DOI: 10.5061/dryad.5fm82
title: Data from: De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome

description: The bryophytes are a morphologically and ecologically diverse group of
 plants that have recently emerged as major model systems for a variety of
 biological processes. In particular, the genome sequence of the moss,
 Physcomitrella patens, has significantly enhanced our understanding of the
 evolution of developmental processes in land plants. However, to fully
 explore the diversity within bryophytes, we need additional genomic
 resources. Here we describe analyses of the transcriptomes of a male and a
 female isolate of the moss, C. purpureus, generated using the 454 FLX
 technology. Comparative analyses between C. purpureus and P. patens
 indicated that this strategy generated nearly complete coverage of the
 protonemal transcriptome. An analysis of the overlap in gene sets between
 C. purpureus and P. patens provides new insights into the evolution of
 gene family composition across the land plants. In spite of the overall
 transcriptomic similarity between the two species, Ka/Ks analysis of P.
 patens and C. purpureus suggest considerable physiological and
 developmental divergence. Additionally, while the codon usage was very
 similar between these two mosses, C. purpureus genes showed a slightly
 greater codon usage bias than P. patens genes potentially because of the
 contrasting mating system of the two species. Finally, we found evidence
 of a genome doubling ~65-76 MYA that likely coincided with the
 contemporaneous polyploidy event inferred for P. patens but postdates the
 divergence of P. patens and C. purpureus. The powerful laboratory tools
 now available for C. purpureus will enable the research community to fully
 exploit these genomic resources.
description: Assembled GG1
 transcriptsWe assembled quality
 filtered and trimmed 454 reads with Newbler for the GG1
 strain.GG1_454Isotigs.zipAssembled R40 transcriptsWe assembled quality filtered and trimmed 454 reads with Newbler for the R40 strain.R40_454Isotigs.zipProtein translation of predicted ORFs for the GG1 transcriptsProtein translations of the predicted ORFs for the GG1 transcripts. We selected the longest ORF prediction for each transcript. The three numbers in the fasta header refer to the frame, the starting and the end coordinates of the predicted ORF on the original transcript sequences.GG1_predicted_PROT.zipProtein translation of predicted ORFs for the R40 transcriptsProtein translations of the predicted ORFs for the R40 transcripts. We selected the longest ORF prediction for each transcript. The three numbers in the fasta header refer to the frame, the starting and the end coordinates of the predicted ORF on the original transcript sequences.R40_predicted_PROT.zipPredicted ORFs for the GG1 transcriptsPredicted ORFs for the GG1 transcripts. We selected the longest ORF prediction for each transcript.GG1_predicted_CDS.zipPredicted ORFs for the R40 transcriptsPredicted ORFs for the R40 transcripts. We selected the longest ORF prediction for each transcript.R40_predicted_CDS.zipTop blast hits of GG1 transcripts in the NCBI nr data baseTop blast hit of each GG1 transcript in the NCBI nr data base using BlastX (e-value threshold 10-3).Table_S1.xlsxTop blast hits of R40 transcripts in the NCBI nr data baseTop blast hit of each R40 transcript in the NCBI nr data base using BlastX (e-value threshold 10-3).Table_S2.zipGO annotation of GG1 transcriptsGO annotation of GG1 transcriptsTable_S3.zipGO annotation of R40 transcriptsGO annotation of R40 transcriptsTable_S4.zipInterproscan analysis of GG1 transcriptsInterproscan analysis of GG1 transcriptsTable_S5.zipInterproscan analysis of R40 transcriptsInterproscan analysis of R40 transcriptsTable_S6.zip