Northern pike (Esox lucius) - Genomic resources

These resources are presented and detailed in:

Rondeau EB, Minkley DR, Leong JS, Messmer AM, Jantzen JR, von Schalburg KR, Lemon C, Bird NH, Koop BF (2014) The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. PLoS ONE. Volume 9: e102089. Link to paper

Assembly information for Contigs, Scaffolds and Chromosome files as well as raw reads are now available in GenBank www.ncbi.nlm.nih.gov/assembly/GCA_000721915.1/
Transcriptome and expression profiles for 13 tissues are available in GenBank through GEO and NT(TSA) databases

We are continuing to improve on these resources! Expanded sequencing and Future assemblies and datasets will be made available on this page. We anticipate a major new release by September 2014.


Sequence Resources

DateResourceLinkInformation
May 30th, 2014Genome v0.9 - scaffoldsDownloadAssembled with ALLPATHS-LG using 180bp, 2kbp and 5kbp Illumina paired reads; 5,688 sequences; Total length: 877,777,613 bp; N50: 700,535 bp; Format: Gzipped Fasta
May 30th, 2014Genome v0.9 - contigsDownloadAssembled with ALLPATHS-LG using 180bp, 2kbp and 5kbp Illumina paired reads; 94,266 sequences; Total length: 823,673,620 bp; N50: 16,910 bp; Format: Gzipped Fasta
May 30th, 2014Reference transcriptome v1.0DownloadAssembled with Trinity using Illumina paired reads; Screened for protein-coding characteristics and redundancy; 38,696 sequences; Format: Gzipped Fasta
May 30th, 2014MAKER2 putative transcripts v1.0DownloadGene predictions from Augustus and MAKER2; 19,601 sequences; Format: Gzipped Fasta


Other Data

DateResourceLinkInformation
June 6th, 2014Expression data from 13 tissues - Reference transcriptome v1.0DownloadFPKM expression data for the Trinity-based reference transcriptome (v1.0), across 13 tissues (Supporting Information Table S2 in PLoS ONE paper) Format: Excel spreadsheet (*.xlsx)
June 6th, 2014Expression data from 13 tissues - MAKER2 putative transcripts v1.0DownloadFPKM expression data for MAKER2 putative transcripts (v1.0), across 13 tissues (Supporting Information Table S3 in PLoS ONE paper) Format: Excel spreadsheet (*.xlsx)

Questions or comments can be directed to the corresponding author, Ben Koop: bkoop@uvic.ca