Mimulus guttatus v1.0
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Please note that the latest data is available at Phytozome.

Status

v1.0: Annoation: Transcript assemblies were constructed using PASA from Mimulus guttatus ESTs (~555K, IM62 and DUN, including some 454 EST reads) and ESTs of related species (~256K, other asterids). Loci were determined by BLAT alignments of above transcript assemblies and/or BLASTX alignments of peptides from arabi (Arabidopsis thaliana), rice, grape genomes or a few tomato, potato and tobacco peptides to repeat-soft-masked M. guttatus genome. Gene models were predicated by homology-based predictors, mainly by FGENESH+ with the addition of GenomeScan if FGENESH+ produced no model at the locus. Predicted genes were UTR-extended and/or improved by PASA. Final gene set was made from gene selection based on ESTs support or peptide homology support subjected to filtering of repeats/transposable elements.

Genome size
 Approximately 321.7Mb arranged in 2216 scaffolds Approximately 300.7Mb arranged in 17831 contigs (~ 6.5% gap) Scaffold N50 (L50) = 81 (1.1 Mbp) Contig N50 (L5) = 1770 (45.5 Kbp) 512 scaffolds larger than 50 Kbp, with 95.7% of the genome in scaffolds larger than 50 Kbp
Loci
   25530 loci containing protein-coding genes
Transcripts
   27504 protein-coding transcripts

Mimulus dataset Links
I would like to use this data to help clone a gene, analyse a gene family, etc. Wonderful! Please feel free to use this data to advance your studies of plant biology. Please reference "Mimulus Genome Project, DoE Joint Genome Institute" as your citation. Also please recognize that this is a preliminary release, which may include various errors. Caveat emptor. I think I found an error.What should I do? If you would like to bring any items to our attention, please email us. I would like to do a large-scale comparison of Mimulus to other genomes, and/or a global analysis of its gene content. Our plans for publication of the Mimulus genome are described below, and are focused on the large-scale analysis of the gene and repetitive content of the genome and its evolutionary dynamics (including synteny and chromosomal/segmental duplication, gene family evolution, gene structure evolution) relative to other angiosperms. The Fort Lauderdale guidelines for large scale sequencing projects aims to balance the value of rapid data release for the user community with respect for the scientific interests of the generators of the data. We ask that you respect these scientific goals as discussed in the Fort Lauderdale guidelines. A plan for the coordinated submission of companion manuscripts to Genome Research will be developed.

Links
We expect that the initial manuscript describing the assembly, annotation, and first analysis of the mimulus genome will be based on an improved, chromosome-scale assembly to be developed by the end of 2010. This assembly and its annotation will be distributed prior to publication. Our target is submission of a manuscript no later than nine months after completion of chromosome-scale assembly and annotation.

Collaborators

  • US Department of Energy Joint Genome Institute (JGI)

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.