Computational protocol: A rice calcium-dependent protein kinase is expressed in cortical root cells during the presymbiotic phase of the arbuscular mycorrhizal symbiosis

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Protocol publication

[…] The full length protein sequences were obtained from the NCBI database and aligned using ClustalW []. The alignment of the various plant CPKs was created with GeneDoc 2.7.0 Software [] and is shown in Additional File .In addition to the 31 CPKs from rice, known full-length CPK sequences from M. truncatula, M. sativa and Zea mays were also used. They were (accession numbers are from Gene Bank at the National Center for Biotechnology Information (NCBI) database http://www.ncbi.nlm.nih.gov/: MtCDPK1 [AAX15706], MtCDPK3 [ABE72958], and MsCDPK3, X96723]; ZmCDPK1 [BAA12338], ZmCDPK2 [AAA69507], ZmCDPK7 [BAA13232], ZmCDPK9 [BAA12715], ZmCDPK10 [CAA07481] and ZmCDPK11 [AAP57564]. As for wheat, up to 20 CPKs have been described from which 14 available sequences were included in this study []. They were: TaCPK1 [ABY59004], TaCPK2 [ABY59005], TaCPK3 [ABY59006], TaCPK4 [ABY59007], TaCPK5 [ABY59008], TaCPK6 [ABY59009], TaCPK7 [ABY59017], TaCPK8 [ABY59010], TaCPK9 [ABY59011], TaCPK12 [ABY59012], TaCPK13 [ABY59018], TaCPK15 [ABY59013], TaCPK18 [ABY59014], TaCPK19 [ABY59015]. Furthermore, CCaMK sequences from rice, wheat and Medicago were included in this analysis, the rice OsCCaMK [Q6AVM3], wheat TaCCaMK [ADK22086] and M. truncatula MtCCaMK [Q6RET7] sequences. Phylogenetic trees were created according to the neighbor-joining method (Figure ) or the maximum-parsimony algorithm (Additional File : Figure S3) using MEGA4 program [,]. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Oryza sativa, Rhizophagus intraradices, Allium cepa
Chemicals Calcium, Carbohydrates