Computational protocol: An APETALA2 Homolog, RcAP2, Regulates the Number of Rose Petals Derived From Stamens and Response to Temperature Fluctuations

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Protocol publication

[…] Sequence analysis and contig assembly were completed using DNAMAN software, while the RcAP2 open reading frame (ORF) was predicted using ORF Finder. Multiple sequences were aligned using ClustalX with default parameters. The alignments were edited and marked using GeneDoc software. Phylogenetic analyses were conducted with MEGA7 using the Neighbor-Joining method and the bootstrap consensus tree was inferred from 1000 replicates. The function prediction of transcription factor using PlantTFDB online tool, the RegRNA 2.0 online tool () was used to identifying the functional motifs and sites of RcAP2. The cis-acting element analyses were completed using online software PlantCARE () and SoftBerry ().The GenBank ID of AP2 protein sequences showed in alignment analyses were as follows: AAL57045.2 Malus domestica; AKN10311.1 Eriobotrya japonica; AJT39804.1 Prunus mume; AEB92231.1 Prunus persica; ACO52508.1 Vitis vinifera; EOX91494.1 Theobroma cacao; AEL29576.1 Betula platyphylla; EXC24730.1 Morus notabilis; AGM20693.1 Populus tomentosa; EEE91165.1 Populus trichocarpa; KYP44918.1 Cajanus cajan; KHN36247.1 Glycine soja; AIS71911.1 Nicotiana tabacum; and AAC13770.1 Arabidopsis thaliana.The GenBank ID of AP2 sequences showed in phylogenetic analyses were as follows: HQ637468.1 Brassica napus; JN247401.1 Actinidia deliciosa; JN247408.1 Betula platyphylla; JF683605.2 Prunus persica; U12546.1 Arabidopsis thaliana; DQ988341.1 Larix marschlinsii; AB495344.1 Nymphaea hybrid; JQ398741.1 Camellia sinensis; HQ113365.1 Actinidia deliciosa; EU883665.1 Poncirus trifoliata; FJ809943.1 Vitis vinifera; DQ988340.1 Larix marschlinsii; KP405836.1 Prunus mume; AB495343.1 Nymphaea hybrid; AF134116.3 Hyacinthus orientalis; AY128328.1 Arabidopsis thaliana; AY069953.1 Hordeum vulgare; AF253971.1 Picea abies; AF253970.1 Picea abies; EU677382.1 Solanum lycopersicum; KT163121.1 Thermopsis textitturcica; KJ482645.1 Brassica juncea; EF216863.2 Ipomoea nil; DQ119837.1 Dendrobium crumenatum; AB195246.1 Gnetum parvifolium; AB195244.1 Ginkgo biloba; AB195242.1 Cycas revoluta; AB101587.1 Pinus thunbergii; AB101586.1 Pinus thunbergii; KM386630.1 Fagopyrum esculentum; KM386629.1 Fagopyrum esculentum; KM386628.1 Fagopyrum esculentum; and GU983666.1 Malus domestica. […]

Pipeline specifications

Software tools DNAMAN, Open Reading Frame Finder, Clustal W, RegRNA
Databases PlantTFDB
Applications Phylogenetics, Transcription analysis
Organisms Hoplobatrachus rugulosus, Arabidopsis thaliana