2009 Maize Meeting Friday Panel Discussion - Question Submission

General Information

At the Friday evening session of the 2009 Maize Meeting, there will be a community forum on "Maize Genome Annotations: What's Next?" The forum will be driven by questions from the maize community that will generate an interactive exchange between the community and the annotation panel. The annotation panel members are: Carolyn Lawrence, Jeff Bennetzen, Yan Fu, Jim Uphaus, Volker Brendel, and Gernot Presting. We are asking the community to submit their top three questions or issues regarding any aspect of maize genome annotation you want to have discussed at this forum. Community members not able to attend the 2009 conference are asked to submit questions as well.

Deadlines

Submissions are due by March 10, 2009 by 5:00 PM.

Submission instructions

The submission period has expired.

List of Submitted Questions
     Is everyone annotating the same GenBank releases? --anonymous

     Will there be a tendency to include all annotations, or will they be heavily filtered to exclude obviously flawed annotations? How will flawed annotations be identified? --anonymous

     How will the existence of complex gene clusters and duplications complicate the interpretation of the sequence relative to gene function? --Ron Philllips, University of Minnesota

     Do you think that analyses of the maize genome will provide clues on how to structurally recognize non-coding sequences that influence the expression of distant genes? --Ron Philllips, University of Minnesota

     Will alternative splicing severely restrict the value of the genome sequence information? --Ron Philllips, University of Minnesota

     For genome browsing in an area of interest, is there an efficient way to see the gene models & their \"motifs\" or \"homologs\" without clicking away to new page? --anonymous

     For genome browsing an area of interest, is there an easy way to scroll in one direction without non-overlapping segment jumps to new areas (i.e. walking)? --anonymous

     What is the most cost-effective way to do the best job, based on jgi and other organizations\' experience? --Ann E. Stapleton, UNCW

     How can we prioritize features needed and ensure feedback to improve raw data from data providers? --Ann E. Stapleton, UNCW

     What can we do BETTER than any other annotation, to attract new researchers? --Ann E. Stapleton, UNCW

     Is there any way to put an birthday and expected expiration date on bp coordinates in the physical map entries? --HW Bass, FSU

     Can linkage maps (like the IBM2 Neighbors Frame 2008, including uncloned mutations) be displayed as co-aligned (with connector-links on/off) with the contig/BAC/gene space views? --HW Bass, FSU

     Can you clarify the similarities and differences between maizesequence.org and maizegdb in terms of data, data structure, interfaces, and utilities? --HW Bass, FSU

     Is there a tool (software) to use synteny with sorghum and rice to define othologous groups? --anonymous

     Is the maize community planning on developing a pathway viewer similar to mapman? --anonymous

     how will we integrate transposon insertions/polymorphisms/EMS-lesions into the gene annotation pipeline? --anonymous

     Are there plans to incorperate data from the Maize SNP Discovery project to enable browsing for allelic/regional diversity? --anonymous

     The relative orientation of many contigs is not known; are there plans to determine contig orientations? --Tom Peterson, Iowa State University

     What will be the process for avoiding duplication of effort and facilitating collaboration among groups with common interests in annotating particular gene families or classes of genes, elements and motifs? --Nick Lauter, USDA-ARS and Iowa State University

     How can existing data sets be used to 1) properly order and orient the fragments of B73 BACs, 2) find genomic positions for the 400+ \"chromosome0\" B73 BAC ctgs, and 3) determine what is not represented by the 16,600 sequenced B73 BAC contigs? --Nick Lauter, USDA-ARS and Iowa State University

     How extensible is yrGATE, and how will it grow to accommodate our community\'s needs as they grow? Also, what can NCBI do for us? --Nick Lauter, USDA-ARS and Iowa State University

     How are multiple names for a gene resolved into a final naming convention (e.g., may have mutation phenotype but gene identified later) --Virginia Dress, Pioneer Hi-Bred Int\'l., Inc.

     How are multiple gene & mutant names linked so that we can see there is/was more than one name used? --Virginia Dress, Pioneer Hi-Bred Int\'l., Inc.

     How are non-coding/non-regulatory genome regions annotated/denoted (e.g., not an ORF, promoter, terminator, enhancer, intron, etc.) --Virginia Dress, Pioneer Hi-Bred Int\'l., Inc.

     What is the contribution of helitron transposable elements in the genetic diversity of maize inbred and hybrid lines? --anonymous

     Are there specific gene loci in maize which brings about differences in their response in in vitro culture and genetic transformation? --anonymous

     when genome sequence will be finished/ to be at a situation similar to rice --murigneux, limagrain

     when structural annotation will be available --murigneux, limagrain

     when functional annotation will be available --murigneux, limagrain

     Is it possible to have access to an evaluation of the annotation pipelines already used to annotate the maize genome? What are the sensitivity and specificity of gene prediction ? --Johann JOETS, INRA

     Do you plan to release annotation data through gff files using physical map bp coordinates rather than bac coordinates ? --Johann JOETS, INRA

     Is it possible to have information about which bac contigs overlap between contiguous BACs ? Is there any plan to go further in bac finishing than the so-called \"improved\" status ? --Johann JOETS, INRA

     Is there a plan to not only annotate genes, but annotate QTL or haplotypes? --anonymous

     How much effort is there in comparative genomics and annotation --anonymous

     The structure of the genome browser looks good, but I get the sense that not much of the data has been incorporated. Is there anyway to know that you did not find your gene because this is a work in progress or because the gene is in a sequence gap? --Sarah Hake

     Will there be a way to quickly see other alleles (such as Mo17 or W22) when they are sequenced so primers could be designed? --Sarah Hake

     Which entity (lab, institution, consortium) will be the official guardian of the maize genome in future years? --Peter Rogowsky, ENS-Lyon

     How can we avoid competing annotations or at least consolidate them into a single annotation that is accepted as reference by the entire maize community? --Peter Rogowsky, ENS-Lyon

     How can we assure that future improvements of the actual sequence (filling gaps between the over 4OO BAC contigs, intra BAC contig order) end up in a single refernce sequence? --Peter Rogowsky, ENS-Lyon

     The current annotation plan does not include providing location information (chromosome number and gene order) to gene names as has been done by all other currently sequences plant genomes (Arabidopsis, Rice, and Sorghum). Can this plan be revised to include this very important information? --anonymous

     Several maize sequences are being considered. A simple system of naming genes, using a modification of TIGR terminology to identify them could be used such as: Mo17xgyyyyyyy and B73xgyyyyyy with x = chromosome and y = to gene order. Is this type of system being considered? --anonymous

     What are the plans to make real nonredundant pseudomolecules for the maize chromosomes? --anonymous

     What is being done to create a well curated (not automated) repeat database for maize? I am aware of the Wessler effort but to my knowledge none of this is in the public domain and/or being used in any maize whole genome annotation efforts. It has to be used soon or it will not be worthwhile. --anonymous

     What are the plans to integreate the MAGIs into the final B73 sequence? Something other than mapping of the MAGIs would be informative --anonymous

     Is there any reason that coding is preferable to use of existing gene nomenclature in the annotation effort? --Ed Coe, University of Missouri and USDA (retired)

     NCBI consistently documents annotations for well-defined Unigenes, AND links to MaizeGDB. Will the Genome Browser provide reciprocal links to NCBI Unigenes? --Ed Coe, University of Missouri and USDA (retired)

     Which parameters will we use for gene predictions? --Joachim Messing, Rutgers University

     Are they any recent whole genome annotations that can serve as a model? --Joachim Messing, Rutgers University

     How do we account for variability of gene copies among inbred lines? --Joachim Messing, Rutgers University

     Where can one get the annotations and contig sequence data in formats that would allow one to perform computational studies and experiments with other genome browsers that might be more appropriate for a particular need such as looking at a lot of genes and regions quickly? --anonymous