Additional file 3: of Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Additional file 1: of Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing

Vijaykumar Veerappan (1861978)
Mehul Jani (3415130)
Khem Kadel (3415115)
Taylor Troiani (3415121)
Ronny Gale (3415136)
Tyler Mayes (3415133)
Elena Shulaev (3415127)
Jiangqi Wen (612044)
Kirankumar Mysore (3415118)
Rajeev Azad (3415139)
Rebecca Dickstein (3415124)

February 2016

List of sequences of all NF11217 flanking sequence tags (FSTs) obtained from R0, R1 and BC1 F2 gener...

Additional file 3: Table S3. of Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Jonna Eriksson (4802400)
Filipe de Sousa (646591)
Yann Bertrand (182077)
Alexandre Antonelli (114105)
Bengt Oxelman (99756)
Bernard Pfeil (3710854)

January 2018

Mean read depth and standard deviation for each accession, across all loci. (DOCX 45 kb

Additional file 1: Table S1. of Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Jonna Eriksson (4802400)
Filipe de Sousa (646591)
Yann Bertrand (182077)
Alexandre Antonelli (114105)
Bengt Oxelman (99756)
Bernard Pfeil (3710854)

January 2018

Species used in this study along with accession numbers. PI and W6 numbers are from United States De...

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Peng Zhou
Kevin A. T. Silverstein
Thiruvarangan Ramaraj
Joseph Guhlin
Roxanne Denny
Junqi Liu
Andrew D. Farmer
Kelly P. Steele
Robert M. Stupar
Jason R. Miller
Peter Tiffin
Joann Mudge
Nevin D. Young

March 2017

Abstract Background Previous studies exploring sequence variation in the model legume, Medicago trun...

Additional file 3: of Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes

Zhihui Wang (88248)
Ke Cheng (161778)
Liyun Wan (204012)
Liying Yan (475923)
Huifang Jiang (118376)
Shengyi Liu (395657)
Yong Lei (337331)
Boshou Liao (118400)

December 2015

The phylogenetic analysis of bZIP proteins based on the bZIP protein sequences from Arabidopsis (71 ...

Additional file 1: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S1. The results of the traditional de novo Arabidopsis thaliana genome assembly generated by f...

Additional file 17: of Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes

Sovanna Tan (6700676)
Frédéric Debellé (681781)
Pascal Gamas (231748)
Florian Frugier (504628)
Mathias Brault (6700679)

May 2019

Domain composition of the different TCS protein families. For each TCS protein family, the domain co...

Additional file 4: Table S3. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

Wen Yao (408229)
Guangwei Li (822910)
Hu Zhao (425380)
Gongwei Wang (1781380)
Xingming Lian (504682)
Weibo Xie (123006)

September 2015

Alignment of contigs of the indica dispensable genome to different sequenced genomes of the Oryza ge...

Additional file 6: Table S1. of Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

L. Karaki (3548669)
P. Da Silva (3548690)
F. Rizk (3548684)
C. Chouabe (3548663)
N. Chantret (3548687)
V. Eyraud (3548675)
F. Gressent (3548678)
C. Sivignon (3548696)
I. Rahioui (3548693)
D. Kahn (3548666)
C. Brochier-Armanet (3548681)
Y. RahbĂŠ (3548672)
C. Royer (31263)

March 2016

Legume species analyzed. Legume species selection data. Genomes with high quality full genomes used ...

Additional file 9: of Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes

Zhihui Wang (88248)
Ke Cheng (161778)
Liyun Wan (204012)
Liying Yan (475923)
Huifang Jiang (118376)
Shengyi Liu (395657)
Yong Lei (337331)
Boshou Liao (118400)

December 2015

Amino acid sequence alignment of the leucine zipper region of 585 legume bZIP proteins. (PDF 4254Â k...

Additional file 3: of Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes

Sovanna Tan (6700676)
Frédéric Debellé (681781)
Pascal Gamas (231748)
Florian Frugier (504628)
Mathias Brault (6700679)

May 2019

List of putative ethylene receptors in the genome of Arabidopsis thaliana, Vitis vinifera and all st...

Additional file 1: of A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

Reema Singh (2793865)
Christina Schilde (2793856)
Pauline Schaap (629913)

November 2016

Excel spreadsheet (.xlsx) listing assembly statistics of the six sequenced genomes before and filter...

Additional file 14: of Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes

Sovanna Tan (6700676)
Frédéric Debellé (681781)
Pascal Gamas (231748)
Florian Frugier (504628)
Mathias Brault (6700679)

May 2019

List of putative RRAs in the genome of Arabidopsis thaliana, Vitis vinifera and all studied legumes....

Additional file 3: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S3. Sequencing libraries and generated sequence data used for the Larix sibirica genome assemb...

Additional file 3: of Characterization of the Esi3/RCI2/PMP3 gene family in the Triticeae

Sabrina Brunetti (6075614)
Michelle Arseneault (6075617)
Patrick Gulick (20267)

December 2018

Table S3. Esi3/RCI2/PMP3 gene family members in eight species with NCBI accession numbers and compar...

Additional file 1: of Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing

Vijaykumar Veerappan (1861978)
Mehul Jani (3415130)
Khem Kadel (3415115)
Taylor Troiani (3415121)
Ronny Gale (3415136)
Tyler Mayes (3415133)
Elena Shulaev (3415127)
Jiangqi Wen (612044)
Kirankumar Mysore (3415118)
Rajeev Azad (3415139)
Rebecca Dickstein (3415124)

February 2016

List of sequences of all NF11217 flanking sequence tags (FSTs) obtained from R0, R1 and BC1 F2 gener...

Additional file 3: Table S3. of Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Jonna Eriksson (4802400)
Filipe de Sousa (646591)
Yann Bertrand (182077)
Alexandre Antonelli (114105)
Bengt Oxelman (99756)
Bernard Pfeil (3710854)

January 2018

Mean read depth and standard deviation for each accession, across all loci. (DOCX 45 kb

Additional file 1: Table S1. of Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Jonna Eriksson (4802400)
Filipe de Sousa (646591)
Yann Bertrand (182077)
Alexandre Antonelli (114105)
Bengt Oxelman (99756)
Bernard Pfeil (3710854)

January 2018

Species used in this study along with accession numbers. PI and W6 numbers are from United States De...

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Peng Zhou
Kevin A. T. Silverstein
Thiruvarangan Ramaraj
Joseph Guhlin
Roxanne Denny
Junqi Liu
Andrew D. Farmer
Kelly P. Steele
Robert M. Stupar
Jason R. Miller
Peter Tiffin
Joann Mudge
Nevin D. Young

March 2017

Abstract Background Previous studies exploring sequence variation in the model legume, Medicago trun...

Additional file 3: of Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes

Zhihui Wang (88248)
Ke Cheng (161778)
Liyun Wan (204012)
Liying Yan (475923)
Huifang Jiang (118376)
Shengyi Liu (395657)
Yong Lei (337331)
Boshou Liao (118400)

December 2015

The phylogenetic analysis of bZIP proteins based on the bZIP protein sequences from Arabidopsis (71 ...

Additional file 1: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S1. The results of the traditional de novo Arabidopsis thaliana genome assembly generated by f...

Additional file 17: of Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes

Sovanna Tan (6700676)
Frédéric Debellé (681781)
Pascal Gamas (231748)
Florian Frugier (504628)
Mathias Brault (6700679)

May 2019

Domain composition of the different TCS protein families. For each TCS protein family, the domain co...

Additional file 4: Table S3. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

Wen Yao (408229)
Guangwei Li (822910)
Hu Zhao (425380)
Gongwei Wang (1781380)
Xingming Lian (504682)
Weibo Xie (123006)

September 2015

Alignment of contigs of the indica dispensable genome to different sequenced genomes of the Oryza ge...

Additional file 6: Table S1. of Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

L. Karaki (3548669)
P. Da Silva (3548690)
F. Rizk (3548684)
C. Chouabe (3548663)
N. Chantret (3548687)
V. Eyraud (3548675)
F. Gressent (3548678)
C. Sivignon (3548696)
I. Rahioui (3548693)
D. Kahn (3548666)
C. Brochier-Armanet (3548681)
Y. RahbĂŠ (3548672)
C. Royer (31263)

March 2016

Legume species analyzed. Legume species selection data. Genomes with high quality full genomes used ...

Additional file 9: of Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes

Zhihui Wang (88248)
Ke Cheng (161778)
Liyun Wan (204012)
Liying Yan (475923)
Huifang Jiang (118376)
Shengyi Liu (395657)
Yong Lei (337331)
Boshou Liao (118400)

December 2015

Amino acid sequence alignment of the leucine zipper region of 585 legume bZIP proteins. (PDF 4254Â k...

Additional file 3: of Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes

Sovanna Tan (6700676)
Frédéric Debellé (681781)
Pascal Gamas (231748)
Florian Frugier (504628)
Mathias Brault (6700679)

May 2019

List of putative ethylene receptors in the genome of Arabidopsis thaliana, Vitis vinifera and all st...

Additional file 1: of A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

Reema Singh (2793865)
Christina Schilde (2793856)
Pauline Schaap (629913)

November 2016

Excel spreadsheet (.xlsx) listing assembly statistics of the six sequenced genomes before and filter...

Additional file 14: of Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes

Sovanna Tan (6700676)
Frédéric Debellé (681781)
Pascal Gamas (231748)
Florian Frugier (504628)
Mathias Brault (6700679)

May 2019

List of putative RRAs in the genome of Arabidopsis thaliana, Vitis vinifera and all studied legumes....

Additional file 3: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S3. Sequencing libraries and generated sequence data used for the Larix sibirica genome assemb...

Additional file 3: of Characterization of the Esi3/RCI2/PMP3 gene family in the Triticeae

Sabrina Brunetti (6075614)
Michelle Arseneault (6075617)
Patrick Gulick (20267)

December 2018

Table S3. Esi3/RCI2/PMP3 gene family members in eight species with NCBI accession numbers and compar...

Additional file 1: of Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing

Vijaykumar Veerappan (1861978)
Mehul Jani (3415130)
Khem Kadel (3415115)
Taylor Troiani (3415121)
Ronny Gale (3415136)
Tyler Mayes (3415133)
Elena Shulaev (3415127)
Jiangqi Wen (612044)
Kirankumar Mysore (3415118)
Rajeev Azad (3415139)
Rebecca Dickstein (3415124)

February 2016

List of sequences of all NF11217 flanking sequence tags (FSTs) obtained from R0, R1 and BC1 F2 gener...

Additional file 3: Table S3. of Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Jonna Eriksson (4802400)
Filipe de Sousa (646591)
Yann Bertrand (182077)
Alexandre Antonelli (114105)
Bengt Oxelman (99756)
Bernard Pfeil (3710854)

January 2018

Mean read depth and standard deviation for each accession, across all loci. (DOCX 45 kb

Additional file 1: Table S1. of Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Jonna Eriksson (4802400)
Filipe de Sousa (646591)
Yann Bertrand (182077)
Alexandre Antonelli (114105)
Bengt Oxelman (99756)
Bernard Pfeil (3710854)

January 2018

Species used in this study along with accession numbers. PI and W6 numbers are from United States De...

Additional file 3: of Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Abstract

Extracted data

Additional file 3: of Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Abstract

Extracted data

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