Additional file 18: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Additional file 2: Table S1. of Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris

Glenna Kramer (4616275)
Justin Nodwell (29871)

November 2017

Predicted gene clusters in C. militaris. Predicted gene clusters are labeled, putative natural produ...

Additional file 1: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

Ahmad Rajeh (5140910)
Jie Lv (235936)
Zhenguo Lin (1984012)

April 2018

Table S1. List of species examined in this study and genome assembly version. (XLSX 16Â kb

Additional file 2: of Molecular and functional evolution of the fungal diterpene synthase genes

Marc Fischer (1778896)
Camille Rustenhloz (3464234)
Véronique Leh-Louis (166350)
Guy Perrière (2074)

October 2015

Fungal exons (blue) and introns (black) in putative di-TPS genes. Fungal species are arranged in the...

Additional file 9: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Table S4. Secondary metabolite clusters found in six T. inflatum strains. (XLXS 17.5 kb

Additional file 17: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Table S6. Blast hits of the Cluster D genes to A. flavus genome and NCBI nr database (XLSX 15.3 kb

Additional file 13: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Table S5. Genome-wide correlation analyses of transposable elements with secondary metabolite cluste...

Additional file 6: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S3. MUMmer plots of complete assemblies for all strains against the reference strain CBS714.7...

Additional file 19: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Table S7. Ortholog analysis of proteomes of all T. inflatum strains to cluster D genes. (XLSX 15 kb

Additional file 12: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S8. Terpene synthase and terpene cyclase phylogenetic trees. (PDF 19.0 Mb

Additional file 3: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S2. Hi-C plot mapping NRRL8044 Hi-C data to the NRRL8044 assembly supports assembly of two un...

Additional file 2: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S1. Mauve alignments of each chromosome showing large inversions. (PDF 930 kb

Additional file 15: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S10. Phylogeny of A-domains of peptaibiotic NRPSs from T. inflatum, T. ophioglossoides, and T...

Additional file 14: 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

Molecular phylogenetic tree of CYP6001 - CYP6003 families (PpoA - PpoD) and colinearity of the genet...

Additional file 8: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

Ahmad Rajeh (5140910)
Jie Lv (235936)
Zhenguo Lin (1984012)

April 2018

Table S6. List of structural variants identified from the genome sequencing data of 216 strains. (XL...

Additional file 2: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

Ahmad Rajeh (5140910)
Jie Lv (235936)
Zhenguo Lin (1984012)

April 2018

Table S2. List of genes in 160 orthologous groups identified in this study. (XLSX 134Â kb

Additional file 2: Table S1. of Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris

Glenna Kramer (4616275)
Justin Nodwell (29871)

November 2017

Predicted gene clusters in C. militaris. Predicted gene clusters are labeled, putative natural produ...

Additional file 1: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

Ahmad Rajeh (5140910)
Jie Lv (235936)
Zhenguo Lin (1984012)

April 2018

Table S1. List of species examined in this study and genome assembly version. (XLSX 16Â kb

Additional file 2: of Molecular and functional evolution of the fungal diterpene synthase genes

Marc Fischer (1778896)
Camille Rustenhloz (3464234)
Véronique Leh-Louis (166350)
Guy Perrière (2074)

October 2015

Fungal exons (blue) and introns (black) in putative di-TPS genes. Fungal species are arranged in the...

Additional file 9: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Table S4. Secondary metabolite clusters found in six T. inflatum strains. (XLXS 17.5 kb

Additional file 17: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Table S6. Blast hits of the Cluster D genes to A. flavus genome and NCBI nr database (XLSX 15.3 kb

Additional file 13: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Table S5. Genome-wide correlation analyses of transposable elements with secondary metabolite cluste...

Additional file 6: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S3. MUMmer plots of complete assemblies for all strains against the reference strain CBS714.7...

Additional file 19: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Table S7. Ortholog analysis of proteomes of all T. inflatum strains to cluster D genes. (XLSX 15 kb

Additional file 12: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S8. Terpene synthase and terpene cyclase phylogenetic trees. (PDF 19.0 Mb

Additional file 3: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S2. Hi-C plot mapping NRRL8044 Hi-C data to the NRRL8044 assembly supports assembly of two un...

Additional file 2: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S1. Mauve alignments of each chromosome showing large inversions. (PDF 930 kb

Additional file 15: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo Olarte (6313925)
Jon Menke (410402)
Ying Zhang (40767)
Shawn Sullivan (6313928)
Jason Slot (6313931)
Yinyin Huang (6313934)
Jonathan Badalamenti (6313937)
Alisha Quandt (6313940)
Joseph Spatafora (3292014)
Kathryn Bushley (6313943)

February 2019

Figure S10. Phylogeny of A-domains of peptaibiotic NRPSs from T. inflatum, T. ophioglossoides, and T...

Additional file 14: 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

Molecular phylogenetic tree of CYP6001 - CYP6003 families (PpoA - PpoD) and colinearity of the genet...

Additional file 8: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

Ahmad Rajeh (5140910)
Jie Lv (235936)
Zhenguo Lin (1984012)

April 2018

Table S6. List of structural variants identified from the genome sequencing data of 216 strains. (XL...

Additional file 2: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

Ahmad Rajeh (5140910)
Jie Lv (235936)
Zhenguo Lin (1984012)

April 2018

Table S2. List of genes in 160 orthologous groups identified in this study. (XLSX 134Â kb

Additional file 2: Table S1. of Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris

Glenna Kramer (4616275)
Justin Nodwell (29871)

November 2017

Predicted gene clusters in C. militaris. Predicted gene clusters are labeled, putative natural produ...

Additional file 1: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

Ahmad Rajeh (5140910)
Jie Lv (235936)
Zhenguo Lin (1984012)

April 2018

Table S1. List of species examined in this study and genome assembly version. (XLSX 16Â kb

Additional file 2: of Molecular and functional evolution of the fungal diterpene synthase genes

Marc Fischer (1778896)
Camille Rustenhloz (3464234)
Véronique Leh-Louis (166350)
Guy Perrière (2074)

October 2015

Fungal exons (blue) and introns (black) in putative di-TPS genes. Fungal species are arranged in the...

Additional file 18: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Abstract

Extracted data

Additional file 18: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Abstract

Extracted data

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