This work is a joint project between EnsemblGenomes at the European Bioinformatics Institute and the group of Doreen Ware at the Cold Spring Harbor Laboratory, who have developed the Gramene database, a resource for plant comparative genomics based on Ensembl technology. A common set of databases are available through EnsemblGenomes and Gramene, and the two groups are collaborating on the integration of content, quality control and the development of new features.

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This release of Ensembl Plants includes the genome of the primitive unicellular red algae, Cyanidioschyzon merolae [1], the first complete algal genome [2]. This photosynthetic eukaryote can be classified as a protist, having a very simple cell architecture and a small genome (16.5 Mbp, about one seventh the size of Arabidopsis thaliana). However, if one defines the kingdom Plantae to mean the Archaeplastida, instead of strictly just the Viridiplantae, red algae is part of the plant kingdom [3,4]. The taxonomic debate has yet to be settled, with recent phylogenetic evidence suggesting alternative algal clades [5]. Unlike plants and fungi, C. merolae lacks a vacuole and has no cell wall [1]. The chloroplast genome of this organism retains several genes not found in those of algae and plants [6].

To accommodate the Oryza species with partial genome assemblies (i.e.the chr 3 short arm projects) we have run a separate gene tree analysis called "Oryza-centered Compara". In addition to the three complete reference genomes for cultivated rice, O. sativa ssp. japonica, O. sativa ssp. indica and O. glaberrima (African rice), and the chromosome 3 short arm assemblies for seven wild Oryza species, these trees include Brachypodium distachyon, Sorghum bicolor, and Arabidopsis thaliana. From a total of 235,561 input proteins, 17,435 families were constructed, comprising 221,563 individual genes.

Screen for putative gene annotation artifacts. The Compara Gene Tree method predicts a special class of within-species paralog called "contiguous_gene_split", identified when two apparently paralogous genes lie on the same strand and in close proximity (<1MB) but have no (or little) overlapping sequence. This phenomenon is commonly related to an annotation artifact wherein a single gene is annotated as two or more genes due to incomplete evidence, but can also result from legitimate evolutionary processes. As a service to the community, we are releasing results of this screen for each of the reference genomes hosted at Gramene and chromosome 3 short arm assemblies for seven wild Oryza species. For more information on the method please read Ensembl documentation on Gene Orthology/Paralogy prediction [7].

References

[1] http://wikipedia.org/wiki/Cyanidioschyzon_merolae

[2] Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. M MATSUZAKI ET. AL. Nature, 2004. http://www.ncbi.nlm.nih.gov/pubmed/15071595

[3] http://merolae.biol.s.u-tokyo.ac.jp/intro_cyanidiaceae.html

[4] An overview of the phylogeny and diversity of eukaryotes. SL BALDAUF. Journal of Systematics and Evolution, 2008. http://www.plantsystematics.com/qikan/epaper/zhaiyao.asp?bsid=15555

[5] Non-random sharing of Plantae genes. CX CHAN AND D BHATTACHARYA. Communicative & integrative biology, 2011. http://www.ncbi.nlm.nih.gov/pubmed/21980581

[6] Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. N OHTA. DNA Research, 2003. http://www.ncbi.nlm.nih.gov/pubmed/12755171

[7] http://useast.ensembl.org/info/docs/compara/homology_method.html