Computational protocol: A Novel Gain-Of-Function Mutation of the Proneural IRX1 and IRX2 Genes Disrupts Axis Elongation in the Araucana Rumpless Chicken

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Protocol publication

[…] DNA samples for six Araucana were acquired from our previous study . Each of the six samples was sequenced on six lanes with an Illumina HiSeq 2000 sequencer. Average genomic coverage was 27.63x and average number of bases sequenced was 29.009 Giga base pairs (). Sequence reads were trimmed using Trimmomatic and aligned to the corresponding region previously identified to be associated with the rumpless phenotype on chromosome 2 of the ICGSC Gallus_gallus-4.0/galGal4 build using Bowtie2 applications , . The mpileup function of SamTools was used to call variants . The view option of bcftools was used to call the genotype at each variant for each individual bird using the bcftools defaults. Variants that were found to be homozygous in all three homozygous rumpless birds, found to be heterozygous in all two heterozygous birds, and were not found in the homozygous tailed bird were considered fixed in the population and targets for genomic variation that may result in the rumpless phenotype. Identified variants were compared against known variants in the Beijing Genomics Institute (BGI) database, and variants that were previously identified not to be involved in rumplessness were removed . […]

Pipeline specifications

Software tools Trimmomatic, Bowtie2, SAMtools, bcftools
Application WGS analysis
Organisms Gallus gallus
Chemicals Tretinoin