How do I work with the cassava Gbrowser browser?

How can I view the cassava sequence and various genomic features?

To facilitate early use of the cassava genome the DOE-JGI and the UC Berkeley Center for Integrative Genomics have developed a simple genome browser using the Gmod/Gbrowse software. Due to the density of information, detailed features are only visible when looking at 70 kb or smaller regions. You may need to zoom in to get to this size. Typically, clicking on a feature will reveal its sequence and alignment to the genome. For gene models, you can also click to bo

How do I retrieve cassava sequence of interest to me?

From the browser, locate the region of interest. With your region in view, select "Download Sequence" from the menu above the Scroll/Zoom bar.  Then click the "Go" button and you'll get your sequence on your browser to cut and paste.  If you click on a gene model, you can retrieve the predicted peptide and coding sequencing.

What happens when I click on a gene on the browser

You'll see a web page that displays the predicted peptide, genomic span of the gene with coding exons shaded, and the (spliced) coding sequence.  From this page you can also launch BLAST vs. the NCBI non-redundant protein database or Phytozome.

Where do the various tracks on the genome browser come from?

How were repeats identified?

Sixteen-base-pair "words" (16-mers) that are over-represented in and clustered on the genome were used to define repetitive regions (J. Chapman, unpublished). These typically represent recently active retrotransposons and simple-sequence-repeats in the cassava genome. Nearly 16% of the assembly appears to be covered by such clustered/over-represented regions.

In a subsequent analysis, RepeatScout (Price & Pevzner, 2005) was used to generate a catalog of 372 over-represented sequences over 500nt long with homology to known transposons in the nr database at NCBI. Known transposon sequences from RepBase (version from 20090604) from Viridiplantae were added to make a custom library of repeats that was used to further mask 9.4% of the genome with RepeatMasker.

How were ESTs aligned?

We aligned the cassava EST sequences using Brian Haas's PASA pipeline which aligns ESTs to the best place in the genome via gmap, then filters hits to ensure proper splice boundaries.

How were plant peptides aligned?

Rice and castor bean peptides were downloaded from TIGR; Arabidopsis peptides were downloaded from TAIR; poplar and soybean proteins were generated in our annotation pipeline. All peptides were aligned to the soft-masked genome using gapped BLASTX; high-scoring sequence pairs (HSPs) are shown. Note that gapped BLAST was used to increase sensitivity, so that in many cases the HSP (shown in orange) spans adjacent exons and the intervening intron(s). Also, small exons are often missed.

How did you determine the cassava gene set?

Gene prediction

To produce the current "Cassava1.1" gene set, we used the homology-based gene prediction program FgenesH predictions provided by Asaf Salamov at JGI, along with the PASA program to integrate over 1.5 million cassava ESTs. The gene set shown on the browser was produced by Simon Prochnik at JGI. Briefly, peptides from diverse angiosperms and cassava EST assemblies (from PASA) were aligned to the genome, and their overlaps used to define putative protein-coding gene loci. The corresponding genomic regions were extended by 1kb in each direction and submitted to FgenesH, along with related angiosperm peptides and/or ORFs from the overlapping EST assemblies. Fgenesh identifies likely protein coding exons, favoring regions that align well to the given homologous peptides. These homology-based predictions were integrated with expressed sequence information using PASA (Haas et al. 2003) using cassava ESTs. The results were filtered to remove genes identified as transposon-related. Genes with apparently truncated ORFs may be prediction errors or pseudogenes.

How come my gene is wrong?

FgenesH is one of the better homology-based gene predictors available, but like all computational gene modeling algorithms is imperfect. In addition, EST and cDNA data are often incomplete. We hope that the aggravation of having an imperfect gene set is partially compensated by the rapid release of the data.

Future gene sets will improve as assembly quality improves along with expressed sequence data and genomic data from related species. But the lesson from the annotation of other well-curated genomes like Arabidopsis and rice is that it can take years to fine tune a gene set even given a high quality genome assembly. So please be patient!

What can I do with the cassava dataset?

I would like to use this data to help clone a gene, analyse a gene family, etc.

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 cassava and other malpighiales. Please cite "Cassava Genome Project 2009, http:://www.phytozome.net/cassava".

I think I found an error. What should I do?

If you would like to bring any items to our attention, please send email to phytozome@jgi-psf.org.

I would like to do a large-scale comparison of cassava to other genomes, and/or a global analysis of its gene content.

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 have released the data prior to any publication because of the importance of this data to the cassava community. Our plans for publication of the genome sequence and associated analyese are still developing, and we would encourage any members of the cassava community who wish to contribute genome-wide, or family-specific analyses to contact us at CassavaGenomics.org.