Genomic GC content



Sources: From Holt et al. (2002) and Zdobnov et al. (2002).

Sources: From Holt et al. (2002) and Zdobnov et al. (2002).

not only the sequence of D. melanogaster but also that of Drosophila pseudobscura, and it will cover those of other Drosophilidae when these become available in the future. The web pages of FlyBase provide an enormous amount of information on genetic maps, cytological maps, genes, alleles, gene products, protein function, protein location, gene expression, transposons, transgene constructs, fruit fly stocks, collections, fly anatomy, literature, references, and fruit fly investigators. For transcription profiling the GeneChip® Drosophila Genome 2.0 Array from Affymetrix is often used. This microarray provides comprehensive coverage of the transcribed Drosophila genome using 18880 probe sets, analyzing over 18500 transcripts.

AnoBase is the An. gambiae genomic and biological database ( The site also contains reference material and links to other mosquito resources, as well as current news and conference information. Anobase works in collaboration with Genoscope, the French Government's sequencing centre, who along with Celera Geno-mics were involved in the initial sequencing of the mosquito genome, and several organizations that specialize in research on tropical diseases, such as The Malaria Research and Reference Reagent Resource Center (MR4). Information on the Aedes aegypti sequencing project can be found on the mosquito genomics server through http://

3.3.4 Plant genomes

The plant kingdom is a monophyletic evolutionary lineage, including green algae, mosses, ferns, and seed plants. Genome sequencing up to now has been completed for one representative from the green algae, Chlamydomonas reinhardtii, and three angiosperms, A. thaliana (thale cress), Oryza sativa (rice, two varieties), and Populus trichocarpa (black cottonwood). Many sequencing projects are being planned and genomic databases, for example collections of ESTs, are being developed worldwide. Researchers often organize themselves around a group of related plant species; for example the Legume Genomics network focuses on Medicago truncatula as a model, the Solanaceae Genomics

Network concerns tomato and potato, collaborators in TreeGenes are interested in forest genetics and the genome sequencing of forest trees, the Multinational Brassica Genome Project addresses the various Brassica species, SoyBase focuses on the soybean Glycine max, and BeanGenes addresses Phaseolus and Vigna species, among others.

As noted in Section 2.2 the very large genome sizes of some agriculturally important plants are a serious obstacle for full-genome sequencing (Table 3.8). This is especially valid for species from the family Poaceae (grasses), which includes the cereals (Triticaceae). Still, it is expected that even the genomes of these plants—despite their very large size—will be sequenced eventually. For some plant species commercial microarrays for geneexpression analysis are already available, even though a complete genome assembly and annotation has not yet been conducted. In these cases the microarrays were developed from publicly accessible databases (for example GenBank) complemented by EST sequences submitted by consortium members. Examples are the Affymetrix GeneChip® Soybean Genome Array, which can be used to study gene expression of over 37500 soybean transcripts, and the Affymetrix GeneChip®

Table 3.8 Genome sizes of some agriculturally important crops, in comparison with Arabidopsis

Species Scientific name Genome size


Species Scientific name Genome size


Thale cress

Arabidopsis thaliana

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