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

Additional file 15: 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

Protein clustering of genes from all Ptr isolates orthologous groups. (TXT 3252Â kb

Additional file 8: Table S5. of Comparative genomics reveals Cyclospora cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens

Shiyou Liu (3469283)
Lin Wang (11986)
Huajun Zheng (38118)
Zhixiao Xu (3469277)
Dawn Roellig (550998)
Na Li (6550)
Michael Frace (210649)
Kevin Tang (3469280)
Michael Arrowood (3452180)
Delynn Moss (3433712)
Longxian Zhang (142384)
Yaoyu Feng (142393)
Lihua Xiao (142413)

April 2016

Members of a major group of paralogs detected in the Cyclospora cayetanensis genome and results of B...

Additional file 16: 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

Enrichment scores for functional annotations of orthologous groups under diversifying selection. (XL...

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 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 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 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 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 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 Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

Jean-FĂŠlix Dallery (4399660)
Nicolas Lapalu (209014)
Antonios Zampounis (4399573)
Sandrine PignĂŠ (3619619)
Isabelle Luyten (4399597)
JoĂŤlle Amselem (4399666)
Alexander Wittenberg (4399579)
Shiguo Zhou (36012)
Marisa de Queiroz (4399582)
Guillaume Robin (4399585)
Annie Auger (4399576)
Matthieu Hainaut (330421)
Bernard Henrissat (31550)
Ki-Tae Kim (1847161)
Yong-Hwan Lee (8162)
Olivier Lespinet (4399591)
David Schwartz (3449264)
Michael Thon (3124980)
Richard OâConnell (4399663)

August 2017

Phylogenetic analysis of 43 cytosine-specific methyltransferase domains (PF00145) from Dnmt1 fungal ...

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 19: of Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

Jean-FĂŠlix Dallery (4399660)
Nicolas Lapalu (209014)
Antonios Zampounis (4399573)
Sandrine PignĂŠ (3619619)
Isabelle Luyten (4399597)
JoĂŤlle Amselem (4399666)
Alexander Wittenberg (4399579)
Shiguo Zhou (36012)
Marisa de Queiroz (4399582)
Guillaume Robin (4399585)
Annie Auger (4399576)
Matthieu Hainaut (330421)
Bernard Henrissat (31550)
Ki-Tae Kim (1847161)
Yong-Hwan Lee (8162)
Olivier Lespinet (4399591)
David Schwartz (3449264)
Michael Thon (3124980)
Richard OâConnell (4399663)

August 2017

Expression analysis of C. higginsianum transposable elements (TEs). (A) Distribution of log (CPM) pe...

Additional file 15: 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

Protein clustering of genes from all Ptr isolates orthologous groups. (TXT 3252Â kb

Additional file 8: Table S5. of Comparative genomics reveals Cyclospora cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens

Shiyou Liu (3469283)
Lin Wang (11986)
Huajun Zheng (38118)
Zhixiao Xu (3469277)
Dawn Roellig (550998)
Na Li (6550)
Michael Frace (210649)
Kevin Tang (3469280)
Michael Arrowood (3452180)
Delynn Moss (3433712)
Longxian Zhang (142384)
Yaoyu Feng (142393)
Lihua Xiao (142413)

April 2016

Members of a major group of paralogs detected in the Cyclospora cayetanensis genome and results of B...

Additional file 16: 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

Enrichment scores for functional annotations of orthologous groups under diversifying selection. (XL...

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 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 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 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 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 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 Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

Jean-FĂŠlix Dallery (4399660)
Nicolas Lapalu (209014)
Antonios Zampounis (4399573)
Sandrine PignĂŠ (3619619)
Isabelle Luyten (4399597)
JoĂŤlle Amselem (4399666)
Alexander Wittenberg (4399579)
Shiguo Zhou (36012)
Marisa de Queiroz (4399582)
Guillaume Robin (4399585)
Annie Auger (4399576)
Matthieu Hainaut (330421)
Bernard Henrissat (31550)
Ki-Tae Kim (1847161)
Yong-Hwan Lee (8162)
Olivier Lespinet (4399591)
David Schwartz (3449264)
Michael Thon (3124980)
Richard OâConnell (4399663)

August 2017

Phylogenetic analysis of 43 cytosine-specific methyltransferase domains (PF00145) from Dnmt1 fungal ...

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 19: of Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

Jean-FĂŠlix Dallery (4399660)
Nicolas Lapalu (209014)
Antonios Zampounis (4399573)
Sandrine PignĂŠ (3619619)
Isabelle Luyten (4399597)
JoĂŤlle Amselem (4399666)
Alexander Wittenberg (4399579)
Shiguo Zhou (36012)
Marisa de Queiroz (4399582)
Guillaume Robin (4399585)
Annie Auger (4399576)
Matthieu Hainaut (330421)
Bernard Henrissat (31550)
Ki-Tae Kim (1847161)
Yong-Hwan Lee (8162)
Olivier Lespinet (4399591)
David Schwartz (3449264)
Michael Thon (3124980)
Richard OâConnell (4399663)

August 2017

Expression analysis of C. higginsianum transposable elements (TEs). (A) Distribution of log (CPM) pe...

Additional file 15: 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

Protein clustering of genes from all Ptr isolates orthologous groups. (TXT 3252Â kb

Additional file 8: Table S5. of Comparative genomics reveals Cyclospora cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens

Shiyou Liu (3469283)
Lin Wang (11986)
Huajun Zheng (38118)
Zhixiao Xu (3469277)
Dawn Roellig (550998)
Na Li (6550)
Michael Frace (210649)
Kevin Tang (3469280)
Michael Arrowood (3452180)
Delynn Moss (3433712)
Longxian Zhang (142384)
Yaoyu Feng (142393)
Lihua Xiao (142413)

April 2016

Members of a major group of paralogs detected in the Cyclospora cayetanensis genome and results of B...

Additional file 16: 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

Enrichment scores for functional annotations of orthologous groups under diversifying selection. (XL...

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

Abstract

Extracted data

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

Abstract

Extracted data

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