Event Title

Session 2C: Analysis of Transposable Elements and Protein Divergence across Diatoms

Session Number

Session 2C: 4th Presentation

Advisor(s)

Matthew Parks, Chicago Botanic Garden

Location

Room A151

Start Date

28-4-2017 10:00 AM

End Date

28-4-2017 11:15 AM

Abstract

Two genomes of unicellular photosynthetic algae known as diatoms have been sequenced and annotated prior to this investigation, but using new techniques, a third diatom genome, Psammoneis, has been sequenced. Analysis of aspects of the Psammoneis genome, including its protein divergence from its relatives as well as its transposable element diversity, could reveal trends about diatoms and heterokonts. Transposable elements (TEs) are portions of the genome which can excise themselves from one portion of the genome and reinsert themselves elsewhere. This investigation characterized the overall distribution of TEs and the distribution of diatom-specific CoDi TEs in the Psammoneis genome as compared to its relatives. Psammoneis had significantly more total transposable elements and CoDi elements. Hidden Markov Models (HMMs) were generated for each species and supplemented with the NCBI database, and searches using these HMMs revealed matches across species, potentially revealing new TEs in the Psammoneis genome. Protein divergence was analyzed using the reciprocal best BLAST hits between the three diatom species. Sequence pairs were aligned using MAFFT and measures of divergence between each pair of sequences were calculated. Using an incomplete Psammoneis genome assembly, there was little significant protein divergence between the species.

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Apr 28th, 10:00 AM Apr 28th, 11:15 AM

Session 2C: Analysis of Transposable Elements and Protein Divergence across Diatoms

Room A151

Two genomes of unicellular photosynthetic algae known as diatoms have been sequenced and annotated prior to this investigation, but using new techniques, a third diatom genome, Psammoneis, has been sequenced. Analysis of aspects of the Psammoneis genome, including its protein divergence from its relatives as well as its transposable element diversity, could reveal trends about diatoms and heterokonts. Transposable elements (TEs) are portions of the genome which can excise themselves from one portion of the genome and reinsert themselves elsewhere. This investigation characterized the overall distribution of TEs and the distribution of diatom-specific CoDi TEs in the Psammoneis genome as compared to its relatives. Psammoneis had significantly more total transposable elements and CoDi elements. Hidden Markov Models (HMMs) were generated for each species and supplemented with the NCBI database, and searches using these HMMs revealed matches across species, potentially revealing new TEs in the Psammoneis genome. Protein divergence was analyzed using the reciprocal best BLAST hits between the three diatom species. Sequence pairs were aligned using MAFFT and measures of divergence between each pair of sequences were calculated. Using an incomplete Psammoneis genome assembly, there was little significant protein divergence between the species.