Event Title

The De Novo Assembly and Analysis of the Soapberry Bug Transcriptome

Presenter Information

Olivia Lang, Colby CollegeFollow

Location

Davis 117

Start Date

30-4-2015 2:45 PM

End Date

30-4-2015 3:55 PM

Project Type

Presentation

Description

We are witnessing the rapid development of technology across all fields in this technological age. Genetics is no exception, particularly as next-generation sequencing technologies get faster and more accurate. In response to these improvements on data collection, processing methods have been developed to keep up with these innovations. In order to identify genes that may play a role in the development of alternate wing lengths exhibited by soapberry bugs, we sequenced its transcriptome. The transcriptome is the collection of all expressed genes in an organism, which is a powerful reference tool to have when conducting research relating to the genetics of an organism, including for comparative purposes. We data from an Illumina 1.5 next-generation sequencer to assemble a de novo transcriptome for the soapberry bug. These raw data were 142.6 million single-end reads of 100 base pairs each from all expressed genes, which leaves the computational question of how to fit these overlapping sequences into individual transcripts (messenger RNAs). I will briefly explain the basic quality check tools for the raw data, followed by an explanation of how the assembler I used, named Trinity, works. Ultimately, I produced a set of about 7398 contigs assembled by Trinity. Using biopython, I conducted a BLAST search for each contig. This annotation compares contigs to sequences in GenBank, the national repository of sequence data. Once annotated these contigs can be used to make comparisons of the genome contents of other species or to select gene sequences for further studies in the soapberry bug.

Faculty Sponsor

Bruce Maxwell

Sponsoring Department

Colby College. Computer Science Dept.

CLAS Field of Study

Natural Sciences

Event Website

http://www.colby.edu/clas

ID

1305

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Apr 30th, 2:45 PM Apr 30th, 3:55 PM

The De Novo Assembly and Analysis of the Soapberry Bug Transcriptome

Davis 117

We are witnessing the rapid development of technology across all fields in this technological age. Genetics is no exception, particularly as next-generation sequencing technologies get faster and more accurate. In response to these improvements on data collection, processing methods have been developed to keep up with these innovations. In order to identify genes that may play a role in the development of alternate wing lengths exhibited by soapberry bugs, we sequenced its transcriptome. The transcriptome is the collection of all expressed genes in an organism, which is a powerful reference tool to have when conducting research relating to the genetics of an organism, including for comparative purposes. We data from an Illumina 1.5 next-generation sequencer to assemble a de novo transcriptome for the soapberry bug. These raw data were 142.6 million single-end reads of 100 base pairs each from all expressed genes, which leaves the computational question of how to fit these overlapping sequences into individual transcripts (messenger RNAs). I will briefly explain the basic quality check tools for the raw data, followed by an explanation of how the assembler I used, named Trinity, works. Ultimately, I produced a set of about 7398 contigs assembled by Trinity. Using biopython, I conducted a BLAST search for each contig. This annotation compares contigs to sequences in GenBank, the national repository of sequence data. Once annotated these contigs can be used to make comparisons of the genome contents of other species or to select gene sequences for further studies in the soapberry bug.

http://digitalcommons.colby.edu/clas/2015/program/237