Aspergillus fumigatus genome sequencing project: December 1999 questionnaire

Authors: Michael Anderson1, David Denning1 Geoff Turner2 Jean-Paul Latgé3and Joan Bennett4
1University of Manchester, UK; 2University of Sheffield, UK; 3Institut Pasteur, France; 4Tulane University, USA.

We wish to canvass opinion about the Aspergillus fumigatus genome sequencing project that has just been initiated. We will be holding planning meetings and seeking collaborations over the next year. We also envisage many aspects of this project involving and affecting experts who work on other Aspergillus species and so we would value your opinions as well. Therefore we would appreciate careful consideration about your requirements and about our proposals (for gene naming, etc) since your responses will determine the nature of future collaborations and our future funding applications. We have provided comments boxes at various points in the questionnaire so that you can give fuller responses if you desire. Alternatively comments can also be emailed directly to any of us. Your details have been requested so that we can contact you if you have expressed an interest in collaborating. However we must emphasize that individual responses will not be singled out.

  1. To what extent do you think the data from the Aspergillus fumigatus genome sequencing project will be useful in your research?

    Essential Very Useful Useful Occasionally useful No use

  2. How do you envisage using the data from the Aspergillus fumigatus genome sequencing project?

    Please tick all the relevant boxes

    1. to identify A. nidulans and other fungal homologues
    2. to continue your study of specific areas of the biology of Aspergillus species
    3. to identify potential pathogenicity factors (animal or plant)
    4. to identify potential diagnostic markers or immunodominant antigens
    5. to identify potential enzymes useful in industry
    6. to identify potential drug targets
    7. to design transcriptome studies
    8. to identify proteins in proteome studies
    9. to carry out comparative and evolutionary studies
    10. to study genome organisation
    11. any other suggestions?

  3. What information from this project would be very useful / useful for your research?

    Please select one column for each section

      Very Useful Useful No Use  
    a) mapping and contig details for the BAC clones
    b) the end-sequence (~500 bp) of the BAC clones
    c) the DNA sequence of individual BAC clones
    d) the DNA sequence of completed contigs and chromosomes
    e) identified ORFs with blast and protein motif searches
    f) identified ORFs with searches as in e) and with comments from experts
    g) identified ORFs with searches as in e) and which incorporate experimentally derived biological data from A. fumigatus (in a manner similar to the YPD database)
    h) identified ORFs with searches as in e) and which incorporate biological data from homologous genes in other Aspergillus species
    i) data about other DNA sequences: e.g. promoters, centromeres, repetitive elements
    j) is there any other data you would like to be made available from this project?

    If this survey shows that there is demand for more comprehensive annotation as suggested in f), g) and h), our current proposal is seek funding for full-time annotators who will co-ordinate data entry and seek advice from the relevant experts. Our current thinking is that a database that covers all the Aspergilli will be most useful. Do you agree?: YES NO

    Any comments:

    If you agree that such a database will be useful, would you be willing to provide expert opinion?: YES NO

    If YES, please indicate your broad areas of expertise from the following list (based on the MIPS functional catalogue for yeast)

    Metabolism
    Energy generation
    Cell growth, cell division and DNA synthesis
    Transcription
    Protein synthesis
    Protein destination
    Transport facilitation
    Intracellular transport
    Cellular biogenesis
    Cellular communication/signal transduction
    Cell rescue, defence, cell death and ageing
    Ionic homeostasis
    Cellular organization

  4. We propose that there should be a standardised approach to the naming of A. fumigatus genes and proteins. However, the standardised name would only be applied to those genes on which some biology has been done within the Aspergilli. Open reading frames which only have a significant hit to a yeast gene for instance would simply be coded in the normal manner for genome sequencing projects.

    a) Do you think that there should be a standardised approach to the naming of genes in A. fumigatus?

    YES NO
    If NO, please click here to continue with question 5.

    b) If YES, which option do you prefer?

    1) A. nidulans naming convention with orthologues in both species assigned the same name: click here for a description.
    2) S. cerevisiae naming convention: click here for a description.

    If you do not want to answer further questions about nomenclature, click here to move onto question 5.

    c) The use of species prefixes: which option do you prefer?
    Option 1) A species prefix would only be used when it is required to prevent confusion i.e. when two species are being compared within a discussion.
    Option 2) A species prefix would be used at all times (e.g. AfucatB and AnicatB).

    d) Choosing names for genes
    We propose the following:

    1) that a standardised list of known gene names be maintained as part of the genome sequencing project (using for instance J. Clutterbuck's list of A. nidulans genetic loci as a starting point)

    2) if an orthologous gene has already been characterised in another Aspergillus species, then the same name should be adopted

    3) if an orthologous gene has only been identified in N. crassa or S. cerevisiae (same function and high level of identity) and the agreement is to use the A. nidulans convention, then the number is transcribed into the equivalent letter e.g. ERG11 becomes ergK.

    4) if different names have already been assigned to the same gene, gene family or orthologue in another Aspergillus species, then the relevant researchers should be contacted to see if a consensus can be established.

    5) if no consensus is possible or if there are other conflicts (for instance the N. crassa and yeast orthologues have different names), then a standard name should be decided upon by a suitable committee.

    Do you agree with the above points YES NO
    Point 1)
    Point 2)
    Point 3)
    Point 4)
    Point 5)
    Any comments?

  5. Do you want other genome-wide studies to be carried out on A. fumigatus?

    YES NO   YES NO
    Transcriptome studies: would you wish to participate?
        what conditions do you think should be studied?
    Proteome studies: would you wish to participate?
    Karyotype studies: would you wish to participate?

  6. a)Would you be willing to provide us with probes for hybridisation work with the BAC library?

    YES NO

    b) Would you want membranes to be available for hybridisation studies?

    YES NO

    (We already plan to make the strain and BAC library clones readily available for a nominal charge to cover packing and delivery costs).

  7. The pilot project will establish the level of synteny between A. fumigatus and A. nidulans by sequencing a 1 Mb region containing loci from chromosome VIII of A. nidulans.

    Do you think equivalent regions in A. fumigatus that have already been sequenced in A. nidulans should be sequenced FIRST or LAST?

  8. Any general comments would be welcome:

  9. Please alert other colleagues about this questionnaire by entering their email addresses (on separate lines) in the box below.

PERSONAL DETAILS  
Title
Name
Position
Institution
E-mail address
 
Michael Anderson

Last modified: Tue May 23 14:11:20 BST 2000

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