Funaria transcriptome

Funaria hygrometrica, Physcomitrium pyriforme and Physcomitrella patens (Funariaceae) share nearly identical vegetative bodies and differ most conspicuously in their sporophyte generation. The species occur in similar general habitats although are not ecologically sympatric. We sought to assess whether ecological and gametophytic similarities would be matched by genomic similarity or if 60 million years of divergence (between Funaria with Physcomitrella-Physcomitrium clade) may be marked by eco-physiological adaptations and reflected by genomic signatures or innovations. We sequenced the transcriptome of three replicates of vegetative tissue (i.e., rhizoids, stem and leaves) of Funaria hygrometrica and three vegetative replicates of Physcomitrium pyriforme by NextSeq 500, then provided a single non-redundant transcriptome reference for each. We then screened the Physcomitrella genome for othologs of the Funaria and Physcomitrium transcripts to estimate their genomic divergence. Specifically, we mapped reads, transcript and protein sequences of each species to the Physcomitrella genome. In addition, their transcriptome were surveyed for evidence of whole genome duplication, and also were subjected to the transcriptome of 49 other mosses by OrthoMCL analysis via ORTHOFINDER to create clustered network used for protein family determination. The rate of changes in their family size was investigated by CAFE analysis.