sees the announcement
in Nature by the Drosophila 12
Genomes Consortium of a further 10 drosophilid genome sequences, which were
the talk of the 48th Annual Drosophila
Research Conference earlier this year.
BioMed Central’s journals are publishing seven open
access companion papers analyzing these genome sequences. The papers in Genome Biology, BMC Genomics, BMC Evolutionary Biology and BMC Bioinformatics span a wide range of topics, including genome-wide surveys
of RNAs, codon usage, comparative genomics of gene families and the evolution
of gene order and sequences.
The
sequencing of the Drosophila
melanogaster genome at the turn of the millennium was a landmark in
genome research, acting as a stepping stone to
the human genome,
and furthering understanding of this
favourite model organism. The publication of the Drosophila
pseudoobscura genome built
upon this. As the Drosophila genus has over 2,000 known species,
there is enormous scope in sequencing further members of this genus to study
the molecular evolution of closely related genomes.
D. simulans and D. yakuba
were sequenced by the Washington University Genome Center, D. erecta, D.
ananassae, D. virilis, D. mojavensis and D. grimshawi were
sequenced by Agencourt, Inc., D. willistoni was sequenced by the J.
Craig Venter Institute, and D. persimilis and D. sechellia were
sequenced by the Broad Institute.
Among the articles published by BioMed Central, a
trio of papers studies global genomic patterns, looking at codon usage, sequence evolution and the evolution of gene order and
chromosome rearrangements.
Two papers study the
conservation of sequence motifs to uncover novel microRNAs and other non-coding RNAs.
On a smaller scale these
sequences allow comparative studies of the evolution of gene families, and two
papers analyze oxidative
phosphorylation genes and the Odorant-Binding Protein family.
The addition of these 10 genomes to the roster of
completed genomes is a further milestone in comparative genomics. As
demonstrated by these companion studies, these sequences, along with the
already well-annotated genome of Drosophila melanogaster, are an
extremely useful tool in exploring speciation, evolution and development, and
should be indispensable for biologists.
- BMC Biology is five years old - 16th December 2008
- Hidden species present conservation challenge; a new Journal of Biology minireview - 24th December 2007
- Hot paper in BMC Bioinformatics - 10th December 2007
While on the surface this seems like an important, intriguing and interesting link, would it not be more helpful if there was a concise listing of the seven abovementioned papers in BMC stable?
The seven articles that analyse the 12 drosophilid genomes are:
Viera FG, Sanchez-Gracia A, Rozas J: Comparative genomic analysis of the Odorant-Binding Protein family in 12 Drosophila genomes: Purifying selection and birth-and-death evolution. Genome Biology 2007, 8:R235
Bhutkar A, Gelbart WM, Smith TF: Inferring genome-scale rearrangement phylogeny and ancestral gene order: A Drosophila case study. Genome Biol 2007, 8:R236
Gu J, Fu H, Zhang X, Li Y: Identifications of conserved 7-mers in 3-UTRs and microRNAs in Drosophila. BMC Bioinformatics 2007, 8:432
Porcelli D, Barsanti P, Pesole G, Caggese C: The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates. BMC Evolutionary Biology 2007, 7:215
Vicario S, Moriyama EN, Powell JR: Codon usage in twelve species of Drosophila. BMC Evol Biol 2007, 7:226
Rose D, Hackermueller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ: Computational RNomics of Drosophilids. BMC Genomics 2007, 8:406
Gallach M, Arnau V, Marin I: Global patterns of sequence evolution in Drosophila. BMC Genomics 2007, 8:408