Computational protocol: Distribution of the Sex-Determining Gene MID and Molecular Correspondence of Mating Types within the Isogamous Genus Gonium (Volvocales, Chlorophyta)

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Protocol publication

[…] Phylogenetic analyses were performed using two data sets. One consists of ClustalX 2.0 -aligned entire protein sequences of eleven MID homologs of the Volvocales (). The other alignment is composed of amino acid sequences (47 aa, ) of RWP-RK domains (the 25 RWP-RK containing proteins recognized in C. reinhardtii and Volvox carteri genome databases, http://www.phytozome.net/ Phytozome v8.0, Joint Genome Institute, Walnut Creek, CA, USA , , and the eleven MID homologs). Maximum likelihood (ML) method, based on Whelan and Goldman model (WAG) by PhyML 3.0 , , and ML and neighbor joining method, using Jones-Taylor-Thornton model by MEGA version 5, were carried out with bootstrap values from 1000 replications –.A molecular evolutionary analysis of non-synonymous and synonymous substitutions was performed by YN00 in the PAML package , . […]

Pipeline specifications

Software tools Clustal W, PhyML, MEGA, PAML
Databases Phytozome
Application Phylogenetics