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TRENDS in Plant Science
Supplementary Material
Origin and evolution of PIN auxin transporters in the green lineage
Tom Viaene 1,2, Charles Delwiche 3, Stefan Rensing 4,5 and Jiří Friml1,2
1Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
2Department of Plant Biotechnology and Genetics, Ghent University, 9052 Gent, Belgium
3Cell Biology and Molecular Genetics, 2108 Biosciences Research Bldg., and the Maryland Agricultural Experiment Station, University of Maryland, College Park, MD 20742, USA
4Faculty of Biology, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
5BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
Corresponding author: Viaene, T. ().
The supplementary material contains information on how the phylogenetic tree in Figure 1 (see main text) was reconstructed, information on the identification of putative outgroup sequences, Figure S1 (see supplementary material online), and information on how the phylogenetic tree in Figure S1 was reconstructed.
Figure 1 (see main text)
Protein sequences were retrieved from Phytozome.org and Genbank. Sequences were aligned with the MUSCLE algorithm and the alignment was manually corrected. The highly variable hydrophilic loop was omitted from the alignment. A Neighbour Joining tree was constructed using the platform on Phylogeny.fr and bootstrap values were calculated from 1000 bootstrap replicates [S1]. PHYML was used to construct a maximum likelihood tree and ProtTest to estimate the correct model (LG + G) [S2, S3]. Bootstrap support (1000 replicates) for the most likely tree was calculated using PHYML. Bayesian inference of phylogeny was estimated using MrBayes with the amino acid model set to pr=mixed (ngen= 500,000) [S4]. The recovered trees only differed in the position of the clade with OsPIN3a and OsPIN3b within the bigger AtPIN1–AtPIN4 and AtPIN7 clade. The most likely tree is shown here. The two PIN proteins from the fern Microlepia sp. (MicPIN1 and MicPIN2) come from an unpublished transcriptome representation (provided by Dr. Stefan Rensing). These sequences, together with the full protein alignment used in this figure can be found in TreeBASE (http://purl.org/phylo/treebase/phylows/study/TB2:S13288?x-access-code=d36aac3bc12cbd2fb9a7fad70de8f7ea&format=html).
Included sequences
TvPIN (XP_001329656), KfPIN (HO482457.1), PpPINA (Pp1s10_17V6.1), PpPINB (Pp1s18_186V6.1), PpPINC (Pp1s32_43V6.1), PpPIND (Pp1s79_126V6.1), SmPIN1-1 (XP_002983754), SmPIN1-2 (XP_002990501), SmPIN2-1 (XP_002975037), SmPIN2-2 (XP_002977457), SmPIN3-1 (XP_002973335), SmPIN3-2 (XP_002976702), SmPIN4-1 (XP_002983791), SmPIN5-1 (XP_002967582), SmPIN5-2 (XP_002981763), PaPIN1 (ACH91613.2), OsPIN9 (Os01g0802700), OsPIN5c (Os08g0529000), OsPIN8 (Os01g0715600), OsPIN5a (OsO1g0919800), OsPIN5b (Os09g0505400), OsPIN3a (Os05g0576900), OsPIN1b (Os11g0137000), OsPIN3b (Os01g0643300), OsPIN2 (OsgOsg0660200), OsPIN1a (Os02g0743400), OsPIN1c (Os06g0232300), VvPIN8 (XP_002282480), VvPIN5b (XP_002272306), VvPIN5a (XP_002279191), VvPIN6 (XP_002278449), VvPIN1a (XP_002282661), VvPIN1b (XP_002282687), VvPIN2 (XP_002266059.1), VvPIN9 (CBI39444), AtPIN1 (Q9C6B8), AtPIN2 (Q9LU77), AtPIN3 (Q9S768), AtPIN4 (Q8RWZ6), AtPIN5 (Q9LFP6) AtPIN6 (Q9SQH6), AtPIN7 (Q940Y5), AtPIN8 (Q9FFFD0).
Outgroups
We performed a BLAST search with PpPIND outside the group of Plantae and identified several putative homologous sequences in other eukaryote groups. Among the best 15 hits, we identified 1 sequence from Protista, 7 sequences from Proteobacteria and 7 sequences from Metazoa. All of these sequences are between 21 and 25% identical over a region of >300 amino acids. When besides TvPIN, all these sequences are added to the matrix, they all form an outgroup to the green plant PINs.
Identified outgroup sequences
Trichomonas vaginalis (TvPIN, XP_001329656), Camponotus floridanus (CpPIN, EFN7449), Nematostella vectensis (NvPIN, XP_001635681), Nasonia vitripennis (NavPIN, XP_001602400), Harpegnathos saltator (HsPIN, EFN76836), Serratia sp. (SerPIN, YP_004498665), Daphnia pulex (DpPIN, EFX75901), Dickeya zeae (DzPIN, YP_003006317), Paenibacillus polymyxa (PpPIN, YP_003947565), Bifidobacterium dentium (BdPIN, ZP_07457627), Metaseiulus occidentalis (MoPIN, XP_003745066), Acyrthosiphon pisum (ApPIN, XP_001944397)
Figure S1 (see supplementary material online)
We selected PIN and PILS proteins from Physcomitrella, Arabidopsis, algae PINs from Klebsormidium and algae PILS from Volvox and Chlamydomonas. Sequences were retrieved from Phytozome.org and Genbank. Using a BLAST search, we identified homologous sequences outside green plants. We used the best hit out of this blast results to reconstruct the phylogeny. Sequences were aligned with the MUSCLE algorithm. A Neighbour Joining tree was constructed using the platform on Phylogeny.fr and bootstrap values were calculated from 1000 bootstrap replicates (S1). PHYML was used to construct a maximum likelihood tree and ProtTest to estimate the correct model (LG + G) [S2, S3]. As the most likely tree was identical to the NJ tree, maximum likelihood bootstraps values were calculated from 1000 bootstraps and put on the tree. The full protein alignment used in this figure can be found in TreeBASE (http://purl.org/phylo/treebase/phylows/study/TB2:S13288?x-access-code=d36aac3bc12cbd2fb9a7fad70de8f7ea&format=html).
Included sequences
KfPIN (HO482457.1), PpPINA (Pp1s10_17V6.1), PpPIND (Pp1s79_126V6.1), AtPIN1 (Q9C6B8), AtPIN5 (Q9LFP6) AtPIN6 (Q9SQH6), AtPIN8 (Q9FFFD0), TvPIN (XP_001329656), VcPILS (Vocar20014819m.g), CrPILS (Cre13.g564850), PpPILS1 (Pp1s174_114V6), PpPILS2 (Pp1s497_6V6.1), PpPILS3 (Pp1s420_20V6), AtPILS2 (AEE35160), AtPILS6 (AED90417), AtPILS5 (AEC06637), AtPILS1 (AEE30042), EFW46187 (Capsospora owczarzaki, CoPIN).
Supplementary references
S1. Dereeper, A. et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. DOI: 10.1093/nar/gkn180 (http://nar.oxfordjournals/org/)
S2. Guindon et al. (2010) New algorithms and methods to estimate Maximum-Likelihood Phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321
S3. Abascal et al. (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105
S4. Ronquist, F. and Huelsenbeck, J.P. (2003) MRBAYES 3:Bayesian Phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574