Gene families gene/protein families
From Purdue Genomics Database Facility
SelmoWikiHome | Selaginella Genomics | JGI | Annotation
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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
- 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
- Cellulose synthase superfamily
- Ubiquitin-mediated proteolysis
- Whole Genome Syntenic Analysis of Haplotypes
- Lack of Synteny Between Selaginella and Physcomitrella patens, Oryza sativa japonica, and Vitis vinifera
Annotation notes
- JGI BLAST searches are run with a 10-7 cutoff
- see JGI naming conventions for more information on what the JGI model names mean. The numerical model ID is the most reliable way to identify specific gene models as the name can be changed.
JGI browser hints
- in the scaffold track, Red = gaps in assembly, black = contigs
- in the Vista tracks, pink= intron/intergene space, blue=exon
- "needs GO" on the transcript annotation page means that there is no appropriate GO term. Do not use this to indicate that GO terms have not been assigned.
Naming Genes
- Do not include prefixes such as selmo or smo
- use a suffix -1 or -2 to indicate the two alleles,for example, CPK5-1 and CPK5-2
- use a three or four letter code followed by a number (such a a gene symbol) for the gene name
- if practical or sensible, try to follow numbering of other plants,
Assignments
Please list the genes, protein families, or other aspects of the genomic sequence that you are committed to working on. Follow the kinase example - it's easy! Note that you have to be logged in to edit pages, see the upper right corner of any page.
Example
Feel free to add to or change this table. The wiki system allows us to recover the old version if you make a mistake. For those new to wikis, here is a hint on editing the table.
A simple version of the table looks like this
{| border="1" cellspacing="0" cellpadding="5"
|- style="1px solid black;"
| Investigator
| Email
| Annotation focus
|-
| Jody Banks
| banksj@purdue.edu
| flagella
|}
the table begins and ends with {| and |}. You can ignore anything that follows the {|; these are formatting commands. In between, the information for each line of the table begins with |-, and each column follows with the information for each column appearing on a separate line beginning with |. So, to add my entry I would add the following before the closing |} line
|- | Michael Gribskov | gribskov@purdue.edu | protein kinases
Assignment Table
If you don't see the edit tab at the top of this page, you must log in first to edit. The tab will then appear.
The order of names and topics in this table have absolutely no significance - please do not get bent out of shape if you are not where you would like to be (feel free to change the table). This table was mostly created by Jody from people's emails, and then converted to the wiki, but in the process was merged with a separate list I had started. If you indicated an interest in more than one family, you probably have entries in multiple sections of the table - we have tried to not arbitrarily remove anyone's innterests. A yes in the fourth column means that you have already worked on this gene family in selaginella. Due to merging Jody's material and mine, there are also some comments about possible collaborations in this column.Gribskov 15:39, 20 September 2007 (EDT)
I'm thinking that we may want to appoint leaders or a establish working groups for broad categories such as protein kinases or transcription factors to handle the details of who is doing what and to make sure that things advance expeditiously. Suggestions on how to do this are welcome.Gribskov 15:39, 20 September 2007 (EDT)
| Hormones (see also signaling) | ||||
|---|---|---|---|---|
| Aldwin Anterola | anterola@plant.siu.edu | terpene synthases isoprenoid pathway genes gibberellin biosynthetic genes | possibly Dr. Sinha on gibberellin biosynthetic genes | |
| Cédric Finet | Cedric.Finet@ens-lyon.fr | Auxin Response Factors (ARFs), auxin signaling enzymes (YUCCA, CYP79B2, AAO1...) | ||
| Guichuan Hou | houg@appstate.edu | genes that function in root development, such as homologs/analogs (if any) in the GRAS and PIN families | Mike Barker? | |
| Neelima Sinha | nrsinha@ucdavis.edu | GA biosynthesis genes | ||
| Rathinasabapathi,Balasubramani | brath@ufl.edu | glutaredoxins and genes in the biosynthesis of pantothenate and beta-alanine | ||
| Alexander Heyl Birgit Pils | heyl@zedat.fu-berlin.de pils@well.ox.ac.uk | cytokinin signaling components | ||
| Victor Albert | victor.albert@nhm.uio.no | ABA receptors | ||
| Tomomichi Fujita | tfujita@sci.hokudai.ac.jp | ABA, Brassinosteroids, ethylene | yes | |
| Naoki Shinohara | shino@nibb.ac.jp | auxin | yes | |
| Minoru Kubo | ku-bo@nibb.ac.jp | cytokinin | yes | |
| Tomoaki Nishiyama | tomoakin@kenroku.kanazawa-u.ac.jp | all | ||
| Protein kinases and signal transduction related genes | ||||
| John Williams Mundy | MUNDY@adm.ku.dk | MAPKs, MAP2Ks, MAP3Ks | ||
| Jake Stout | stout0@purdue.edu | G-protein alpha, G-protein beta, G-protein coupled receptors | ||
| Gerard Manning Michael Gribskov | manning@salk.edu gribskov@purdue.edu | all | yes | |
| Martin Potocky | potocky@ueb.cas.cz | phospholipid and phosphoinositide signalling genes | ||
| Neelima Sinha | nrsinha@ucdavis.edu | Aux/IAA family | ||
| Eric Engstrom | emengs@wm.edu | GRAS genes, ethylene signaling genes | ||
| Chi-Kuang Wen | cwen@sippeac.cn | ethylene signaling genes, | ||
| Hong Ma | hxm16@psu.edu | Cyclins and CDKs | ||
| John Larkin | jlarkin@lsu.edu | CDK inhibitors, both SIM-like and KRP-like, and Cyclins, CDKs, and other cell cycle genes | ||
| Masaki Ishikawa | ishikam@nibb.ac.jp | Cell cycle | yes | |
| Michael J. Prigge | mprigge@indiana.edu | Auxin signaling (TIR1/AFB, ARF, Aux/IAA, PIN, AUX1/LAX, PINOID-like, YUCCA/FLOOZY, Trp aminotransferase, GH3, IRL1/ILL, SAURs(?), IAN Nitrilase-like, ABP, AXR4, IBR5, DIAGEOTROPICA, Class III HD-Zips, TOPLESS, SGT1, AXR1-like (and other SCF-concerning components), Inositol kinases) | ||
| Aldwin Anterola | anterola@plant.siu.edu | Lipoxygenase/Jasmonate pathway genes | ||
| Sheila McCormick | sheilamc@nature.berkeley.edu | Rop-GEFs, other signaling components in RLK pathways | ||
| Saori Miyazaki | saori@nibb.ac.jp | development related Receptor like kinases | ||
| Tomoaki Nishiyama | tomoakin@kenroku.kanazawa-u.ac.jp | all related to development | ||
| Transcription factors | ||||
| Bernd Mueller-Roeber | bmr@rz.uni-potsdam.de | all | Diego Riaño (diriano@uni-potsdam.de), Luiz Gustavo Guedes Corrêa (correa@uni-potsdam.de) | |
| Stefan Rensing | stefan.rensing@biologie.uni-freiburg.de | all | ||
| Neelima Sinha | nrsinha@ucdavis.edu | KNOX genes | ||
| Zengyan Xie | xiezy@mail.cbi.pku.edu.cn | HAP3 genes | ||
| Jill Harrison | jill.harrison@plants.ox.ac.uk | genes involved in meristem function | yes | |
| Tsuyoshi Aoyama | t_aoyama@nibb.ac.jp | Shoot meristem, axillary meristem, Root and lateral root | yes | |
| Guenter Theissen | guenter.theissen@uni-jena.de | MADS-box genes | ||
| Victor Albert | victor.albert@nhm.uio.no | TCPs, and YABBY-like genes | yes | |
| Patricia Springer | pspringer@ucr.edu | LBDs, and perhaps help with MYBs, bHLHs, GRAS domain, and others | ||
| Hong Ma | hxm16@psu.edu | bHLH, possibly Myb, possibly homeodomain, Cohesins and condensins, Proteosome and ubiquitination pathways, SKP1, F-box genes, ubiquitin, SUMOs, etc. | ||
| Elizabeth Barker | barker.e@gmail.com | MADS-box and KNOX | yes | |
| Amy Litt | alitt@nybg.org | MADS-box, AP2/ERF | ||
| Erik Vollbrecht | vollbrec@iastate.edu | C2H2 zinc finger proteins | ||
| Barbara Ambrose | b.ambrose@massey.ac.nz | MADS-box | ||
| Christian Schulz | Christian.Schulz-3@ruhr-uni-bochum.de; cschulz@nybg.org | MADS-box | ||
| John Mundy | MUNDY@adm.ku.dk, mcs@bio.ku.dk, simonb@bio.ku.dk | WRKY protein family | ||
| Minoru Kubo | ku-bo@nibb.ac.jp | vascular development | ||
| Tomoaki Nishiyama | tomoakin@kenroku.kanazawa-u.ac.jp | all related to development | ||
| Transporters and membrane proteins (except receptor protein kinases | ||||
| Michael Gutensohn | gutensohn@pflanzenphys.uni-halle.de | chloroplast protein transport machineries; components of the Toc and Tic machineries involved in the the translocation of nuclear encoded chloroplast proteins across the two chloroplast envelope membranes | ||
| Alonso Rodriguez-Navarro | alonso.rodriguez@upm.es | potassium and sodium transporters starting with HKT and HAK continuing to potassium channels and K-Na/H exchangers | ||
| Ingo Dreyer | dreyer@uni-potsdam.de | K channels and cyclic nucleotide gated channels (CNGC) | yes | |
| Uener Kolukisaoglu | uener.kolukisaoglu@uni-rostock.de | ABC transporters | ||
| Burkard Schulz | bschulz@purdue.edu | ABC transporters | yes | |
| Jeff Gustin | jgustin@purdue.edu | Cation Diffusion Facilitator (CDF) Family | ||
| Sylvie Lalonde & Wolf Frommer | wfrommer@stanford.edu | glucose and sucrose transporters | ||
| Dominique Loque & Wolf Frommer | wfrommer@stanford.edu | ammonium transporters | ||
| Koji Mikami | Phosphoinositides (PIs) | komikami@fish.hokudai.ac.jp | yes | |
| Nakako Shibagaki | NShibagaki@lbl.gov | sulfate transporters | ||
| Chromatin proteins/RNAi associated proteins | ||||
| Carolyn Napoli | cnapoli@Ag.arizona.edu | all | ||
| Lingjing Chen | lchen2@nature.berkeley.edu | polycomb group(PcG) genes | ||
| Mari Obara | mobara@nibb.ac.jp | RISC complex, epigenetics | yes | |
| Yasuko Oguri | yoguri@nibb.ac.jp | epigenetics | yes | |
| Sachiko Wakazuki | mo_wakazuki@yahoo.co.jp | epigenetics | yes | |
| Tomoaki Nishiyama | tomoakin@kenroku.kanazawa-u.ac.jp | all | ||
| MicroRNA and small RNA-producing regions of the genome | ||||
| Michael Axtell | mja18@psu.edu | all, including microRNA target predictions | yes | |
| DNA recombination and repair | ||||
| Cliff Weil | cweil@purdue.edu | all | ||
| Dorothy Shippen | dshippen@neo.tamu.edu | all, plus telomere related genes | ||
| Hong Ma | hxm16@psu.edu | RAD50, RAD51, RAD52, RAD54, RAD55, RAD57, etc, and MSHs, MLHs, DNA helicases, ligases | ||
| Light | ||||
| Ken Karol | kkarol@nybg.org | cryptochromes, phytochromes and phototropins | ||
| Todd P. Michael | tmichael@waksman.rutgers.edu | circadian, light signaling and flowering time genes | ||
| Dion Durnford | durnford@unb.ca | Light-harvesting complexes and relatives (ELIPs, SEPs, OHPs). Light-stress related genes. | ||
| Yoshikatsu Sato | yoshi@nibb.ac.jp | Light signaling and Circadian clock | yes | |
| Tadayoshi Hirai | thirai@gene.tsukuba.ac.jp | Light signaling and Circadian clock | yes | |
| Nagisa Sugimoto | nagisa91@nibb.ac.jp | Light signaling and Circadian clock | yes | |
| Secondary Metabolism | ||||
| Clint Chapple | chapple@purdue.edu | cytochrome P450-dependent monooxygenases, serine carboxypeptidase-like proteins, BAHD acyltransferases, all enzymes of phenylpropanoid metabolism | yes | |
| Victor Albert | victor.albert@nhm.uio.no | chalcone/pyrone synthase and related downstream pathways (but...considerable overlap w/ Clint Chapple) | ||
| Seiichi Matsuda | matsuda@rice.edu | sterol and triterpene Biosynthesis | ||
| Minoru Kubo | ku-bo@nibb.ac.jp | vascular development (Lignin etc.) | ||
| Transposable elements | ||||
| Jeff Bennetzen | maize@uga.edu | all | ||
| Primary metabolism | ||||
| Victor Albert | victor.albert@nhm.uio.no | cytochrome c oxidase subunits, other proteins in the respiratory pathway | ||
| Jin Miao | jin.miao@pku.edu.cn | Glutaredoxin family genes | ||
| Uener Kolukisaoglu | uener.kolukisaoglu@uni-rostock.de | C2 cycle genes and amino acid racemases | ||
| Bala Rathinasabapathi | brath@ufl.edu | glutaredoxins, pantothenate and beta-alanine biosynthesis | ||
| Mitochondrial genome | ||||
| Ken Karol | kkarol@nybg.org | all | ||
| Victor Albert | victor.albert@nhm.uio.no | coding | ||
| Chloroplast genome | ||||
| Ken Karol | kkarol@nybg.org | genes that are typically found in the plastid genome but have been lost in the Selaginella cp genome | yes | |
| Cell biology | ||||
| Alison Roberts | aro1844u@postoffice.uri.edu | Cellulose synthase superfamily | yes | |
| Henrik Scheller | hscheller@lbl.gov | cell wall related glycosyltransferases (excl GT2) | ||
| John Fowler | fowlerj@science.oregonstate.edu | ROP GTPase-related genes (eg, ROPs, RICs, etc),select genes related to vesicle trafficking (exocyst, possibly some Rabs) and in the actin cytoskeleton | ||
| Marek Elias | melias@natur.cuni.cz | Ras superfamily GTPases (including ROPs and RABs) | ||
| Burkard Schulz | bschulz@purdue.edu | immunophilin genes, FKBPs and cyclophilins | yes | |
| Takashi Murata | cytoskeleton | tkmurata@nibb.ac.jp | yes | |
| Jody Banks | banksj@purdue.edu | flagella proteins (and other genes lost in the angiosperm lineage) | ||
| Hong Ma | hxm16@psu.edu | Motor proteins, kinesins, myosins, dyneins | ||
| Robert Pruitt | pruittr@purdue.edu | organ fusion genes (fiddlehead, hothead, etc.) | ||
| Genome Evolution | ||||
| Stefan Rensing | stefan.rensing@biologie.uni-freiburg.de | large scale duplication issues | ||
| Mike Barker | msbarker@indiana.edu | Gene and genome duplications | ||
| Stefan Rensing | stefan.rensing@biologie.uni-freiburg.de | Comparison to Physcomitrella & synteny | ||
| John Cushman | jcushman@unr.edu | Comparison to S. lepidophylla, transcriptome comparisons; LEA genes | ||
| Mel Oliver | Mel.Oliver@ars.usda.gov | transcriptome comparisons | ||
| Mike Barker | msbarker@indiana.edu | evolutionary stats for gene families (Ka, Ks, Ka/Ks,and NJ and ML trees) | ||
| Victor Albert | victor.albert@nhm.uio.no | intragenic repeats | ||
| Tomoaki Nishiyama | tomoakin@kenroku.kanazawa-u.ac.jp | Conservation and diversification of genes related to development. | ||
| Genes of unknown function | ||||
| John Williams Mundy | MUNDY@adm.ku.dk | Genes of unknown function | ||
| Sporogenesis and gametogenesis | ||||
| Harry T Horner | hth@iastate.edu | sporogenesis | ||
| Sheila McCormick | sheilamc@nature.berkeley.edu | gametophytes | ||
| Saori Miyazaki | saori@nibb.ac.jp | homologues of pollen development related genes | ||
| 'Flowering time' genes; promoters/repressors of reproduction | ||||
| Victor Albert | victor.albert@nhm.uio.no | all; would also like to cooperate! | yes | |
| RNA recognition motif (RRM) containing proteins | ||||
| Victor Albert | victor.albert@nhm.uio.no | all | ||
| WW domain containing proteins | ||||
| Victor Albert | victor.albert@nhm.uio.no | all | ||
| Pentatricopeptide repeat (PPR) motif containing proteins | ||||
| Mamoru Sugita | sugita@gene.nagoya-u.ac.jp | all | yes | |
| Development related genes (functional aspects rather than gene family) | ||||
| Yuji Hiwatashi | hiwatash@nibb.ac.jp | Shoot meristem and axillary meristem | yes | |
| Tsuyoshi Aoyama | t_aoyama@nibb.ac.jp | Shoot meristem, axillary meristem, Root and lateral root | yes | |
| Tomomichi Fujita | tfujita@sci.hokudai.ac.jp | Seeds | ||

