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Fig. 8 | BMC Plant Biology

Fig. 8

From: Identification of novel superoxide dismutase isoenzymes in the olive (Olea europaea L.) pollen

Fig. 8

Molecular phylogenetic analysis of superoxide dismutase nucleotide sequences by Maximum Likelihood (ML) method based on the General Time Reversible (GTR) model and conducted in MEGA7 [79]. The bootstrap consensus tree was inferred from 100 replicates. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (100 replicates) are shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites [4 categories (+G, parameter = 1,9145)]. The analysis involved 35 nucleotide sequences [AtCSD1 (NCBI accession no. AY091168); AtCSD2 (AY133756); AtCSD3 (BT003689), AtFSD1 (AF324711), AtFSD2 (BT005116), AtFSD3 (AY091225), AtMSD1 (NM111929), BnFSD2 (XM_013827408.1), BoFSD2 (XM_013774046.1), BrFSD1 (HQ258931.1), BrMSD1 (XM_009124281.2), CsFSD2 (XM_010444287.2), CsMSD2 (KP189420.1), DlFSD3 (KT894098.1), DoMSD3 (JQ797737.1), EgFSD3 (KU904638.1), GhCSD3 (EU597270.1), InCSD2 (XM_019331435.1), NaCSD1 (JN869247.1), OeCSD1.1A (transcript code po11_olive_011703), OeCSD1.1B (po11_olive_018096), OeCSD1.2 (po11_olive_018137), OeCSD1.3 (po11_olive_027139), OeCSD2 (po11_olive_021051 + po11_olive_016542), OeCSD3 (po11_olive_018653), OeFSD2 (po11_olive_023570), OeMSD1 (po11_olive_008559), PfCSD1 (GU731670.1), PmCSD2 (XM_008228408.1), RsFSD2 (XM_018621411.1), RsMSD1 (XM_018578014.1), SbCSD2 (HQ395747.1), SeCSD1 (JQ074238.2), SiCSD2 (XM_011090495.1), VvCSD1 (JQ692111.2)]. Olive pollen SOD sequences are in red. Blue, orange and green squares represent Cu,Zn-, Mn- and Fe-SODs, respectively. Among the Cu,Zn-SODs, the three subclades corresponding to the cytosolic, chloroplastidic and peroxisomal forms are indicated with brackets. Abbreviations: At, Arabidopsis thaliana; Bn, Brassica napus; Bo, Brassica oleracea; Br, Brassica rapa; Cs, Camelina sativa; Dl, Dimocarpus longan; Do, Diospyros oleifera; Eg, Eucalyptus grandis; Gh, Gossypium hirsutum; In, Ipomoea nil; Na, Neosinocalamus affinis; Oe, Olea europaea; Pf, Pleioblastus fortunei; Pm, Prunus mume; Rs, Raphanus sativus; Sb, Scutellaria baicalensis; Se, Salicornia europaea; Si, Sesamum indicum; Vv, Vitis vinifera

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