PDB-file 1z63 chain A was used as a template for comparative modeling which was sharing 24% with SMARCAL1 protein sequence of Bos taurus.
Divergence time between the two haplotypes of chamois was estimated with BEAST after the analysis of the sequences of Bos, Ovis, Capra and Rupicapra.
S2) When the Cox1 protein sequences of both Euplotes species are compared with the Cox1 protein sequence of Bos taurus a large insert in frame of 380 amino acids was identified between positions 119-120.
The phylogenetic relationships of these haplotypes with the available sequences of other Caprinae in the GenBank, Capra, Ovis and Ammotragus were investigated using the sequence of Bos taurus as outgroup.
In order to calculate the mutation rate for the studied region of the D-loop, we extended to compile a separate data matrix comprising all yak halotypes, seven sequences (U12864, U12936, U12946, U12948, U12955, U12956 and U12959) of Bison bison (the sister group of yak, [ 19]) and one sequence of Bos incus (L27714, outgroup).
We generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST.
The Btau and UMD masked sequences of each Bos taurus chromosome were first compared using the GenAlyzer software [ 13].
Protein sequences of cow (Bos taurus), dog (Canis familiaris), human (Homo sapiens), mouse (Mus musculus), and pig (Sus scrofa) were downloaded from the Ensembl database version 72.
Primers for the genes under study were designed based on cervid sequences or on conserved regions of Bos taurus sequences when cervid sequences were not available.
The close relationship of Brassica to Arabidopsis motivated NSF-funded low-coverage (0.6×) sequencing of B. oleracea (BO) genotype TO 1000 [ 25].
