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The current red jungle fowl (Gallus gallus) genome assembly, GRCg6a, was sequenced and assembled with single molecule real time (SMRT) sequencing technology to a depth of approximately 80x. The same DNA reference source, a female known as "RJF #256" ... from an inbred line (UCD 001), was sequenced on the Pacific Biosciences RSII instrument (a relatively equal split of P6 and P5 chemistry reads) and all reads were assembled with the FALCON assembler. In recognition of the need for improvement in assembly contiguity and representation of chromosomes we generated a high chromatin proximity map to aid in the order and orientation of assembled sequences. The creation of the improved chromosomal sequences proceeded in a way similar to that described for the Gallus_gallus-5.0 release. To avoid loss of sequence in the transition from Gallus_gallus-5.0 to GRCg6a, finished RJF BAC clones found in the former assembly were incorporated into the final chromosomal sequences, replacing underlying WGS contigs where appropriate. For more information see: https://www.ncbi.nlm.nih.gov/grc/chicken. Funding for the sequence characterization of the chicken genome was provided by the USDA, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH) and Cobb Vantress.
GRCg6a differs from the earlier GRCg6 version only in the elimination of four redundant unlocalized scaffolds.  more

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