Computational protocol: Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 Locus

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Protocol publication

[…] NRPD2-type sequences from diverse plant lineages were obtained through tblastn searches of Phytozome (www.phytozome.net) and BrachyBase (http://blast.brachybase.org/) using ZmNRPD2a or AtNRPD2a as queries. When necessary, gene models were predicted with FGENESH+ (www.softberry.com) using similarity to either ZmNRPD2a or AtNRPD2a. Some sequence names were altered for clarity in . Full-length names are as follows: AtNRPB2 = At4g21710, OsNRPB2 = Os03g44484, AtNRPD2a = At3g23780.1, PtNRPD2 = XP_002324332, VvNRPD2 = XP_002283296, for maize sequences add GRM to the beginning of the sequence name, for Brachypodium sequences substitute super for Bd. Sequences were aligned using MAFFT (http://align.bmr.kyushu-u.ac.jp/mafft/online/server/) and a maximum likelihood tree was constructed with Phyml (http://mobyle.pasteur.fr/cgi-bin/portal.py) using the JTT amino acid substitution model and NNI+SPR tree topology search operation. The tree was edited with Dendroscope 2.2.2 . The alignment was edited using GeneDoc 2.6.04 as previously described . Homoeologous regions were identified using ESTs, simple sequence repeat markers, and genes to identify sequence similarity on chromosomes 2S and 10L. Features used and the corresponding BACs they identify are as follows: AY111545 (AC206980, AC190732), nrpd2a (AC191113), ZM2G128427 (AC199156), AY112227 (AC209428, AC197497), AY110965 (AC215994, AC204716), AY105682 (AC186195, AC183941), AY109473 (AC177886, AC214263), p-umc44b, p-umc44a, b1 (AC191025), r1 (AC199387). […]

Pipeline specifications

Software tools TBLASTN, MAFFT, PhyML, [email protected], Dendroscope
Databases Phytozome
Applications Phylogenetics, Amino acid sequence alignment
Organisms Zea mays, Arabidopsis thaliana