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Fig. 1 | BMC Genomics

Fig. 1

From: A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees

Fig. 1

Phylogenetic analysis of SCAMP gene families and transmembrane topology analysis of P. trichocarpa SCAMP proteins. a The gene families were retrieved from the Joint Genome Institute (JGI) (http://genome.jgi.doe.gov/). The SCAMP genes are evm_27.model.AmTr_v1.0_scaffold00003.345 and evm_27.model.AmTr_v1.0_scaffold00048.82 in Amborella trichopoda, AT1G61250 (AthSCAMP1), AT1G11180 (AthSCAMP2) AT2G20840 (AthSCAMP3), AT1G03550 (AthSCAMP4) and AT1G32050 (AthSCAMP5) in Arabidopsis thaliana, Phpat.001G082700 (Pp3c1_21730V3.1.p), Phpat.002G068200 (Pp3c2_16160V3.1.p), Phpat.025G032600 (Pp3c25_8700V3.1.p), Phpat.010G037000 (Pp3c10_9510V3.1.p) and Phpat.005G053500 (Pp3c5_14240V3.1.p) in Physcomitrella patens, Potri.004G036600 (PtrSCAMP1), Potri.011G045100 (PtrSCAMP2), Potri.019G104000 (PtrSCAMP3), Potri.001G134100 (PtrSCAMP4), Potri.003G099300 (PtrSCAMP5), Potri.013G144700 (PtrSCAMP6), Potri.011G045200 (PtrSCAMP7) and Potri.004G036700 (PtrSCAMP8) in Populus trichocarpa, and 141,352 and 92,029 in Selaginella moellendorffii. The evolutionary history was inferred using the WAG substitution model [58]. Evolutionary analyses were conducted in R (https://www.R-project.org/) using the phangorn package (v2.2.0) and visualised using the ggtree extension for ggplot2. Numbers are bootstrap support values based on 1000 runs. b Transmembrane topology prediction was performed using Phobius and visualised using ggplot2. The NPF motif and the tyrosine sorting motif YXXF were identified using the regular expressions NPF and YXXF, respectively, in R (https://www.R-project.org/)

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