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An overview of the updated and annotated fathead minnow genome
Citation:
Biales, A., Greg Toth, J. Martinson, W. Huang, D. Bencic, R. Flick, Mary Jean See, D. Gordon, AND M. Kostich. An overview of the updated and annotated fathead minnow genome. SETAC North America, Toronto, ON, CANADA, November 03 - 07, 2019.
Impact/Purpose:
This presentation will overview the MIB effort to assemble and annotate the FHM genome
Description:
The Fathead Minnow (FHM; Pimephales promelas) is an important and widely used organism in aquatic toxicology. Modern 'omics methods are being employed to characterize FHM responses to toxicants, and the genetic basis of differences in stressor susceptibility. These efforts have been hampered by the lack of a reference genome sequence or a complete collection of annotated full-length gene models for FHM. Assembly of the genome has been difficult due to the highly repetitive and polymorphic nature of the genome, which in turn interfered with development of gene models. Recent advances in long-read DNA sequencing, assembly algorithms and scaffolding technologies have allowed us to generate a more complete, more contiguous genome assembly. This assembly provided the basis for identification and classification of repetitive elements across the FHM genome. We also conducted mRNA of multiple developmental stages and tissues as well as more limited small-RNA sequencing, facilitating delineation of protein coding and non-coding genes. This FHM gene collection allowed us to explore the effects of different RNA-sequencing parameters and other experimental choices on the performance of RNA-seq used for gene expression profiling. We also compared the performance of RNA-seq and microarrays for developing gene expression-based multivariate classifiers of toxicant exposure. Subsequently, we used RNA-seq to evaluate the effects of using various fish ages and durations of exposure on the sensitivity, specificity and functional interpretability of observed gene expression changes after toxicant exposure. We also compared results from mRNA sequencing with miRNA sequencing and mRNA 3'-end targeted sequencing on cost/performance trade-offs of multi-gene toxicant detection assays developed using those types of data.