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. 2015 Sep 7;6:912. doi: 10.3389/fmicb.2015.00912

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Copyright © 2015 Iwai, Hori, Sasaki-Sekimoto, Shimojima and Ohta.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Phylogenetic tree analysis of SQD2. A phylogeny incorporating eukaryotic SQD2, cyanobacterial sqdX and the glycosyl transferase proteins of other organisms was constructed using Bayesian inference, maximum likelihood and neighbor-joining algorithms. It is based on a protein comparison. The topologies and branch lengths were calculated using maximum likelihood. Bootstrap values (maximum likelihood and neighbor-joining) higher than 70 and Bayesian posterior probabilities (Bayesian inference) higher than 0.9 are indicated under each branch (maximum likelihood/neighbor-joining/Bayesian inference). The scale bar represents 0.2 amino acid substitutions per site. Sequence accession numbers or sequence resources for the phylogenetic tree are as follows: Archaea glycosyl transferase: Methanocella paludicola (YP_003355097), Methanocella sp. (YP_685710) and Haloferax volcanii (YP_003535220); Alpha-proteobacteria glycosyl transferase: Caulobacter crescentus (YP_002516166), Novosphingobium aromaticivorans (WP_011446186), and Maricaulis maris (WP_011642337); Cyanobacteria sqdX: Cyanothece sp. 1 (WP_015784192), Cyanothece sp. 2 (WP_012629991), Synechococcus elongatus (WP_011243256), Synechococcus sp. (WP_011429929), and Cyanothece sp. 3 (WP_015956855); Other bacterial glycosyl transferases: Truepera radiovictrix (WP_013178429), Rubrobacter xylanophilus (WP_011564279), and Alicyclobacillus acidocaldarius (WP_012810695); Rhodophyta SQD2: Chondrus crispus (XP_005715110), and Cyanidioschyzon merolae (XP_005538341); Stramenopile SQD2: Nannochloropsis sp. NIES-2145 (DDBJ Accession LC061442), Nannochloropsis oceanica IMET1 (BioProject: PRJNA202418, scaffold00247.g6721), Nannochloropsis granulata CCMP529 (BioProject: PRJNA65111, evm.model.NODE_3998_length_11613_cov_18.861534.4), Nannochloropsis salina CCMP537 (BioProject: PRJNA62503, evm.model.NODE_9973_length_179428_cov_24.782236.3), Nannochloropsis gaditana (EWM27152), Phaeodactylum tricornutum (JGI Protein ID: 50356), Fragilariopsis cylindrus 1 (JGI Protein ID: 207999), Fragilariopsis cylindrus 2 (JGI Protein ID: 158007), Pseudo-nitzschia multiseries 1 (JGI Protein ID: 252457), Pseudo-nitzschia multiseries 2 (JGI Protein ID: 145536), Thalassiosira pseudonana (JGI Protein ID: 38775), [Chlorophyta] Ostreococcus tauri (JGI Protein ID: 3203), Micromonas sp. (JGI Protein ID: 58169), Chlorella sp. (JGI Protein ID: 33086), Volvox carteri (Phytozome Transcript Name: Vocar20009459m), Chlamydomonas reinhardtii 1 (Phytozome Transcript Name: Cre01.g038550.t1.3), and Chlamydomonas reinhardtii 2 (Phytozome Transcript Name: Cre16.g689150.t1.2); Charophyta: Klebsormidium flaccidum 1 (BioProject: PRJDB718, kfl00392_0070) and Klebsormidium flaccidum 2 (BioProject: PRJDB718, kfl00041_0140), and Embryophyta (Phytozome Transcript Name): Arabidopsis thaliana (AT5G01220.1), Populus trichocarpa 1 (Potri.006G097600.1), Populus trichocarpa 2 (Potri.016G112600.1), Oryza sativa 1 (Os07g01030.1), Oryza sativa 2 (Os01g04920.1), Oryza sativa 3 (Os03g15840.1), Selaginella moellendorffii (170091), and Physcomitrella patens (Pp1s24_194V6.1).