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

Additional file 6: of Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity

Paula Moolhuijzen (171379)
Pao See (5132903)
James Hane (3539561)
Gongjun Shi (5132906)
Zhaohui Liu (189380)
Richard Oliver (2411857)
Caroline Moffat (5132900)

April 2018

M4 plot of large segmental duplications. Circos plot displays M4 genome LTR positions and segmental ...

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 1: Figure S1. of Several steps of lateral gene transfer followed by events of âbirth-and-deathâ evolution shaped a fungal sorbicillinoid biosynthetic gene cluster

Irina Druzhinina (3492278)
Eva Kubicek (3492284)
Christian Kubicek (3426419)

December 2016

Architecture of Trire2: 73618 and Trire2:73621. The bar specifies the size of the proteins (in amino...

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 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 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 18: 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 S12. RAxML trees for homologs of each gene within T. inflatum CBS567.84 and CBS824.70 cluster...

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 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 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 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 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 1: Figure S1. of Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris

Glenna Kramer (4616275)
Justin Nodwell (29871)

November 2017

Coverage across chromosomes. Coverage across chromosomes from SMRT analysis resequencing protocol as...

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 4: 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

Figure S1. Examples of significant variation of pGOD among different chromosomal regions in Saccharo...

Additional file 6: of Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity

Paula Moolhuijzen (171379)
Pao See (5132903)
James Hane (3539561)
Gongjun Shi (5132906)
Zhaohui Liu (189380)
Richard Oliver (2411857)
Caroline Moffat (5132900)

April 2018

M4 plot of large segmental duplications. Circos plot displays M4 genome LTR positions and segmental ...

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 1: Figure S1. of Several steps of lateral gene transfer followed by events of âbirth-and-deathâ evolution shaped a fungal sorbicillinoid biosynthetic gene cluster

Irina Druzhinina (3492278)
Eva Kubicek (3492284)
Christian Kubicek (3426419)

December 2016

Architecture of Trire2: 73618 and Trire2:73621. The bar specifies the size of the proteins (in amino...

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 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 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 18: 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 S12. RAxML trees for homologs of each gene within T. inflatum CBS567.84 and CBS824.70 cluster...

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 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 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 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 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 1: Figure S1. of Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris

Glenna Kramer (4616275)
Justin Nodwell (29871)

November 2017

Coverage across chromosomes. Coverage across chromosomes from SMRT analysis resequencing protocol as...

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 4: 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

Figure S1. Examples of significant variation of pGOD among different chromosomal regions in Saccharo...

Additional file 6: of Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity

Paula Moolhuijzen (171379)
Pao See (5132903)
James Hane (3539561)
Gongjun Shi (5132906)
Zhaohui Liu (189380)
Richard Oliver (2411857)
Caroline Moffat (5132900)

April 2018

M4 plot of large segmental duplications. Circos plot displays M4 genome LTR positions and segmental ...

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 1: Figure S1. of Several steps of lateral gene transfer followed by events of âbirth-and-deathâ evolution shaped a fungal sorbicillinoid biosynthetic gene cluster

Irina Druzhinina (3492278)
Eva Kubicek (3492284)
Christian Kubicek (3426419)

December 2016

Architecture of Trire2: 73618 and Trire2:73621. The bar specifies the size of the proteins (in amino...

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

Abstract

Extracted data

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

Abstract

Extracted data

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