Rieske-Kinney, Lynne K

Transcriptome analysis of pine bark beetles and their fungal associates

Illumina HiSeq mRNA sequencing of Ips spp. and Dendroctonus spp. bark beetles will be used to investigate and characterize genes involved in chemosensory and gustatory processes. Raw short nucleotide sequence reads will be assembled using de novo assembly algorithms, then chemosensory genes characterized in related and model beetle species from genetic databases will be used to find related matches in the transcriptomes. Additionally, transcriptomes from fungal associates of the beetles will be assembled to gather information relevant to future work planned involving transformations to insert hairpin RNA for gene silencing research.

Students:

Beth Kyre (Graduate Student), 03/17/2021

Flavia Pampolini (Graduate Student), 03/17/2021

Mary Wallace (Graduate Student), 03/17/2021

Hannah Hollowell (Graduate Student), 03/17/2021

Zachary Bragg (Graduate Student), 03/17/2021

Software:

De novo transcriptome assembly - Trinity - Available at UK, but may require run times in excess of 7 days and may consume 100-500 GB RAM
Read mapping - RSEM - Available at UK, may require 100-500 GB RAM

Genome assembly improvement tool - Pilon - Available at UK
Sequence similarity searching - NCBI Blast 2.2.28+ - Available at UK
Functional annotation - BLAST2GO - Available at UK, but free version is limited in functionality. Commercially available versions would be helpful if accessible.
Representation analysis - DAVID, PANTHER - Available at UK

Tools for using data from the INSDC - sratoolkit - Available at UK

Alignment tool – Burrows-Wheeler aligner - Available at UK

Tools for interacting with high-throughput sequencing data - SAMTools - Available at UK

Alignment program for mapping next-generation sequencing - HiSat2 - Available at UK
Transcript quantification from RNA-seq data - Salmon - Available at UK

The software listed above are all under active development and improvement. Genome and transcriptome assembly, read mapping, and functional annotation represent areas of rapid innovation and other software packages may be utilized as they become available.

Grants:

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