The Aspergillus fumigatus genome sequencing project: December 1999 questionnaire was set up to canvass opinion from the Aspergillus research community about the sequencing project. Two email shots were sent out in December 1999 to approximately 5700 people directing them to the questionnaire on The Aspergillus Web site and as of 04/02/00, there have been 110 replies. Twelve of the responses had to be disregarded either because they were from patients simply expressing support or because the responses were set to the defaults only. Some responses were also incompletely filled in and so it was not always possible to collate data for each section from every reply. This preliminary analysis will review only the salient results from the questionnaire and a complete breakdown of the data will be posted later. Fourteen responses were from industry, including such companies as Eli Lilly, SmithKline Beecham, Bristol-Myers Squibb, Genome Therapeutics, Paradigm Genetics, Novartis, Cereon Genomics and Novo Nordisk. There were 79 responses from the academic and governmental communities with the largest proportion of respondents of professorial status (22 responses; 31%). In section 2 of the questionnaire, we asked the respondents: How do you envisage using the data from the Aspergillus fumigatus genome sequencing project? The table below details the responses to this question. In addition, some respondents said that they would wish to use the data to identify secondary metabolic pathways.
| a) | to identify A. nidulans and other fungal homologues | 59 |
| b) | to continue your study of specific areas of the biology of Aspergillus species | 64 |
| c) | to identify potential pathogenicity factors (animal or plant) | 49 |
| d) | to identify potential diagnostic markers or immunodominant antigens | 30 |
| e) | to identify potential enzymes useful in industry | 30 |
| f) | to identify potential drug targets | 56 |
| g) | to design transcriptome studies | 23 |
| h) | to identify proteins in proteome studies | 32 |
| i) | to carry out comparative and evolutionary studies | 42 |
| j) | to study genome organization | 34 |
In section 3 of the questionnaire, we proposed that we could seek funding to employ full-time annotators who would co-ordinate data entry and seek advice from the relevant experts in order to construct a database which would include experimentally derived biological data about the genes identified during the sequencing project. Eighty of the respondents considered that a database that included data from all the Aspergilli would be most useful and 63 were willing to provide expert opinion (see section below). Only two respondents did not agree. In reply to the questions in section 5, 22 of the respondents expressed a desire to participate in transcriptome studies, 13 expressed a desire to participate in proteome studies and 12 in karyotype studies. In addition, comments boxes were provided throughout the questionnaire. We received several messages supporting the Aspergillus fumigatus genome sequencing project as a whole and specifically the idea of an annotated database containing experimentally derived data for specific genes and from transcriptome analyses as and when these were generated (see below).
In summary, the questionnaire has been useful in showing that the data from the Aspergillus fumigatus genome sequencing project will be used by theAspergillus research community to study many areas of Aspergillus and fungal biology and will in addition be used to initiate functional genome projects in A. fumigatus and other Aspergillus species. Explicitly and by implication, there was support for a centralised data warehouse containing experimentally derived data as well as the sequence which could be used with the appropriate bio-informatics tools to enable this research.
The questionnaire respondents were asked to define their areas of expertise using the MIPS functional classification system for yeast. This classification is listed below along the number of ORFs coding for yeast proteins within the class (given as an indication of the size of the class). The number of people who expressed a desire to help annotate within each class is also listed.
| Class | No of ORFs | No of experts |
|---|---|---|
| Metabolism | 1047 | 25 |
| Energy generation | 247 | 7 |
| Cell growth, cell division and DNA synthesis | 798 | 27 |
| Transcription | 751 | 17 |
| Protein synthesis | 347 | 9 |
| Protein destination | 543 | 7 |
| Transport facilitation | 305 | 7 |
| Intracellular transport | 453 | 8 |
| Cellular biogenesis | 192 | 9 |
| Cellular communication/signal transduction | 128 | 13 |
| Cell rescue, defence, cell death and ageing | 356 | 8 |
| Ionic homeostatis | 121 | 1 |
| Cellular organisation | 2211 | 9 |
Just emphasizing a comparison to other Aspergilli very, very useful and important. I'd be interesting in helping in a project coordinating data from the different Aspergilli.
It will be useful to have a database for all the Aspergilli.
My responses are from an industrial perspective so may be quite different to those of academics. Without well annotated sequence we would not even consider a drug development program in Aspergillus. Therefore I think the sequencing project will ultimately be of clinical benefit by allowing smaller companies to participate in anti-Aspergillus drug development.
I support the annotation, but not being a developmental biologist or a physiologist, I cannot help annotate.
Yes, it would be best to do pan-Aspergillus annotation... Note that, in Saccharomyces cerevisiae, the databases that are now the most popular (SGD and YPD) were set up by groups that were not closely involved in the sequencing project itself... My point is that the tasks of sequencing and database curation can, and probably should, be separated.