Title

Will Improved Assembly Approaches Lead to Improved Biological Inferences?

Presenter Information

Olivia Kleyn
Wenbin Mei

Document Type

Oral Presentation

Location

SURC 137B

Start Date

21-5-2015

End Date

21-5-2015

Keywords

NGS Assembly, Chloroplast Genomics

Abstract

The ability to determine the DNA sequences of genomes has provided an excellent source of data for biological studies. Next generation sequencing (NGS) techniques have expanded our ability to determine genome sequences as they are relatively inexpensive; however, they are potentially less accurate due to the read length being shorter than in first generation techniques, giving a higher probability of incorrect assemblies. The short NGS reads must be assembled into genome sequences, and computer programs to do this work are improving all the time. The goal of my work is to analyze the impact of those changes on chloroplast genome assembly and see if they can lead to improved biological inferences. To do this, we compared chloroplast assemblies of genomes from NGS data for six species within Araucariaceae. Wenbin Mei analyzed these data using the assembly methods available in 2010; we have reanalyzed these reads using newer assembly techniques in combination with a new tool to remove nucleotides of low quality. The assemblies we made were compared both to each other and to Wenbin’s assemblies. We found that all of our new methods returned a greater percentage of the genome than the earlier methods. In addition, our methods showed improvement in numerous other statistics used to characterize assemblies. Once the best of the new methods has been determined, that method will be applied to the additional 20 species of Araucariaceae for which NGS data are available, and biological analyses will be conducted and compared to Wenbin’s results.

Faculty Mentor(s)

Linda Raubeson

Department/Program

Biological Sciences

Additional Mentoring Department

Biological Sciences

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May 21st, 1:10 PM May 21st, 1:30 PM

Will Improved Assembly Approaches Lead to Improved Biological Inferences?

SURC 137B

The ability to determine the DNA sequences of genomes has provided an excellent source of data for biological studies. Next generation sequencing (NGS) techniques have expanded our ability to determine genome sequences as they are relatively inexpensive; however, they are potentially less accurate due to the read length being shorter than in first generation techniques, giving a higher probability of incorrect assemblies. The short NGS reads must be assembled into genome sequences, and computer programs to do this work are improving all the time. The goal of my work is to analyze the impact of those changes on chloroplast genome assembly and see if they can lead to improved biological inferences. To do this, we compared chloroplast assemblies of genomes from NGS data for six species within Araucariaceae. Wenbin Mei analyzed these data using the assembly methods available in 2010; we have reanalyzed these reads using newer assembly techniques in combination with a new tool to remove nucleotides of low quality. The assemblies we made were compared both to each other and to Wenbin’s assemblies. We found that all of our new methods returned a greater percentage of the genome than the earlier methods. In addition, our methods showed improvement in numerous other statistics used to characterize assemblies. Once the best of the new methods has been determined, that method will be applied to the additional 20 species of Araucariaceae for which NGS data are available, and biological analyses will be conducted and compared to Wenbin’s results.