Andersen, Mikael Rørdam

Baker, Scott E.

de Vries, R. P.

Frisvad, Jens Christian

Grigoriev, Igor V.

Kogle, Martin Engelhard

Kuo, Alan

Lyhne, Ellen Kirstine

Mortensen, Uffe Hasbro

Nielsen, Kristian Fog

Rasmussen, Jane Lind Nybo

Riley, Robert

Theobald, Sebastian

Vesth, Tammi Camilla

In the era of high-throughput sequencing, comparative genomics can be applied for evaluating species diversity. In this project we aim to compare the genomes of 300 species of filamentous fungi from the Aspergillus genus, a complex task. To be able to define species, clade, and core features, this project uses BLAST on the amino acid level to discover orthologs. With a potential of 300 Aspergillus species each having ~12,000 annotated genes, traditional clustering will demand supercomputing. Instead, our approach reduces the search space by identifying isoenzymes within each genome creating intragenomic protein families (iPFs), and then connecting iPFs across all genomes. The initial findings in a set of 31 species show that ~48% of the annotated genes are core genes (genes shared between all species) and 2-24% of the genes are defining the individual species. The methods presented here will allow for detailed investigation into mapping of genotype to phenotype across a very large set of genomes without loosing information

Online Research Database In Technology

Genome mining of the genetic diversity in the Aspergillus genus - from a collection of morethan 30 Aspergillus species - DTU Orbit (08/11/2017) Genome mining of the genetic diversity in the Aspergillus genus - from a collection of more than 30 Aspergillus speciesIntheeraofhigh-throughputsequencing,comparativegenomicscanbeappliedforevaluatingspeciesdiversity.Inthisprojectweaimtocomparethegenomesof300speciesoffilamentousfungifromtheAspergillusgenus,acomplextask.Tobeabletodefinespecies,clade,andcorefeatures,thisprojectusesBLASTontheaminoacidleveltodiscoverorthologs.Withapotentialof300Aspergillusspecieseachhaving~12,000annotatedgenes,traditionalclusteringwilldemandsupercomputing.Instead,ourapproachreducesthesearchspacebyidentifyingisoenzymeswithineachgenomecreatingintragenomicproteinfamilies(iPFs),andthenconnectingiPFsacrossallgenomes.Theinitialfindingsinasetof31speciesshowthat~48%oftheannotatedgenesarecoregenes(genessharedbetweenallspecies)and2-24%ofthegenesaredefiningtheindividualspecies.Themethodspresentedherewillallowfordetailedinvestigationintomappingofgenotypetophenotypeacrossaverylargesetofgenomeswithoutloosinginformation. General informationState: PublishedOrganisations: Department of Systems Biology, Network Engineering of Eukaryotic Cell Factories, Fungal Chemodiversity, Metabolomics Platform, Eucaryotic Molecular Cell Biology, Joint Genome Institute, CBS-KNAW Fungal BiodiversityCentre, Joint Bioenergy InstituteAuthors: Rasmussen, J. L. N. (Intern), Vesth, T. C. (Intern), Theobald, S. (Intern), Frisvad, J. C. (Intern), Nielsen, K. F.(Intern), Lyhne, E. K. (Intern), Kogle, M. E. (Intern), Kuo, A. (Ekstern), Riley, R. (Ekstern), de Vries, R. P. (Ekstern),Grigoriev, I. V. (Ekstern), Mortensen, U. H. (Intern), Baker, S. E. (Ekstern), Andersen, M. R. (Intern)Number of pages: 1Publication date: 2015Event: Abstract from Exploring the genomic complexity and diversity of eukaryotes, Sant Feliu de Guixols, Spain.Main Research Area: Technical/natural sciencesSource: PublicationPreSubmissionSource-ID: 123998371Publication: Research - peer-review › Conference abstract for conference – Annual report year: 2016 

Genome mining of the genetic diversity in the <i>Aspergillus </i>genus - from a collection of more than 30 <i>Aspergillus </i>species

http://orbit.dtu.dk/en/publications/genome-mining-of-the-genetic-diversity-in-the-aspergillus-genus--from-a-collection-of-more-than-30-aspergillus-species(4aa38390-a10d-4b06-a992-0ca2eee5190f).pdf?nofollow=true&rendering=long

Genome mining of the genetic diversity in the <i>Aspergillus </i>genus - from a collection of more than 30 <i>Aspergillus </i>species

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