Computational protocol: Congenic Strain Analysis Reveals Genes That Are Rapidly Evolving Components of a Prezygotic Isolation Mechanism Mediating Incipient Reinforcement

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Protocol publication

[…] All animal manipulation was performed humanely and under appropriate Animal Welfare Guidelines under University of Arizona IACUC protocol 08-138. Methods are summarized here; details appear in File S5.Polymerase chain reaction (PCR) was run as previously described using genomic DNAs either purchased (Jackson Laboratory) or purified from tail tips and the products sequenced either by the UAGC facility at the University of Arizona or by MCLAB (http://www.mclab.com/). DNA sequence traces were edited with Chromas 2.3 (http://www.technelysium.com.au). DNA sequence alignment, coding region assembly, and in silico translation were done using the DNAsis Max program 2.0 (Hitachi).Salivary gland protein expression data sets were obtained by searching “mouse salivary gland" on the NCBI Gene Expression Omnibus website (www.ncbi.nlm.nih.gov/geo/). Data was downloaded and cross-referenced with Amersham Codelink UniSet Mouse 1 Bioarray, and protein information for each probe target was gathered by searching probe accession numbers on MGI (http://www.informatics.jax.org/), the international database resource for the laboratory mouse. The data in the region of interest was also sorted on the sample signal intensity from the array, which ranged from 0 to 250–400 in the six data sets, and only those with values of 10 or above were retained for this study.Positive selection was assessed in the program CODEML in the PAML package –. The three-dimensional structures of mouse a27, bg26 and bg27 were modeled using the PHYRE2 (version 2.0) threading program (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index; ), and the resulting models were visualized using PYMOL (open-source 1.2.8; http://www.pymol.org/). Sites under positive selection were mapped onto the structural models using PYMOL and incorporated into a figure. […]

Pipeline specifications

Software tools Chromas, DNASIS Max, PAML, Phyre, PyMOL
Applications Sanger sequencing, Nucleotide sequence alignment
Organisms Mus musculus