Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon (Salmo salar)

acceptedVersio

Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway

acceptedVersio

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Abstract: Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions: Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone

A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut

Acknowledgements For facilitating sampling of Atlantic Halibut, we thank: Bruce Chapman of the Atlantic Halibut Council, Gerry and Gary Dedrick of the Shelburne County Quota Group, Lori Baker from the Eastern Shore Fisherman’s Protective Association, Erin Caruthers and Miranda McGrath from FFAW-Unifor, Albert Moore and Dylan Buchanan and Fisheries Observers from Javitech Atlantic, and Derrick Lambert and Fisheries Observers from Seawatch, Inc. We thank Michael Kersula and the Maine Department of Marine Resources, and Esther Román-Marcotte and Jose Luis Del Rio from the Spanish Institute of Oceanography for providing Atlantic Halibut tissue samples. We thank Christopher McGuire and Jocelyn Runnebaum of The Nature Conservancy, Richard McBride from the National Oceanic and Atmospheric Administration, George Maynard of the Cape Cod Commercial Fishermen’s Alliance, and Scott Elzey from the Massachusetts Division of Marine Fisheries for additional coordination of collection of Atlantic Halibut Samples. We thank Lorraine Hamilton for organizing RAD library preparation, and the McGill University and Génome Québec Innovation Centre for genotyping RAD libraries. Sequencing of the reference genome sequence was conducted by the Vertebrate Genome Project. This research was enabled by computing resources provided by ACENet and Compute Canada. Funding Funding and support for this project was through the Ocean Frontier Institute and the Department of Fisheries and Oceans Canada Genomics Research and Development Initiative, as well as an NSERC Visiting Postdoctoral Fellowship.Peer reviewedPostprin

Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs

Funding information Natural Sciences and Engineering Research Council of Canada; Department of Fisheries and Oceans Canada Genomic Research and Development Initiative ACKNOWLEDGEMENTS Thanks to Parks Canada, the Nunatsiavut Government, the NunatuKavut Community Council, the Sivunivut Inuit Community Corporation, the Innu Nation, the Labrador Hunting and Fishing Association, and Newfoundland DFO Salmonids section, for sup- port of this study and tissue collection. Significant portions of labo- ratory work for genotyping were conducted by staff at Aquatic Biotechnology Laboratory at the Bedford Institute of Oceanography. Computing resources for bioinformatic analyses were provided by Compute Canada. Support for this study was provided by the Ocean Frontier Institute, a Genomics Research and Development Initiative (GRDI) Grant, a Natural Sciences and Engineering Research Council (NSERC) Discovery Grant and Strategic Project Grant to I.R.B., the Weston Family Award for research at the Torngat Mountains Base Camp and an Atlantic Canada Opportunities Agency and Department of Tourism, Culture, Industry and Innovation grant al- located to the Labrador Institute.Peer reviewedPostprin