Biology Reference
In-Depth Information
Sequencing and analysis of the genome of
D. discoideum
was completed
in 2005.
4
This genome consists of six chromosomes with a total of 34 million
base pairs of DNA. It is predicted to harbor about 13 000 protein-
coding genes — a number comparable with that of the fruit fly,
Drosophila
.
The introns and intergenic regions are usually more than 90% AT-rich, mak-
ing them easily distinguishable from the GC-rich protein-coding regions
and facilitating the prediction of open reading frames (ORFs).
The predicted proteome supports the hypothesis that
Dictyostelium
represents an early branch in the eukaryotic tree of life that diverged after
the split between animals, plants, and fungi, with Dictyostelium and other
amebae more closely related to animals. Therefore, many
Dictyostelium
proteins are more similar to their human orthologs than they are to those
of the yeast
Saccharomyces cerevisiae
.
1.3. The Dictyostelium discoideum Proteome
at DictyBase
dictyBase (dictybase.org), created in June 2003, is the model organism
database (MOD) for D. discoideum
.
5
It houses and maintains the
genome sequence, and integrates biological knowledge obtained from
experimental studies. Currently, 5372 gene models have already been
manually checked and annotated, and 7515 genes have a product
description assigned either manually or automatically, representing 40%
and 60% of the estimated number of genes, respectively.
1.4. The Dictyostelium Annotation Project at UniProt
Among the large number of species contained within UniProtKB, a
subset — targets of large-scale genome sequencing and mapping projects —
has been selected. Dedicated annotation programs have been initiated
around these priority organisms to concentrate annotation efforts on
these species. The Human Proteomics Initiative (HPI) aims to anno-
tate all known human protein sequences and orthologous sequences
from other mammals such as other primates, mouse, rat, cow, pig, and
rabbit. The Plant Proteome Annotation Project (PPAP) focuses on the
annotation of plant-specific proteins with efforts directed primarily
