 nt).

Maël Bessaud (344554)
Marie-Line Joffret (344555)
Barbara Holmblat (344557)
Richter Razafindratsimandresy (138306)
Francis Delpeyroux (67572)

February 2013

<p>The length of the branches is proportional to the number of nucleotide changes (percent divergenc...

Different GCRV isolates and their species assignments.

Max L. Nibert (121828)
Roy Duncan (43455)

July 2013

a<p>The first isolate listed for each species is the approved or suggested prototype strain for that...

Sequences of the Six <i>D. desulfuricans</i> ND132 Gaps.

Richard A. Hurt Jr (146044)
Steven D. Brown (146049)
Mircea Podar (146055)
Anthony V. Palumbo (146061)
Dwayne A. Elias (146066)

July 2012

a<p>Location of gaps in the genome according to updated genome GenBank (CP003220) sequence.</p

Distribution of nucleotide substitutions along the genome of the isolates P37, P47, P49 and SD9.

David Sánchez (644850)
Margarita Gomila (644851)
Antonio Bennasar (644852)
Jorge Lalucat (644853)
Elena García-Valdés (644854)

October 2014

<p>Distribution of nucleotide substitutions along the genome of the isolates P37, P47, P49 and SD9.<...

Isolates of origin of the 485 orthologs shared by 16 out of the 17 tested genomes.

Benoît Valot (68921)
Christophe Guyeux (625819)
Julien Yves Rolland (736837)
Kamel Mazouzi (736838)
Xavier Bertrand (114101)
Didier Hocquet (114103)

May 2015

<p>Isolates of origin of the 485 orthologs shared by 16 out of the 17 tested genomes.</p

Gaps and complex structurally variant loci in phased genome assemblies

Evan E. Eichler
Mitchell R. Vollger
William T. Harvey
Allison N. Rozanski
Peter Ebert
Glenn Hickey
Patrick Hasenfeld
Ashley D. Sanders
Catherine Stober
Jan O. Korbel
Benedict Paten
Tobias Marschall
Evan E. Eichler

June 2022

Supplementary data including code for an science article 'Gaps and complex structurally variant loci...

Details of isolates sequenced in current study.

Jason W. Sahl (276694)
Christopher J. Allender (189556)
Rebecca E. Colman (254707)
Katy J. Califf (710313)
James M. Schupp (193214)
Bart J. Currie (131288)
Kristopher E. Van Zandt (710314)
H. Carl Gelhaus (710315)
Paul Keim (69765)
Apichai Tuanyok (78029)

March 2015

<p>*genome has been sequenced previously</p><p>Details of isolates sequenced in current study.</p

Strain Information for all 40 HPIV-1 Genomes Sequenced.

Eric T. Beck (132995)
Jie He (132999)
Martha I. Nelson (52455)
Michael E. Bose (133005)
Jiang Fan (133009)
Swati Kumar (133013)
Kelly J. Henrickson (133018)

September 2012

*<p>These sequences still have some gaps. Gene sequences with gaps in the coding region were not use...

Metagenome coverage of isolate genomes.<sup>1</sup>

Emily B. Hollister (156772)
Andrea K. Forrest (156777)
Heather H. Wilkinson (156780)
Daniel J. Ebbole (156786)
Susannah G. Tringe (43680)
Stephanie A. Malfatti (124718)
Mark T. Holtzapple (156792)
Terry J. Gentry (156799)

June 2012

1<p>Ranges provided for isolate genome protein coding gene counts and coverage values are in cases w...

Number of duplicate genes located in syntenic gaps and on chromosome ends<sup>a</sup>.

Jeremy D. DeBarry (275965)
Jessica C. Kissinger (14009)

June 2014

a<p>Includes genes within 1 kb of either end of a syntenic gap.</p>b<p>Counts are for individual gen...

Conservation of Sequence Features between 3D7 and Kilifi Field Isolates

Peter C Bull (42879)
Matthew Berriman (5353)
Sue Kyes (42880)
Michael A Quail (42881)
Neil Hall (12782)
Moses M Kortok (42882)
Kevin Marsh (9406)
Chris I Newbold (42883)

February 2013

<div><p>(A) Distribution of sequence features within the 3D7 genome (black bars) and in Kilifi seque...

Variant calling in the 12-mer datasets at genome positions with depth larger than 100 × (except for position 31 in the K-12N condition) and minor nucleotide percentage of at least 10%.

Toon Rosseel (313761)
Steven Van Borm (313768)
Frank Vandenbussche (313767)
Bernd Hoffmann (191620)
Thierry van den Berg (371067)
Martin Beer (222377)
Dirk Höper (193333)

September 2013

<p>Variant calling in the 12-mer datasets at genome positions with depth larger than 100 × (except f...

Distribution of genotypes isolated by year.

Wolfgang Beyer (179591)
Steve Bellan (179596)
Gisela Eberle (179602)
Holly H. Ganz (179608)
Wayne M. Getz (24543)
Renate Haumacher (179617)
Karen A. Hilss (179624)
Werner Kilian (179633)
Judith Lazak (179639)
Wendy C. Turner (179645)
Peter C. B. Turnbull (179649)

March 2012

<p>The total number of isolates per year and per GT. GTs 2, 3, 6, 9, 18, and 22 (highlighted in grey...

Distribution of K13 mutations among different years and sites in the NW region.

Mei Li (217363)
Hui Liu (33624)
Linhua Tang (563240)
Henglin Yang (17373490)
Maria Dorina Geluz Bustos (17373493)
Hong Tu (558392)
Pascal Ringwald (80272)

November 2023

Distribution of K13 mutations among different years and sites in the NW region.</p

General features of draft genomes of incipient isolates.

Winnie Ridderberg (435656)
Signe Maria Nielsen (789060)
Niels Nørskov-Lauritsen (789061)

August 2015

<p>*Number of coding sequences as determined by RAST.</p><p>General features of draft genomes of inc...

Phylogenetic relationships between Madagascan CV-A13 field strains and other CV-A13 isolates for which sequences are available in GenBank, based on 3′ one-third of the VP1 region (∼300 nt).

Maël Bessaud (344554)
Marie-Line Joffret (344555)
Barbara Holmblat (344557)
Richter Razafindratsimandresy (138306)
Francis Delpeyroux (67572)

February 2013

<p>The length of the branches is proportional to the number of nucleotide changes (percent divergenc...

Different GCRV isolates and their species assignments.

Max L. Nibert (121828)
Roy Duncan (43455)

July 2013

a<p>The first isolate listed for each species is the approved or suggested prototype strain for that...

Sequences of the Six <i>D. desulfuricans</i> ND132 Gaps.

Richard A. Hurt Jr (146044)
Steven D. Brown (146049)
Mircea Podar (146055)
Anthony V. Palumbo (146061)
Dwayne A. Elias (146066)

July 2012

a<p>Location of gaps in the genome according to updated genome GenBank (CP003220) sequence.</p

Distribution of nucleotide substitutions along the genome of the isolates P37, P47, P49 and SD9.

David Sánchez (644850)
Margarita Gomila (644851)
Antonio Bennasar (644852)
Jorge Lalucat (644853)
Elena García-Valdés (644854)

October 2014

<p>Distribution of nucleotide substitutions along the genome of the isolates P37, P47, P49 and SD9.<...

Isolates of origin of the 485 orthologs shared by 16 out of the 17 tested genomes.

Benoît Valot (68921)
Christophe Guyeux (625819)
Julien Yves Rolland (736837)
Kamel Mazouzi (736838)
Xavier Bertrand (114101)
Didier Hocquet (114103)

May 2015

<p>Isolates of origin of the 485 orthologs shared by 16 out of the 17 tested genomes.</p

Gaps and complex structurally variant loci in phased genome assemblies

Evan E. Eichler
Mitchell R. Vollger
William T. Harvey
Allison N. Rozanski
Peter Ebert
Glenn Hickey
Patrick Hasenfeld
Ashley D. Sanders
Catherine Stober
Jan O. Korbel
Benedict Paten
Tobias Marschall
Evan E. Eichler

June 2022

Supplementary data including code for an science article 'Gaps and complex structurally variant loci...

Details of isolates sequenced in current study.

Jason W. Sahl (276694)
Christopher J. Allender (189556)
Rebecca E. Colman (254707)
Katy J. Califf (710313)
James M. Schupp (193214)
Bart J. Currie (131288)
Kristopher E. Van Zandt (710314)
H. Carl Gelhaus (710315)
Paul Keim (69765)
Apichai Tuanyok (78029)

March 2015

<p>*genome has been sequenced previously</p><p>Details of isolates sequenced in current study.</p

Strain Information for all 40 HPIV-1 Genomes Sequenced.

Eric T. Beck (132995)
Jie He (132999)
Martha I. Nelson (52455)
Michael E. Bose (133005)
Jiang Fan (133009)
Swati Kumar (133013)
Kelly J. Henrickson (133018)

September 2012

*<p>These sequences still have some gaps. Gene sequences with gaps in the coding region were not use...

Metagenome coverage of isolate genomes.<sup>1</sup>

Emily B. Hollister (156772)
Andrea K. Forrest (156777)
Heather H. Wilkinson (156780)
Daniel J. Ebbole (156786)
Susannah G. Tringe (43680)
Stephanie A. Malfatti (124718)
Mark T. Holtzapple (156792)
Terry J. Gentry (156799)

June 2012

1<p>Ranges provided for isolate genome protein coding gene counts and coverage values are in cases w...

Number of duplicate genes located in syntenic gaps and on chromosome ends<sup>a</sup>.

Jeremy D. DeBarry (275965)
Jessica C. Kissinger (14009)

June 2014

a<p>Includes genes within 1 kb of either end of a syntenic gap.</p>b<p>Counts are for individual gen...

Conservation of Sequence Features between 3D7 and Kilifi Field Isolates

Peter C Bull (42879)
Matthew Berriman (5353)
Sue Kyes (42880)
Michael A Quail (42881)
Neil Hall (12782)
Moses M Kortok (42882)
Kevin Marsh (9406)
Chris I Newbold (42883)

February 2013

<div><p>(A) Distribution of sequence features within the 3D7 genome (black bars) and in Kilifi seque...

Variant calling in the 12-mer datasets at genome positions with depth larger than 100 × (except for position 31 in the K-12N condition) and minor nucleotide percentage of at least 10%.

Toon Rosseel (313761)
Steven Van Borm (313768)
Frank Vandenbussche (313767)
Bernd Hoffmann (191620)
Thierry van den Berg (371067)
Martin Beer (222377)
Dirk Höper (193333)

September 2013

<p>Variant calling in the 12-mer datasets at genome positions with depth larger than 100 × (except f...

Distribution of genotypes isolated by year.

Wolfgang Beyer (179591)
Steve Bellan (179596)
Gisela Eberle (179602)
Holly H. Ganz (179608)
Wayne M. Getz (24543)
Renate Haumacher (179617)
Karen A. Hilss (179624)
Werner Kilian (179633)
Judith Lazak (179639)
Wendy C. Turner (179645)
Peter C. B. Turnbull (179649)

March 2012

<p>The total number of isolates per year and per GT. GTs 2, 3, 6, 9, 18, and 22 (highlighted in grey...

Distribution of K13 mutations among different years and sites in the NW region.

Mei Li (217363)
Hui Liu (33624)
Linhua Tang (563240)
Henglin Yang (17373490)
Maria Dorina Geluz Bustos (17373493)
Hong Tu (558392)
Pascal Ringwald (80272)

November 2023

Distribution of K13 mutations among different years and sites in the NW region.</p

General features of draft genomes of incipient isolates.

Winnie Ridderberg (435656)
Signe Maria Nielsen (789060)
Niels Nørskov-Lauritsen (789061)

August 2015

<p>*Number of coding sequences as determined by RAST.</p><p>General features of draft genomes of inc...

Phylogenetic relationships between Madagascan CV-A13 field strains and other CV-A13 isolates for which sequences are available in GenBank, based on 3′ one-third of the VP1 region (∼300 nt).

Maël Bessaud (344554)
Marie-Line Joffret (344555)
Barbara Holmblat (344557)
Richter Razafindratsimandresy (138306)
Francis Delpeyroux (67572)

February 2013

<p>The length of the branches is proportional to the number of nucleotide changes (percent divergenc...

Different GCRV isolates and their species assignments.

Max L. Nibert (121828)
Roy Duncan (43455)

July 2013

a<p>The first isolate listed for each species is the approved or suggested prototype strain for that...