SelmoWikiHome | Selaginella Genomics | JGI | Annotation

Articles

• Brief History of the Selaginella genome project and taxonomy
• Contamination
  analysis
• Distribution of genes
• Flagellar Proteins
• Protein kinases
• transcription factors
• Evolution of developmental genes
• Meristems
• Root
• Vascular system
• Cytoskeletons
• Epidermal cell differentiation
• Pollen
• ABA
• Seed
• Ethylene
• Brassinosteroids
• Gibberellins
• Cytokinin
• Evolution of cytokinin signaling
• Auxin
• Phosphoinositides
• Evolution of auxin signaling
• Epigenetic gene regulation
• Phase transition
• Cell cycle
• Circadian clock
• Light signalling
• small RNAs
• PEBP gene family
• Potassium channels
• PPR gene family
• Cyclic Nucleotide Gated Channels
• YABBY gene family
• Ras superfamily GTPases
• LUMINIDEPENDENS (LD)
• UNUSUAL FLORAL ORGANS (UFO)
• STERILE APETALA (SAP)
• PESCADILLO - Wnt-like signaling?
• KEGG differences
• The NTMC2 genes of embryophytes
• BRK1 and apical growth
• MADS-box genes
• Lignin monomer biosynthesis
• BAHD family acyltransferases
• SCPL (serine carboxypeptidase-like) enzymes
• Cytochrome P450
• MAP Kinases
• Light Harvesting Complexes
• Transcription factors involved in senescence
• Phylogenetic_Patterns
• Metallothionein
• Duplicate Gene Analyses
• HAP3 gene family
• Sucrose transporter gene family
• Hexose/hexitol transporter gene family
• Amino acid transporter gene family
• Ammonium transporter gene family
• plastidic maltose transporter gene family
• Telomeres, subtelomeres and telomere-related genes
• Sulfate transporter gene family
• proton/urea cotransporter
• Cell wall composition and glycosyltransferases involved in cell wall formation
• KNOX Genes

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This Wiki provides a means for the Selaginella moellendorffii community to share information on the use of Selaginella as an experimental organism, and on the Selaginella genome and proteome.

The JGI Selaginella portal is now available to registered users. The Purdue Selaginella Genomics web page also provides information about the Selaginella genome. There are links to both of these sites in the navigation bar at the top of the page.

Announcements

If you would like to participate in another JGI tutorial on how to use the annotation site, please contact Jody Banks. The JGI tutorials cover the mechanics of how to use their website but not how to decide on what the correct annotation is. That is up to you, the expert.

News

7 May - Tomoaki Nishiyama and Mitsuyasu Hasebe have provided some guidelines for phylogenetic analysis, which can be viewed at http://moss.nibb.ac.jp/treedb/TreeforSelmo.html. If you need any help with your analyses, please contact them by email: Mitsuyasu Hasebe <mhasebe@nibb.ac.jp> Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>. As John Bowman has pointed out, long branch attraction can be a problem with some analyses. This is an issue the steering committee is discussing and will have to be dealt with in the final manuscript.

8 March - Please register on the Selaginella homepage (http://selaginella.genomics.purdue.edu/cgi-bin/participants.cgi) if you wish to receive occasional emails.

28 February - The new account approval process appears to work, I have approved two new acounts.

25 February - You may have noticed that we are seeing some spam posted to pages on the wiki. Jody and I have been cleaning this up as we see it and I have blocked a number of suspicious accounts. To cut down on this activity, new accounts have to be approved. This is done automatically through the wiki registration page and should involve no delays. If you cannot log in, please contact me - it probably means I inactivated your account as suspicious. Gribskov 13:08, 25 February 2008 (EST)

21 January - Students at Catholic University of Chile help annotate genome.

21 December - JGI Selaginella portal is officially open to the public.

• Please use the new URL for annotation http://www.jgi.doe.gov/Selaginella.
• Sign up for annotation at http://genome.jgi-psf.org:8080/annotator/servlet/jgi.annotation.Annotation?pDb=Selmo1&pStateVar=Register.
• There is an online tutorial for the annotation interface at http://genome.jgi-psf.org/Tutorial/

17 December - At the steering committee teleconference, we decided to complete the initial genome paper by the end of February. This will require Your help. Please let us know what we can do to expedite your work.

17 December 2007 - Andreas Zimmer and Stefan Rensing have provided a contaminant analysis of the Selaginella genome. Click "Contamination analysis" under Topics to review their results.

17 December 2007 - note that JGI has added an "Allelic Variants" link to the protein pages. If a gene in the GeneCatalog has an allelic variant, the preferred copy is the one on the lowest numbered scaffold, e.g. usually the one on the largest scaffold.

31 October 2007 - JGI announces pre-release of assembled genome. A few factoids

Nuclear genome size (Mbp)                 212.5
Sequencing read coverage depth             7.0x (for diploid genome)
Number of contigs                         5,156
Number of nuclear scaffolds >2 Kbp          726
Nuclear scaffold N/L50               38/1.7 Mbp
Three largest Scaffolds (Mbp)               7.0, 6.2, 4.5
                                             

See details for more information about the release and JGI naming conventions, or the JGI Selaginella portal or the JGI release notesfor more information.