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Green algal transcriptomes for phylogenetics and comparative genomics

posted on 17.03.2016, 15:11 by Endymion CooperEndymion Cooper, Charles Delwiche

For technical details please see the README

Green algal transcriptomes for phylogenetics and comparative genomics.

The incredible diversity of green plants traces its origins to a single, unicellular common ancestor. The Green Algal Tree of Life project (www.gratol.org) aims to reconstruct the evolutionary history of these globally important organisms.

Here we provide the results of our transcriptome sequencing initiative. The 32 (from 31 species) high-coverage transcriptome assemblies, consisting of >2.7 million contigs with a mean length ~1.3kb, provides a rich resource for phylogenetics and evolutionary comparative genomics. Our focus on high-coverage sequencing means that these transcriptomes include a larger fraction of the expressed genome, and more full-length coding sequences, than other previous and contemporary sequencing efforts.

The recovery of a full-length homolog of the Arabidopsis BIG gene (a huge 5098 amino acid protein) provides an example of the completeness of these transcriptomes. With a dataset of over 1600 orthologs (<10% missing sequences) we are identifying and isolating disparate evolutionary signals, and reconstructing deep phylogenetic relationships with unprecedented confidence. Transcriptome wide comparative analyses are revealing broad scale patterns of gene content evolution and implicating recurrent whole genome duplications in major evolutionary transitions. Detailed analyses of key molecular genetic mechanisms are providing insights into the origins and evolution of: developmental regulation of three-dimensional growth, plant hormones, photorespiration, and desiccation tolerance.

At present no publication is available for citation purposes. We therefore ask that all users of this data cite it using the figshare DOI(s) as appropriate. In addition, until we have can provide a publication for citation purposes we ask that for large scale analyses of these data, users contact us to discuss their plans and thereby avoid conflict or overlap.

Cooper, Endymion; Delwiche, Charles (2016): Green algal transcriptomes for phylogenetics and comparative genomics. figshare.https://dx.doi.org/10.6084/m9.figshare.1604778

For additional information please contact Professor Charles Delwiche (delwiche@umd.edu).


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