men12284-sup-0001-FigS1.pdfapplication/PDF278KFig. S1 Length distribution and read coverage of the GG1 and R40 isotigs assembled.
men12284-sup-0002-FigS2.pdfapplication/PDF481KFig. S2 Contamination analysis of the GG1 and R40 transcriptomes based on a megan analysis.
men12284-sup-0003-FigS3.pdfapplication/PDF237KFig. S3 Relative abundances of gene ontology terms (associated with a minimum of 150 isogroups) in the Biological Process, Cellular Component and Molecular Function ontologies in the GG1 and R40 assemblies.
men12284-sup-0004-FigS4.pdfapplication/PDF366KFig. S4 Gene ontology terms (associated with a minimum of 150 isogroups) significantly enriched (FDR < 0.05, Fisher exact test) in the gene sets expressed in the Physcomitrella patens chloronema and in the Ceratodon purpureus GG1 control protonema tissues relative to the P. patens genomic gene set.
men12284-sup-0005-FigS5.pdfapplication/PDF796KFig. S5 Gene ontology terms (Biological process ontology) enriched in the plaza version 2.5 gene families which Ceratodon purpureus transcripts was assigned to.
men12284-sup-0006-FigS6.pdfapplication/PDF417KFig. S6 Genetic divergence of the Ceratodon purpureus and Physcomitrella patens proteomes at the protein (proportion of identical amino acid residues in alignment) and at the nucleotide level (Ks: number of synonymous substitutions per synonymous sites, Ka: number of nonsynonymous substitutions per nonsynonymous sites).
men12284-sup-0007-FigS7.pdfapplication/PDF254KFig. S7 Gene ontology terms (Biological Process ontology) of which genes show a significantly greater evolutionary rate (Ka/Ks ratio) between the Ceratodon purpureus strains and Physcomitrella patens than the average of the total ortholog list.
men12284-sup-0008-FigS8.pdfapplication/PDF214KFig. S8 Histogram of Ks values of Physcomitrella patens (red) and Ceratodon purpureus GG1 (green) paralog clusters and P. patens and C. purpureus GG1 orthologs (grey, reciprocal best hits).
men12284-sup-0009-FigS9.pdfapplication/PDF953KFig. S9 Gene ontology bias results on the genes belonging to the groups identified by emmix for the (K4) GG1 strain and (K3) R40 strain.
men12284-sup-0010-TableS1.xlsxapplication/msexcel2420KTable S1 Top blast hit of each GG1 transcript in the NCBI nr database using blastx.
men12284-sup-0011-TableS2.xlsxapplication/msexcel2072KTable S2 Top blast hit of each R40 transcript in the NCBI nr database using blastx.
men12284-sup-0012-TableS3.xlsxapplication/msexcel1749KTable S3 Gene ontology annotation of GG1 transcripts.
men12284-sup-0013-TableS4.xlsxapplication/msexcel1510KTable S4 Gene ontology annotation of R40 transcripts.
men12284-sup-0014-TableS5.xlsxapplication/msexcel4490KTable S5 Interproscan analysis of GG1 transcripts.
men12284-sup-0015-TableS6.xlsxapplication/msexcel3937KTable S6 Interproscan analysis of R40 transcripts.
men12284-sup-0016-TableS7.xlsxapplication/msexcel16KTable S7 Codon preferences in Ceratodon purpureus GG1, R40 and Physcomitrella patens.
men12284-sup-0017-TableS8.xlsxapplication/msexcel10KTable S8 Results of the emmix analysis for the Ks distribution of the GG1 and R40 assemblies.
men12284-sup-0018-TableS9.xlsxapplication/msexcel10KTable S9 Inferred age (Ks) of the putative large-scale duplication events for the GG1 and R40 assemblies.

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