This Hub contains rock pigeon and peregrine falcon chromosome assemblies, and the comparative data reported in Damas et al. 2016.
How to access the data
1. Go to UCSC custom track Hubs.
2. Paste http://sftp.rvc.ac.uk/rvcpaper/birdsHUB/hub.txt on the URL box and click "Add Hub".
3. To access peregrine falcon or pigeon chromosome assemblies select the species from the "ChromosomeAssembliesGR Hub Assembly".
4. To access the comparative data using chicken as a reference, select chicken from the "Represented species" tree.
Description
Each chromosome assembly contains:
- Assembly track: scaffolds, predicted chromosome fragments (PCFs) and BAC clones used to upgrade species genome assembly to chromosome level.
- Genes: converted original scaffold assembly gene annotations.
- Synteny track: pairwise homologous synteny blocks (HSBs) between the target species and the chicken and zebra finch genomes, and the lineage-specific evolutionary breakpoint regions (EBRs).
- Repeats track: converted original scaffold assembly repeat annotations.
The chicken genome contains:
- Conservation track: conservation scores, conserved elements (CEs) and conserved non-coding elements (CNEs) obtained from 21 avian genome alignments. More details.
- Chicken BACs: BAC clones predicted to hybridize with ≥85% probability with phylogenetically distant avian species. More details.
- Avian universal panel BACs: BAC clones comprising the final universal BAC clone panel reported in Damas et al. 2016.
References
- Damas et al. 2016. Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research. doi:10.1101/gr.213660.116
- Shapiro et al. 2013. Genomic diversity and evolution of the head crest in the rock pigeon. Science 339: 1063-1067. doi:10.1126/science.1230422
- Zhan et al. 2013. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nat Genet 45: 563-566. doi:10.1038/ng.2588
- Zhang et al. 2014. Comparative genomic data of the Avian Phylogenomics Project. GigaScience 3: 26. doi:10.1186/2047-217X-3-26
If you have further questions contact jdamas@rvc.ac.uk or dlarkin@rvc.ac.uk.