Additional file 7: of Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

Additional file 37: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Ronald de Vries (3464225)
Robert Riley (11626)
Ad Wiebenga (218081)
Guillermo Aguilar-Osorio (3546917)
Sotiris Amillis (3747547)
Cristiane Uchima (3512723)
Gregor Anderluh (145545)
Mojtaba Asadollahi (3747562)
Marion Askin (3747604)
Kerrie Barry (276529)
Evy Battaglia (510411)
Özgür Bayram (150583)
Tiziano Benocci (3747532)
Susanna Braus-Stromeyer (3747565)
Camila Caldana (76564)
David Cánovas (609771)
Gustavo Cerqueira (3747541)
Fusheng Chen (298630)
Wanping Chen (298625)
Cindy Choi (819115)
Alicia Clum (111778)
Renato dos Santos (3747505)
André Damásio (3613712)
George Diallinas (148998)
Tamás Emri (3747502)
Erzsébet Fekete (658292)
Michel Flipphi (586744)
Susanne Freyberg (3747544)
Antonia Gallo (3747571)
Christos Gournas (3747598)
Rob Habgood (3747511)
Matthieu Hainaut (330421)
María Harispe (3747607)
Bernard Henrissat (31550)
Kristiina Hildén (520583)
Ryan Hope (3747601)
Abeer Hossain (3542657)
Eugenia Karabika (3747526)
Levente Karaffa (658296)
Zsolt Karányi (213679)
Nada Kraševec (629660)
Alan Kuo (260458)
Harald Kusch (444862)
Kurt LaButti (114830)
Ellen Lagendijk (364626)
Alla Lapidus (6321)
Anthony Levasseur (45449)
Erika Lindquist (116964)
Anna Lipzen (194340)
Antonio Logrieco (3061605)
Andrew MacCabe (3747550)
Miia Mäkelä (563196)
Iran Malavazi (81124)
Petter Melin (3747592)
Vera Meyer (436900)
Natalia Mielnichuk (3747613)
Márton Miskei (213668)
Ákos Molnár (3747508)
Giuseppina Mulé (3747586)
Chew Ngan (3505151)
Margarita Orejas (3412205)
Erzsébet Orosz (3747595)
Jean Ouedraogo (3747523)
Karin Overkamp (3542666)
Hee-Soo Park (132707)
Giancarlo Perrone (415847)
Francois Piumi (88016)
Peter Punt (2278426)
Arthur Ram (3454442)
Ana Ramón (3747535)
Stefan Rauscher (3747529)
Eric Record (818818)
Diego Riaño-Pachón (3430481)
Vincent Robert (92227)
Julian Röhrig (550487)
Roberto Ruller (113949)
Asaf Salamov (116970)
Nadhira Salih (3747538)
Rob Samson (3747556)
Erzsébet Sándor (658294)
Manuel Sanguinetti (3747577)
Tabea Schütze (3747517)
Kristina Sepčić (14662)
Ekaterina Shelest (615653)
Gavin Sherlock (827)
Vicky Sophianopoulou (3747610)
Fabio Squina (3406874)
Hui Sun (107933)
Antonia Susca (3747580)
Richard Todd (1615972)
Adrian Tsang (9935)
Shiela Unkles (3747568)
Nathalie van de Wiele (229065)
Diana van Rossen-Uffink (3747589)
Juliana Oliveira (3747553)
Tammi Vesth (399962)
Jaap Visser (3451127)
Jae-Hyuk Yu (34724)
Miaomiao Zhou (91821)
Mikael Andersen (3533219)
David Archer (203725)
Scott Baker (41660)
Isabelle Benoit (209030)
Axel Brakhage (3747520)
Gerhard Braus (3506639)
Reinhard Fischer (182192)
Jens Frisvad (3747583)
Gustavo Goldman (271482)
Jos Houbraken (415850)
Berl Oakley (3747559)
István Pócsi (3747574)
Claudio Scazzocchio (763578)
Bernhard Seiboth (51869)
Patricia vanKuyk (3546932)
Jennifer Wortman (59749)
Paul Dyer (3747514)
Igor Grigoriev (760696)

February 2017

HMM file used for the identification of protein classes of interest related to signal transduction. ...

Additional file 1: of Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea

Mudassir Iqbal (537102)
Mukesh Dubey (5944586)
Mikael Gudmundsson (5743373)
Maria Viketoft (2916590)
Dan Jensen (3815518)
Magnus Karlsson (150089)

November 2018

Table S1. Protease genes in different fungal genomes arranged according to MEROPS peptidase database...

Additional file 6: of Identification of novel genes in the carotenogenic and oleaginous yeast Rhodotorula toruloides through genome-wide insertional mutagenesis

Yanbin Liu (231378)
Chong Koh (3493988)
Sihui Yap (3493991)
Minge Du (4874146)
Mya Hlaing (4874143)
Lianghui Ji (231384)

February 2018

Figure S3. T-DNA organizations in contructs used in this study. All binary vectors have the same pPZ...

Additional file 5: Figure S1. of Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

Nicolás Bellora (45255)
Martín Moliné (3488867)
Márcia David-Palma (3165348)
Marco Coelho (3488864)
Chris Hittinger (821003)
José Sampaio (3488870)
Paula Gonçalves (129720)
Diego Libkind (3158151)

November 2016

Secondary protein structure features of the homeodomain transcription factors and pheromone receptor...

Additional file 7: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

Amelia Lindsey (4349380)
Yogeshwar Kelkar (599810)
Xin Wu (10164)
Dan Sun (140898)
Ellen Martinson (5237861)
Zhichao Yan (470852)
Paul Rugman-Jones (446257)
Daniel Hughes (3401426)
Shwetha Murali (3401390)
Jiaxin Qu (297542)
Shannon Dugan (39796)
Sandra Lee (273007)
Hsu Chao (3401423)
Huyen Dinh (273005)
Yi Han (194901)
Harsha Doddapaneni (3548552)
Kim Worley (3401444)
Donna Muzny (54293)
Gongyin Ye (343853)
Richard Gibbs (144333)
Stephen Richards (1495)
Soojin Yi (713141)
Richard Stouthamer (359680)
John Werren (2557927)

May 2018

Table S18. Comparisons to a sexual genome. Proteins and overrepresented GO terms for proteins most d...

Additional file 18: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Ronald de Vries (3464225)
Robert Riley (11626)
Ad Wiebenga (218081)
Guillermo Aguilar-Osorio (3546917)
Sotiris Amillis (3747547)
Cristiane Uchima (3512723)
Gregor Anderluh (145545)
Mojtaba Asadollahi (3747562)
Marion Askin (3747604)
Kerrie Barry (276529)
Evy Battaglia (510411)
Özgür Bayram (150583)
Tiziano Benocci (3747532)
Susanna Braus-Stromeyer (3747565)
Camila Caldana (76564)
David Cánovas (609771)
Gustavo Cerqueira (3747541)
Fusheng Chen (298630)
Wanping Chen (298625)
Cindy Choi (819115)
Alicia Clum (111778)
Renato dos Santos (3747505)
André Damásio (3613712)
George Diallinas (148998)
Tamás Emri (3747502)
Erzsébet Fekete (658292)
Michel Flipphi (586744)
Susanne Freyberg (3747544)
Antonia Gallo (3747571)
Christos Gournas (3747598)
Rob Habgood (3747511)
Matthieu Hainaut (330421)
María Harispe (3747607)
Bernard Henrissat (31550)
Kristiina Hildén (520583)
Ryan Hope (3747601)
Abeer Hossain (3542657)
Eugenia Karabika (3747526)
Levente Karaffa (658296)
Zsolt Karányi (213679)
Nada Kraševec (629660)
Alan Kuo (260458)
Harald Kusch (444862)
Kurt LaButti (114830)
Ellen Lagendijk (364626)
Alla Lapidus (6321)
Anthony Levasseur (45449)
Erika Lindquist (116964)
Anna Lipzen (194340)
Antonio Logrieco (3061605)
Andrew MacCabe (3747550)
Miia Mäkelä (563196)
Iran Malavazi (81124)
Petter Melin (3747592)
Vera Meyer (436900)
Natalia Mielnichuk (3747613)
Márton Miskei (213668)
Ákos Molnár (3747508)
Giuseppina Mulé (3747586)
Chew Ngan (3505151)
Margarita Orejas (3412205)
Erzsébet Orosz (3747595)
Jean Ouedraogo (3747523)
Karin Overkamp (3542666)
Hee-Soo Park (132707)
Giancarlo Perrone (415847)
Francois Piumi (88016)
Peter Punt (2278426)
Arthur Ram (3454442)
Ana Ramón (3747535)
Stefan Rauscher (3747529)
Eric Record (818818)
Diego Riaño-Pachón (3430481)
Vincent Robert (92227)
Julian Röhrig (550487)
Roberto Ruller (113949)
Asaf Salamov (116970)
Nadhira Salih (3747538)
Rob Samson (3747556)
Erzsébet Sándor (658294)
Manuel Sanguinetti (3747577)
Tabea Schütze (3747517)
Kristina Sepčić (14662)
Ekaterina Shelest (615653)
Gavin Sherlock (827)
Vicky Sophianopoulou (3747610)
Fabio Squina (3406874)
Hui Sun (107933)
Antonia Susca (3747580)
Richard Todd (1615972)
Adrian Tsang (9935)
Shiela Unkles (3747568)
Nathalie van de Wiele (229065)
Diana van Rossen-Uffink (3747589)
Juliana Oliveira (3747553)
Tammi Vesth (399962)
Jaap Visser (3451127)
Jae-Hyuk Yu (34724)
Miaomiao Zhou (91821)
Mikael Andersen (3533219)
David Archer (203725)
Scott Baker (41660)
Isabelle Benoit (209030)
Axel Brakhage (3747520)
Gerhard Braus (3506639)
Reinhard Fischer (182192)
Jens Frisvad (3747583)
Gustavo Goldman (271482)
Jos Houbraken (415850)
Berl Oakley (3747559)
István Pócsi (3747574)
Claudio Scazzocchio (763578)
Bernhard Seiboth (51869)
Patricia vanKuyk (3546932)
Jennifer Wortman (59749)
Paul Dyer (3747514)
Igor Grigoriev (760696)

February 2017

Identified secreted proteins (A. sydowii, A. tubingensis, A. wentii, A. zonatus). (XLSX 34 kb

Additional file 28: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Ronald de Vries (3464225)
Robert Riley (11626)
Ad Wiebenga (218081)
Guillermo Aguilar-Osorio (3546917)
Sotiris Amillis (3747547)
Cristiane Uchima (3512723)
Gregor Anderluh (145545)
Mojtaba Asadollahi (3747562)
Marion Askin (3747604)
Kerrie Barry (276529)
Evy Battaglia (510411)
Özgür Bayram (150583)
Tiziano Benocci (3747532)
Susanna Braus-Stromeyer (3747565)
Camila Caldana (76564)
David Cánovas (609771)
Gustavo Cerqueira (3747541)
Fusheng Chen (298630)
Wanping Chen (298625)
Cindy Choi (819115)
Alicia Clum (111778)
Renato dos Santos (3747505)
André Damásio (3613712)
George Diallinas (148998)
Tamás Emri (3747502)
Erzsébet Fekete (658292)
Michel Flipphi (586744)
Susanne Freyberg (3747544)
Antonia Gallo (3747571)
Christos Gournas (3747598)
Rob Habgood (3747511)
Matthieu Hainaut (330421)
María Harispe (3747607)
Bernard Henrissat (31550)
Kristiina Hildén (520583)
Ryan Hope (3747601)
Abeer Hossain (3542657)
Eugenia Karabika (3747526)
Levente Karaffa (658296)
Zsolt Karányi (213679)
Nada Kraševec (629660)
Alan Kuo (260458)
Harald Kusch (444862)
Kurt LaButti (114830)
Ellen Lagendijk (364626)
Alla Lapidus (6321)
Anthony Levasseur (45449)
Erika Lindquist (116964)
Anna Lipzen (194340)
Antonio Logrieco (3061605)
Andrew MacCabe (3747550)
Miia Mäkelä (563196)
Iran Malavazi (81124)
Petter Melin (3747592)
Vera Meyer (436900)
Natalia Mielnichuk (3747613)
Márton Miskei (213668)
Ákos Molnár (3747508)
Giuseppina Mulé (3747586)
Chew Ngan (3505151)
Margarita Orejas (3412205)
Erzsébet Orosz (3747595)
Jean Ouedraogo (3747523)
Karin Overkamp (3542666)
Hee-Soo Park (132707)
Giancarlo Perrone (415847)
Francois Piumi (88016)
Peter Punt (2278426)
Arthur Ram (3454442)
Ana Ramón (3747535)
Stefan Rauscher (3747529)
Eric Record (818818)
Diego Riaño-Pachón (3430481)
Vincent Robert (92227)
Julian Röhrig (550487)
Roberto Ruller (113949)
Asaf Salamov (116970)
Nadhira Salih (3747538)
Rob Samson (3747556)
Erzsébet Sándor (658294)
Manuel Sanguinetti (3747577)
Tabea Schütze (3747517)
Kristina Sepčić (14662)
Ekaterina Shelest (615653)
Gavin Sherlock (827)
Vicky Sophianopoulou (3747610)
Fabio Squina (3406874)
Hui Sun (107933)
Antonia Susca (3747580)
Richard Todd (1615972)
Adrian Tsang (9935)
Shiela Unkles (3747568)
Nathalie van de Wiele (229065)
Diana van Rossen-Uffink (3747589)
Juliana Oliveira (3747553)
Tammi Vesth (399962)
Jaap Visser (3451127)
Jae-Hyuk Yu (34724)
Miaomiao Zhou (91821)
Mikael Andersen (3533219)
David Archer (203725)
Scott Baker (41660)
Isabelle Benoit (209030)
Axel Brakhage (3747520)
Gerhard Braus (3506639)
Reinhard Fischer (182192)
Jens Frisvad (3747583)
Gustavo Goldman (271482)
Jos Houbraken (415850)
Berl Oakley (3747559)
István Pócsi (3747574)
Claudio Scazzocchio (763578)
Bernhard Seiboth (51869)
Patricia vanKuyk (3546932)
Jennifer Wortman (59749)
Paul Dyer (3747514)
Igor Grigoriev (760696)

February 2017

Number of flavohemoglobins and protein IDs found in the genome sequences of the Aspergillus species....

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 1: of Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA

Inmaculada García-Romero (3462461)
Antonio Pérez-Pulido (3462458)
Yolanda González-Flores (3462464)
Francisca Reyes-Ramírez (458207)
Eduardo Santero (12083)
Belén Floriano (3462455)

February 2016

Analysis of the oriC genomic region. A. Genetic organization around the predicted oriC region in sev...

Additional file 8: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S5. Heatmap of gene orthologues differentially abundant between the two F. prausnitzii genomo...

Additional file 6: of Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723

Swati Sinha (5225981)
Choy-Eng Nge (1701916)
Chung Leong (6701474)
Veronica Ng (6701477)
Sharon Crasta (6701480)
Mohammad Alfatah (4584019)
Falicia Goh (117265)
Kia-Ngee Low (6701483)
Huibin Zhang (5979632)
Prakash Arumugam (303310)
Alexander Lezhava (186379)
Swaine Chen (3453932)
Yoganathan Kanagasundaram (6701486)
Siew Ng (3523106)
Frank Eisenhaber (1700)
Birgit Eisenhaber (7248)

May 2019

Figure S8. Phylogenetic tree analysis of the functional distribution of C domains using MEGA7 (Maxim...

Additional file 3: of Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis

Zhiquan Song (1841773)
Jason Stajich (5225312)
Yunxuan Xie (2234497)
Xianhua Liu (2201038)
Yaodong He (5022107)
Jinfeng Chen (118034)
Glenn Hicks (722947)
Guangyi Wang (204937)

July 2018

Figure S2. Phylogenetic tree of all proteins containing IPR001019 domains. Total 18 species were ass...

Additional file 5: 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 S5. Histogram of average distances within ortholog groups, including single- and multi-copy i...

Additional file 5: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S3. De novo orthologous protein groups (nâ=â10,630) encoded in 31âF. prausnitzii genome...

Additional file 3: Table S2. of Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

Daniel Penselin (3362783)
Martin Münsterkötter (13742)
Susanne Kirsten (3362777)
Marius Felder (21057)
Stefan Taudien (47210)
Matthias Platzer (11284)
Kevin Ashelford (254162)
Konrad Paskiewicz (3529364)
Richard Harrison (824846)
David Hughes (47111)
Thomas Wolf (136760)
Ekaterina Shelest (615653)
Jenny Graap (3362765)
Jan Hoffmann (323101)
Claudia Wenzel (3362756)
Nadine Wöltje (3529370)
Kevin King (70030)
Bruce Fitt (3529367)
Ulrich Güldener (13741)
Anna Avrova (3362771)
Wolfgang Knogge (3362762)

November 2016

(A) Core meiotic recombination machinery genes. (B) Genes involved in sexual reproduction in the asp...

Additional file 37: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Ronald de Vries (3464225)
Robert Riley (11626)
Ad Wiebenga (218081)
Guillermo Aguilar-Osorio (3546917)
Sotiris Amillis (3747547)
Cristiane Uchima (3512723)
Gregor Anderluh (145545)
Mojtaba Asadollahi (3747562)
Marion Askin (3747604)
Kerrie Barry (276529)
Evy Battaglia (510411)
Özgür Bayram (150583)
Tiziano Benocci (3747532)
Susanna Braus-Stromeyer (3747565)
Camila Caldana (76564)
David Cánovas (609771)
Gustavo Cerqueira (3747541)
Fusheng Chen (298630)
Wanping Chen (298625)
Cindy Choi (819115)
Alicia Clum (111778)
Renato dos Santos (3747505)
André Damásio (3613712)
George Diallinas (148998)
Tamás Emri (3747502)
Erzsébet Fekete (658292)
Michel Flipphi (586744)
Susanne Freyberg (3747544)
Antonia Gallo (3747571)
Christos Gournas (3747598)
Rob Habgood (3747511)
Matthieu Hainaut (330421)
María Harispe (3747607)
Bernard Henrissat (31550)
Kristiina Hildén (520583)
Ryan Hope (3747601)
Abeer Hossain (3542657)
Eugenia Karabika (3747526)
Levente Karaffa (658296)
Zsolt Karányi (213679)
Nada Kraševec (629660)
Alan Kuo (260458)
Harald Kusch (444862)
Kurt LaButti (114830)
Ellen Lagendijk (364626)
Alla Lapidus (6321)
Anthony Levasseur (45449)
Erika Lindquist (116964)
Anna Lipzen (194340)
Antonio Logrieco (3061605)
Andrew MacCabe (3747550)
Miia Mäkelä (563196)
Iran Malavazi (81124)
Petter Melin (3747592)
Vera Meyer (436900)
Natalia Mielnichuk (3747613)
Márton Miskei (213668)
Ákos Molnár (3747508)
Giuseppina Mulé (3747586)
Chew Ngan (3505151)
Margarita Orejas (3412205)
Erzsébet Orosz (3747595)
Jean Ouedraogo (3747523)
Karin Overkamp (3542666)
Hee-Soo Park (132707)
Giancarlo Perrone (415847)
Francois Piumi (88016)
Peter Punt (2278426)
Arthur Ram (3454442)
Ana Ramón (3747535)
Stefan Rauscher (3747529)
Eric Record (818818)
Diego Riaño-Pachón (3430481)
Vincent Robert (92227)
Julian Röhrig (550487)
Roberto Ruller (113949)
Asaf Salamov (116970)
Nadhira Salih (3747538)
Rob Samson (3747556)
Erzsébet Sándor (658294)
Manuel Sanguinetti (3747577)
Tabea Schütze (3747517)
Kristina Sepčić (14662)
Ekaterina Shelest (615653)
Gavin Sherlock (827)
Vicky Sophianopoulou (3747610)
Fabio Squina (3406874)
Hui Sun (107933)
Antonia Susca (3747580)
Richard Todd (1615972)
Adrian Tsang (9935)
Shiela Unkles (3747568)
Nathalie van de Wiele (229065)
Diana van Rossen-Uffink (3747589)
Juliana Oliveira (3747553)
Tammi Vesth (399962)
Jaap Visser (3451127)
Jae-Hyuk Yu (34724)
Miaomiao Zhou (91821)
Mikael Andersen (3533219)
David Archer (203725)
Scott Baker (41660)
Isabelle Benoit (209030)
Axel Brakhage (3747520)
Gerhard Braus (3506639)
Reinhard Fischer (182192)
Jens Frisvad (3747583)
Gustavo Goldman (271482)
Jos Houbraken (415850)
Berl Oakley (3747559)
István Pócsi (3747574)
Claudio Scazzocchio (763578)
Bernhard Seiboth (51869)
Patricia vanKuyk (3546932)
Jennifer Wortman (59749)
Paul Dyer (3747514)
Igor Grigoriev (760696)

February 2017

HMM file used for the identification of protein classes of interest related to signal transduction. ...

Additional file 1: of Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea

Mudassir Iqbal (537102)
Mukesh Dubey (5944586)
Mikael Gudmundsson (5743373)
Maria Viketoft (2916590)
Dan Jensen (3815518)
Magnus Karlsson (150089)

November 2018

Table S1. Protease genes in different fungal genomes arranged according to MEROPS peptidase database...

Additional file 6: of Identification of novel genes in the carotenogenic and oleaginous yeast Rhodotorula toruloides through genome-wide insertional mutagenesis

Yanbin Liu (231378)
Chong Koh (3493988)
Sihui Yap (3493991)
Minge Du (4874146)
Mya Hlaing (4874143)
Lianghui Ji (231384)

February 2018

Figure S3. T-DNA organizations in contructs used in this study. All binary vectors have the same pPZ...

Additional file 5: Figure S1. of Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

Nicolás Bellora (45255)
Martín Moliné (3488867)
Márcia David-Palma (3165348)
Marco Coelho (3488864)
Chris Hittinger (821003)
José Sampaio (3488870)
Paula Gonçalves (129720)
Diego Libkind (3158151)

November 2016

Secondary protein structure features of the homeodomain transcription factors and pheromone receptor...

Additional file 7: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

Amelia Lindsey (4349380)
Yogeshwar Kelkar (599810)
Xin Wu (10164)
Dan Sun (140898)
Ellen Martinson (5237861)
Zhichao Yan (470852)
Paul Rugman-Jones (446257)
Daniel Hughes (3401426)
Shwetha Murali (3401390)
Jiaxin Qu (297542)
Shannon Dugan (39796)
Sandra Lee (273007)
Hsu Chao (3401423)
Huyen Dinh (273005)
Yi Han (194901)
Harsha Doddapaneni (3548552)
Kim Worley (3401444)
Donna Muzny (54293)
Gongyin Ye (343853)
Richard Gibbs (144333)
Stephen Richards (1495)
Soojin Yi (713141)
Richard Stouthamer (359680)
John Werren (2557927)

May 2018

Table S18. Comparisons to a sexual genome. Proteins and overrepresented GO terms for proteins most d...

Additional file 18: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Ronald de Vries (3464225)
Robert Riley (11626)
Ad Wiebenga (218081)
Guillermo Aguilar-Osorio (3546917)
Sotiris Amillis (3747547)
Cristiane Uchima (3512723)
Gregor Anderluh (145545)
Mojtaba Asadollahi (3747562)
Marion Askin (3747604)
Kerrie Barry (276529)
Evy Battaglia (510411)
Özgür Bayram (150583)
Tiziano Benocci (3747532)
Susanna Braus-Stromeyer (3747565)
Camila Caldana (76564)
David Cánovas (609771)
Gustavo Cerqueira (3747541)
Fusheng Chen (298630)
Wanping Chen (298625)
Cindy Choi (819115)
Alicia Clum (111778)
Renato dos Santos (3747505)
André Damásio (3613712)
George Diallinas (148998)
Tamás Emri (3747502)
Erzsébet Fekete (658292)
Michel Flipphi (586744)
Susanne Freyberg (3747544)
Antonia Gallo (3747571)
Christos Gournas (3747598)
Rob Habgood (3747511)
Matthieu Hainaut (330421)
María Harispe (3747607)
Bernard Henrissat (31550)
Kristiina Hildén (520583)
Ryan Hope (3747601)
Abeer Hossain (3542657)
Eugenia Karabika (3747526)
Levente Karaffa (658296)
Zsolt Karányi (213679)
Nada Kraševec (629660)
Alan Kuo (260458)
Harald Kusch (444862)
Kurt LaButti (114830)
Ellen Lagendijk (364626)
Alla Lapidus (6321)
Anthony Levasseur (45449)
Erika Lindquist (116964)
Anna Lipzen (194340)
Antonio Logrieco (3061605)
Andrew MacCabe (3747550)
Miia Mäkelä (563196)
Iran Malavazi (81124)
Petter Melin (3747592)
Vera Meyer (436900)
Natalia Mielnichuk (3747613)
Márton Miskei (213668)
Ákos Molnár (3747508)
Giuseppina Mulé (3747586)
Chew Ngan (3505151)
Margarita Orejas (3412205)
Erzsébet Orosz (3747595)
Jean Ouedraogo (3747523)
Karin Overkamp (3542666)
Hee-Soo Park (132707)
Giancarlo Perrone (415847)
Francois Piumi (88016)
Peter Punt (2278426)
Arthur Ram (3454442)
Ana Ramón (3747535)
Stefan Rauscher (3747529)
Eric Record (818818)
Diego Riaño-Pachón (3430481)
Vincent Robert (92227)
Julian Röhrig (550487)
Roberto Ruller (113949)
Asaf Salamov (116970)
Nadhira Salih (3747538)
Rob Samson (3747556)
Erzsébet Sándor (658294)
Manuel Sanguinetti (3747577)
Tabea Schütze (3747517)
Kristina Sepčić (14662)
Ekaterina Shelest (615653)
Gavin Sherlock (827)
Vicky Sophianopoulou (3747610)
Fabio Squina (3406874)
Hui Sun (107933)
Antonia Susca (3747580)
Richard Todd (1615972)
Adrian Tsang (9935)
Shiela Unkles (3747568)
Nathalie van de Wiele (229065)
Diana van Rossen-Uffink (3747589)
Juliana Oliveira (3747553)
Tammi Vesth (399962)
Jaap Visser (3451127)
Jae-Hyuk Yu (34724)
Miaomiao Zhou (91821)
Mikael Andersen (3533219)
David Archer (203725)
Scott Baker (41660)
Isabelle Benoit (209030)
Axel Brakhage (3747520)
Gerhard Braus (3506639)
Reinhard Fischer (182192)
Jens Frisvad (3747583)
Gustavo Goldman (271482)
Jos Houbraken (415850)
Berl Oakley (3747559)
István Pócsi (3747574)
Claudio Scazzocchio (763578)
Bernhard Seiboth (51869)
Patricia vanKuyk (3546932)
Jennifer Wortman (59749)
Paul Dyer (3747514)
Igor Grigoriev (760696)

February 2017

Identified secreted proteins (A. sydowii, A. tubingensis, A. wentii, A. zonatus). (XLSX 34 kb

Additional file 28: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Ronald de Vries (3464225)
Robert Riley (11626)
Ad Wiebenga (218081)
Guillermo Aguilar-Osorio (3546917)
Sotiris Amillis (3747547)
Cristiane Uchima (3512723)
Gregor Anderluh (145545)
Mojtaba Asadollahi (3747562)
Marion Askin (3747604)
Kerrie Barry (276529)
Evy Battaglia (510411)
Özgür Bayram (150583)
Tiziano Benocci (3747532)
Susanna Braus-Stromeyer (3747565)
Camila Caldana (76564)
David Cánovas (609771)
Gustavo Cerqueira (3747541)
Fusheng Chen (298630)
Wanping Chen (298625)
Cindy Choi (819115)
Alicia Clum (111778)
Renato dos Santos (3747505)
André Damásio (3613712)
George Diallinas (148998)
Tamás Emri (3747502)
Erzsébet Fekete (658292)
Michel Flipphi (586744)
Susanne Freyberg (3747544)
Antonia Gallo (3747571)
Christos Gournas (3747598)
Rob Habgood (3747511)
Matthieu Hainaut (330421)
María Harispe (3747607)
Bernard Henrissat (31550)
Kristiina Hildén (520583)
Ryan Hope (3747601)
Abeer Hossain (3542657)
Eugenia Karabika (3747526)
Levente Karaffa (658296)
Zsolt Karányi (213679)
Nada Kraševec (629660)
Alan Kuo (260458)
Harald Kusch (444862)
Kurt LaButti (114830)
Ellen Lagendijk (364626)
Alla Lapidus (6321)
Anthony Levasseur (45449)
Erika Lindquist (116964)
Anna Lipzen (194340)
Antonio Logrieco (3061605)
Andrew MacCabe (3747550)
Miia Mäkelä (563196)
Iran Malavazi (81124)
Petter Melin (3747592)
Vera Meyer (436900)
Natalia Mielnichuk (3747613)
Márton Miskei (213668)
Ákos Molnár (3747508)
Giuseppina Mulé (3747586)
Chew Ngan (3505151)
Margarita Orejas (3412205)
Erzsébet Orosz (3747595)
Jean Ouedraogo (3747523)
Karin Overkamp (3542666)
Hee-Soo Park (132707)
Giancarlo Perrone (415847)
Francois Piumi (88016)
Peter Punt (2278426)
Arthur Ram (3454442)
Ana Ramón (3747535)
Stefan Rauscher (3747529)
Eric Record (818818)
Diego Riaño-Pachón (3430481)
Vincent Robert (92227)
Julian Röhrig (550487)
Roberto Ruller (113949)
Asaf Salamov (116970)
Nadhira Salih (3747538)
Rob Samson (3747556)
Erzsébet Sándor (658294)
Manuel Sanguinetti (3747577)
Tabea Schütze (3747517)
Kristina Sepčić (14662)
Ekaterina Shelest (615653)
Gavin Sherlock (827)
Vicky Sophianopoulou (3747610)
Fabio Squina (3406874)
Hui Sun (107933)
Antonia Susca (3747580)
Richard Todd (1615972)
Adrian Tsang (9935)
Shiela Unkles (3747568)
Nathalie van de Wiele (229065)
Diana van Rossen-Uffink (3747589)
Juliana Oliveira (3747553)
Tammi Vesth (399962)
Jaap Visser (3451127)
Jae-Hyuk Yu (34724)
Miaomiao Zhou (91821)
Mikael Andersen (3533219)
David Archer (203725)
Scott Baker (41660)
Isabelle Benoit (209030)
Axel Brakhage (3747520)
Gerhard Braus (3506639)
Reinhard Fischer (182192)
Jens Frisvad (3747583)
Gustavo Goldman (271482)
Jos Houbraken (415850)
Berl Oakley (3747559)
István Pócsi (3747574)
Claudio Scazzocchio (763578)
Bernhard Seiboth (51869)
Patricia vanKuyk (3546932)
Jennifer Wortman (59749)
Paul Dyer (3747514)
Igor Grigoriev (760696)

February 2017

Number of flavohemoglobins and protein IDs found in the genome sequences of the Aspergillus species....

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 1: of Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA

Inmaculada García-Romero (3462461)
Antonio Pérez-Pulido (3462458)
Yolanda González-Flores (3462464)
Francisca Reyes-Ramírez (458207)
Eduardo Santero (12083)
Belén Floriano (3462455)

February 2016

Analysis of the oriC genomic region. A. Genetic organization around the predicted oriC region in sev...

Additional file 8: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S5. Heatmap of gene orthologues differentially abundant between the two F. prausnitzii genomo...

Additional file 6: of Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723

Swati Sinha (5225981)
Choy-Eng Nge (1701916)
Chung Leong (6701474)
Veronica Ng (6701477)
Sharon Crasta (6701480)
Mohammad Alfatah (4584019)
Falicia Goh (117265)
Kia-Ngee Low (6701483)
Huibin Zhang (5979632)
Prakash Arumugam (303310)
Alexander Lezhava (186379)
Swaine Chen (3453932)
Yoganathan Kanagasundaram (6701486)
Siew Ng (3523106)
Frank Eisenhaber (1700)
Birgit Eisenhaber (7248)

May 2019

Figure S8. Phylogenetic tree analysis of the functional distribution of C domains using MEGA7 (Maxim...

Additional file 3: of Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis

Zhiquan Song (1841773)
Jason Stajich (5225312)
Yunxuan Xie (2234497)
Xianhua Liu (2201038)
Yaodong He (5022107)
Jinfeng Chen (118034)
Glenn Hicks (722947)
Guangyi Wang (204937)

July 2018

Figure S2. Phylogenetic tree of all proteins containing IPR001019 domains. Total 18 species were ass...

Additional file 5: 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 S5. Histogram of average distances within ortholog groups, including single- and multi-copy i...

Additional file 5: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S3. De novo orthologous protein groups (nâ=â10,630) encoded in 31âF. prausnitzii genome...

Additional file 3: Table S2. of Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

Daniel Penselin (3362783)
Martin Münsterkötter (13742)
Susanne Kirsten (3362777)
Marius Felder (21057)
Stefan Taudien (47210)
Matthias Platzer (11284)
Kevin Ashelford (254162)
Konrad Paskiewicz (3529364)
Richard Harrison (824846)
David Hughes (47111)
Thomas Wolf (136760)
Ekaterina Shelest (615653)
Jenny Graap (3362765)
Jan Hoffmann (323101)
Claudia Wenzel (3362756)
Nadine Wöltje (3529370)
Kevin King (70030)
Bruce Fitt (3529367)
Ulrich Güldener (13741)
Anna Avrova (3362771)
Wolfgang Knogge (3362762)

November 2016

(A) Core meiotic recombination machinery genes. (B) Genes involved in sexual reproduction in the asp...

Additional file 37: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Ronald de Vries (3464225)
Robert Riley (11626)
Ad Wiebenga (218081)
Guillermo Aguilar-Osorio (3546917)
Sotiris Amillis (3747547)
Cristiane Uchima (3512723)
Gregor Anderluh (145545)
Mojtaba Asadollahi (3747562)
Marion Askin (3747604)
Kerrie Barry (276529)
Evy Battaglia (510411)
Özgür Bayram (150583)
Tiziano Benocci (3747532)
Susanna Braus-Stromeyer (3747565)
Camila Caldana (76564)
David Cánovas (609771)
Gustavo Cerqueira (3747541)
Fusheng Chen (298630)
Wanping Chen (298625)
Cindy Choi (819115)
Alicia Clum (111778)
Renato dos Santos (3747505)
André Damásio (3613712)
George Diallinas (148998)
Tamás Emri (3747502)
Erzsébet Fekete (658292)
Michel Flipphi (586744)
Susanne Freyberg (3747544)
Antonia Gallo (3747571)
Christos Gournas (3747598)
Rob Habgood (3747511)
Matthieu Hainaut (330421)
María Harispe (3747607)
Bernard Henrissat (31550)
Kristiina Hildén (520583)
Ryan Hope (3747601)
Abeer Hossain (3542657)
Eugenia Karabika (3747526)
Levente Karaffa (658296)
Zsolt Karányi (213679)
Nada Kraševec (629660)
Alan Kuo (260458)
Harald Kusch (444862)
Kurt LaButti (114830)
Ellen Lagendijk (364626)
Alla Lapidus (6321)
Anthony Levasseur (45449)
Erika Lindquist (116964)
Anna Lipzen (194340)
Antonio Logrieco (3061605)
Andrew MacCabe (3747550)
Miia Mäkelä (563196)
Iran Malavazi (81124)
Petter Melin (3747592)
Vera Meyer (436900)
Natalia Mielnichuk (3747613)
Márton Miskei (213668)
Ákos Molnár (3747508)
Giuseppina Mulé (3747586)
Chew Ngan (3505151)
Margarita Orejas (3412205)
Erzsébet Orosz (3747595)
Jean Ouedraogo (3747523)
Karin Overkamp (3542666)
Hee-Soo Park (132707)
Giancarlo Perrone (415847)
Francois Piumi (88016)
Peter Punt (2278426)
Arthur Ram (3454442)
Ana Ramón (3747535)
Stefan Rauscher (3747529)
Eric Record (818818)
Diego Riaño-Pachón (3430481)
Vincent Robert (92227)
Julian Röhrig (550487)
Roberto Ruller (113949)
Asaf Salamov (116970)
Nadhira Salih (3747538)
Rob Samson (3747556)
Erzsébet Sándor (658294)
Manuel Sanguinetti (3747577)
Tabea Schütze (3747517)
Kristina Sepčić (14662)
Ekaterina Shelest (615653)
Gavin Sherlock (827)
Vicky Sophianopoulou (3747610)
Fabio Squina (3406874)
Hui Sun (107933)
Antonia Susca (3747580)
Richard Todd (1615972)
Adrian Tsang (9935)
Shiela Unkles (3747568)
Nathalie van de Wiele (229065)
Diana van Rossen-Uffink (3747589)
Juliana Oliveira (3747553)
Tammi Vesth (399962)
Jaap Visser (3451127)
Jae-Hyuk Yu (34724)
Miaomiao Zhou (91821)
Mikael Andersen (3533219)
David Archer (203725)
Scott Baker (41660)
Isabelle Benoit (209030)
Axel Brakhage (3747520)
Gerhard Braus (3506639)
Reinhard Fischer (182192)
Jens Frisvad (3747583)
Gustavo Goldman (271482)
Jos Houbraken (415850)
Berl Oakley (3747559)
István Pócsi (3747574)
Claudio Scazzocchio (763578)
Bernhard Seiboth (51869)
Patricia vanKuyk (3546932)
Jennifer Wortman (59749)
Paul Dyer (3747514)
Igor Grigoriev (760696)

February 2017

HMM file used for the identification of protein classes of interest related to signal transduction. ...

Additional file 1: of Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea

Mudassir Iqbal (537102)
Mukesh Dubey (5944586)
Mikael Gudmundsson (5743373)
Maria Viketoft (2916590)
Dan Jensen (3815518)
Magnus Karlsson (150089)

November 2018

Table S1. Protease genes in different fungal genomes arranged according to MEROPS peptidase database...

Additional file 6: of Identification of novel genes in the carotenogenic and oleaginous yeast Rhodotorula toruloides through genome-wide insertional mutagenesis

Yanbin Liu (231378)
Chong Koh (3493988)
Sihui Yap (3493991)
Minge Du (4874146)
Mya Hlaing (4874143)
Lianghui Ji (231384)

February 2018

Figure S3. T-DNA organizations in contructs used in this study. All binary vectors have the same pPZ...

Additional file 7: of Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

Abstract

Extracted data

Additional file 7: of Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

Abstract

Extracted data

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