Conserved synteny in Trichoderma reesei with related filamentous ascomycetes

D. Martinez, Markku Saloheimo, R. Berka, B. Henrissat, M.A. Nelson

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

Abstract

The current pace of whole genome sequencing has made it almost trivial to produce nearly complete fungal sequences. This now gives us the ability to perform whole genome comparisons of fungi to investigate biological questions and genome evolution. To this end, syntenic regions between Trichoderma reesei and four other filamentous fungi (Fusarium graminearum, Neurospora crassa, Magnaporthe grisea and Aspergillus nidulans) were identified. An algorithm was designed that takes homologs from two fungi and places them side by side, optimizing homolog density, and minimizing gaps between homologs and the number of homologs in a syntenic region. As would be expected, the percent coverage of synteny between T. reesei and the other four ascomycetes declines with time since the last common ancestor, with F. graminearum having the highest synteny and A. nidulans the lowest. This approach enabled the identification of regions in the T. reesei genome that were conserved in multiple genomes as well as highlighting regions of the T. reesei genome that have changed dramatically. Finally, for genes within these highly conserved regions and for the gaps, GO terms and Enzyme Commission codes were assigned. These results were used to assess the possibility that there is selective pressure to force genes that are in the same biochemical pathway, have similar function or are involved in similar processes to maintain or gain proximity.
Original languageEnglish
Title of host publication3rd European Federation of Biotechnology Conference
Subtitle of host publicationPhysiology of Yeasts and Filamentous Fungi PYFF3
Place of PublicationEspoo
PublisherVTT Technical Research Centre of Finland
Pages55
ISBN (Electronic)978-951-38-6314-2
ISBN (Print)978-951-38-6313-5
Publication statusPublished - 2007
Event3rd European Federation of Biotechnology Conference : Physiology of Yeasts and Filamentous Fungi - Helsinki, Finland
Duration: 13 Jun 200716 Jun 2007

Publication series

SeriesVTT Symposium
Number245
ISSN0357-9387

Conference

Conference3rd European Federation of Biotechnology Conference
Abbreviated titlePYFF3
CountryFinland
CityHelsinki
Period13/06/0716/06/07

Fingerprint

Trichoderma reesei
Ascomycota
genome
Aspergillus nidulans
Fusarium graminearum
fungi
Neurospora crassa
Magnaporthe grisea
biochemical pathways
ancestry
genes
enzymes

Cite this

Martinez, D., Saloheimo, M., Berka, R., Henrissat, B., & Nelson, M. A. (2007). Conserved synteny in Trichoderma reesei with related filamentous ascomycetes. In 3rd European Federation of Biotechnology Conference: Physiology of Yeasts and Filamentous Fungi PYFF3 (pp. 55). [P4] Espoo: VTT Technical Research Centre of Finland. VTT Symposium, No. 245
Martinez, D. ; Saloheimo, Markku ; Berka, R. ; Henrissat, B. ; Nelson, M.A. / Conserved synteny in Trichoderma reesei with related filamentous ascomycetes. 3rd European Federation of Biotechnology Conference: Physiology of Yeasts and Filamentous Fungi PYFF3. Espoo : VTT Technical Research Centre of Finland, 2007. pp. 55 (VTT Symposium; No. 245).
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Martinez, D, Saloheimo, M, Berka, R, Henrissat, B & Nelson, MA 2007, Conserved synteny in Trichoderma reesei with related filamentous ascomycetes. in 3rd European Federation of Biotechnology Conference: Physiology of Yeasts and Filamentous Fungi PYFF3., P4, VTT Technical Research Centre of Finland, Espoo, VTT Symposium, no. 245, pp. 55, 3rd European Federation of Biotechnology Conference , Helsinki, Finland, 13/06/07.

Conserved synteny in Trichoderma reesei with related filamentous ascomycetes. / Martinez, D.; Saloheimo, Markku; Berka, R.; Henrissat, B.; Nelson, M.A.

3rd European Federation of Biotechnology Conference: Physiology of Yeasts and Filamentous Fungi PYFF3. Espoo : VTT Technical Research Centre of Finland, 2007. p. 55 P4 (VTT Symposium; No. 245).

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

TY - CHAP

T1 - Conserved synteny in Trichoderma reesei with related filamentous ascomycetes

AU - Martinez, D.

AU - Saloheimo, Markku

AU - Berka, R.

AU - Henrissat, B.

AU - Nelson, M.A.

PY - 2007

Y1 - 2007

N2 - The current pace of whole genome sequencing has made it almost trivial to produce nearly complete fungal sequences. This now gives us the ability to perform whole genome comparisons of fungi to investigate biological questions and genome evolution. To this end, syntenic regions between Trichoderma reesei and four other filamentous fungi (Fusarium graminearum, Neurospora crassa, Magnaporthe grisea and Aspergillus nidulans) were identified. An algorithm was designed that takes homologs from two fungi and places them side by side, optimizing homolog density, and minimizing gaps between homologs and the number of homologs in a syntenic region. As would be expected, the percent coverage of synteny between T. reesei and the other four ascomycetes declines with time since the last common ancestor, with F. graminearum having the highest synteny and A. nidulans the lowest. This approach enabled the identification of regions in the T. reesei genome that were conserved in multiple genomes as well as highlighting regions of the T. reesei genome that have changed dramatically. Finally, for genes within these highly conserved regions and for the gaps, GO terms and Enzyme Commission codes were assigned. These results were used to assess the possibility that there is selective pressure to force genes that are in the same biochemical pathway, have similar function or are involved in similar processes to maintain or gain proximity.

AB - The current pace of whole genome sequencing has made it almost trivial to produce nearly complete fungal sequences. This now gives us the ability to perform whole genome comparisons of fungi to investigate biological questions and genome evolution. To this end, syntenic regions between Trichoderma reesei and four other filamentous fungi (Fusarium graminearum, Neurospora crassa, Magnaporthe grisea and Aspergillus nidulans) were identified. An algorithm was designed that takes homologs from two fungi and places them side by side, optimizing homolog density, and minimizing gaps between homologs and the number of homologs in a syntenic region. As would be expected, the percent coverage of synteny between T. reesei and the other four ascomycetes declines with time since the last common ancestor, with F. graminearum having the highest synteny and A. nidulans the lowest. This approach enabled the identification of regions in the T. reesei genome that were conserved in multiple genomes as well as highlighting regions of the T. reesei genome that have changed dramatically. Finally, for genes within these highly conserved regions and for the gaps, GO terms and Enzyme Commission codes were assigned. These results were used to assess the possibility that there is selective pressure to force genes that are in the same biochemical pathway, have similar function or are involved in similar processes to maintain or gain proximity.

M3 - Conference abstract in proceedings

SN - 978-951-38-6313-5

T3 - VTT Symposium

SP - 55

BT - 3rd European Federation of Biotechnology Conference

PB - VTT Technical Research Centre of Finland

CY - Espoo

ER -

Martinez D, Saloheimo M, Berka R, Henrissat B, Nelson MA. Conserved synteny in Trichoderma reesei with related filamentous ascomycetes. In 3rd European Federation of Biotechnology Conference: Physiology of Yeasts and Filamentous Fungi PYFF3. Espoo: VTT Technical Research Centre of Finland. 2007. p. 55. P4. (VTT Symposium; No. 245).