Transcriptomics and Genomics

Project Description

We have conducted transcriptomic (RNA-seq) studies to identify genes of interest in a variety of vertebrate taxa, including lake sturgeon, tiger salamanders, and kangaroo rats.  We have also conducted genome sequencing to identify novel genetic markers and genes of interest; our genome projects include the golden eagle, the bananaquit, and a whale (forthcoming).transcriptomics

Matt Hale
Soo Hyung Eo
Jackie Doyle
Nick Marra
Jennifer Antonides
Andrew DeWoody


Hale M.C., McCormick C.R., Jackson J.R. & DeWoody J.A. (2009) Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics 10:203 (Highly Accessed).

Hale M.C., Jackson J.R. & DeWoody J.A. (2010) Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens). Genetica 138:745-756. DOI: 10.1007/s10709-010-9455-y

Eo, S.H. & DeWoody J.A. (2012) The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts. BMC Genomics 13:259 | DOI:10.1186/1471-2164-13-259.

Marra N.J., Eo S.H., Hale M.C., Waser P.M., & DeWoody J.A. (2012) A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat). Comparative Biochemistry and Physiology Part D 2012:328-339.

Doyle J.M., Siegmund G., Ruhl J.D., Eo S.H., Hale M.C., Marra N.J., Waser P.M. & DeWoody J.A. (2013) Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis). Genome 56:407-414.

Doyle J.M., Katzner T.E., Bloom P.H., Ji Y., Wijayawardena B.K. & DeWoody J.A. (2014) The genome sequence of a widespread apex predator, the Golden Eagle (Aquila chrysaetos). PLoS ONE 9(4): e95599. DOI: 10.1371/journal.pone.0095599.

Marra N.J., Romero A. & DeWoody J.A. (2014) Natural selection and the genetic basis of osmoregulation in Heteromyid rodents as revealed by RNA-seq. Molecular Ecology 23:2699–2711.

Marra N.J. & DeWoody J.A. (2014) Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents. BMC Genomics 15:929 | DOI:10.1186/1471-2164-15-929

Abts K.C., Ivy J. & DeWoody J.A. (2015) Immunomics of the koala (Phascolarctos cinereus). Immunogenetics, in press.

Ji Y., Marra N.M. & DeWoody J.A. (2015) Comparative analysis of active retrotransposons in the transcriptomes of three species of Heteromyid rodents. Gene, in press.