One Thousand Land Plant Transcriptomes: Challenges, Developments, and Status

Data from one thousand land plant transcriptomes has been produced.  The challenges involve the selection of species for sampling and developing a method to successfully extract RNA from across the land plant tree of life.  The selection of species centered around three criteria: having representatives of clades that would encompass taxonomic diversity, making sure the species represent major innovations on the tree of life, and if possible represent an economic or otherwise important species.  Additionally, an attempt was made to select at least two species from major lineages, one that would be sister to that lineage and another that would represent derived features within that lineage.  From the non-seed plant lineages, there are nearly 150 species plus appropriate outgroups. Some key questions being addressed by this comparative transcriptome analysis are: a) the switch from dominant gametophytes to dominant sporophytes by sampling both haploid and diploid generations in a selection of plants chosen to elucidate this major shift in life-history, adaption and diversification to a land habit and habitat, b) indeterminate growth of the sporophyte, c) the acquisition of vascular tissue and equivalents, and d) the independent development of heterospory in several lineages.