The solution was then diluted fourfold with 10 mM Tris-HCl, pH 8


The solution was then diluted fourfold with 10 mM Tris-HCl, pH 8.0 followed by overnight digestion with trypsin (sequencing grade, Promega, Mannheim, c-met-IN-1 Germany) at 37C with shaking at 350 rpm. alkaline regions. (XLSX) pone.0201480.s004.xlsx (6.7M) GUID:?8E202CD6-E1C5-4657-B78D-6F6AEB52F930 S5 Table: Chara_australis_AllUnigene5-3_AA_only_longest (FASTA). (FA) pone.0201480.s005.fa (9.7M) GUID:?2135D5BD-0957-4686-ABE5-8EDE20720AEC S1 Fig: Characean thallus and cortical cytoplasm of an internodal cell. (A) Thallus of annotation. The c-met-IN-1 percentage of all annotations of unigenes to orthologous sequences of selected species is presented. The NCBI non-redundant (NR) database was searched.(JPG) pone.0201480.s008.jpg (171K) GUID:?D3638F4B-3347-4351-ADE3-6E4E6F971B7E S4 Fig: Classification of the transcriptome to COG categories. The identified sequences were arranged into functional categories according to the COG (Clusters of Orthologous Genes) database.(TIF) pone.0201480.s009.tif (291K) GUID:?54C727DE-692C-4B2D-9B41-3B35566E64FE S5 Fig: Summary of GO classes. Identified transcripts of cells are classified according to the GO (Gene Ontology) categories.(TIF) pone.0201480.s010.tif (382K) GUID:?3D58FDC0-F3B4-4ED9-9721-D3458A47302C S6 Fig: Distribution of unigenes into MapMan BINs. Assembled unigenes were searched against TAIR (release 10), PPAP (Swiss-Prot Plant Protein), and sequence databases with enabled InterProScan using Mercator software and classified into BIN classes ( Pies slices correlate with percentages of unigenes in the respective class. Number of BIN class and description is given in the legend with total unigenes numbers in brackets. Not assigned unigenes (ca. 60%) were omitted. The pie chart starts with ?photosynthesis at 12 oclock with subsequent categories in counter-clockwise order (arrow).(JPG) pone.0201480.s011.jpg (341K) GUID:?C40C8F7C-436F-4D77-88F3-61D1F4805CC3 S7 Fig: Alignment of PM H+ ATPase sequences of unigenes. unigenes homologous to sequences of the PM H+ ATPase were translated into amino acid sequences and aligned with META7 software (MUSCLE algorithm). The PM H+ ATPase CaHA1 was obtained from another sequencing project (access.-no. “type”:”entrez-nucleotide”,”attrs”:”text”:”MF196972″,”term_id”:”1381324743″,”term_text”:”MF196972″MF196972, Foissner & Hoepflinger, unpublished). The AHA2 protein of (“type”:”entrez-protein”,”attrs”:”text”:”P19456.2″,”term_id”:”114335″,”term_text”:”P19456.2″P19456.2) serves as a template to indicate specific domains: Transmembrane domains of AHA2 (Aramemnon, topology, AramTmMultiCon), peptide sequences identified in membrane proteome, Phosphorylation site of phospho-intermediate state, C-terminus with Regulatory Domain I and Regulatory Domain II. Rabbit Polyclonal to FAKD3 Amino acids numbering is following the AHA2 sequence. Transmembrane domains of CaHA1 were determined by TMPred ([50]; ( pone.0201480.s012.pdf (167K) GUID:?DF2B4D51-7EC9-4C7A-AFEF-F13F90129BE9 S8 Fig: Whole original membranes/gels of Western blots. Lanes marked with red stars are shown in figures.(PDF) pone.0201480.s013.pdf (558K) GUID:?A296A3C3-0549-4DDC-9624-9B02CFD8CA85 S9 Fig: Phylogenetic analysis of PM H+ ATPase sequences. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [71]. The bootstrap consensus tree inferred from 500 replicates [72] is taken to represent the evolutionary history of the taxa analysed [73]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches [72]. Initial tree for the heuristic search were obtained automatically by applying Neighbour-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The analysis involved 14 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 806 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [72].(TIF) pone.0201480.s014.tif (19K) c-met-IN-1 GUID:?5A25F82A-51E5-4C45-A811-CCC9195E74B5 Data Availability StatementRNA seq data files are available from the EBI-ENA database (accession number ERP023711), the sequence of the Chara PM H+ ATPase was deposited at NCBI (accession no. MF196972). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (44) partner repository with the dataset identifier PXD006785. Abstract The Characeae are multicellular.