Evolution of genes and genomes on the Drosophila phylogeny

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Abstract

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

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Figure 1: Phylogram of the 12 sequenced species of Drosophila.
Figure 2: Gene models in 12 Drosophila genomes.
Figure 3: Synteny plots for Muller elements B and C with respect to D. melanogaster gene order.
Figure 4: Patterns of constraint and positive selection among GO terms.
Figure 5: Deviations in codon bias from D. melanogaster in 11 Drosophila species.
Figure 6: Substitution rate of site classes within miRNAs.

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Acknowledgements

Agencourt Bioscience Corporation, The Broad Institute of MIT and Harvard and the Washington University Genome Sequencing Center were supported by grants and contracts from the National Human Genome Research Insititute (NHGRI). T.C. Kaufman acknowledges support from the Indian Genomics Initiative.

Author Contributions The laboratory groups of A. G. Clark (including A. M. Larracuente, T. B. Sackton, and N. D. Singh) and Michael B. Eisen (including V. N. Iyer and D. A. Pollard) played the part of coordinating the primary writing and editing of the manuscript with the considerable help of D. R. Smith, C. M. Bergman, W. M. Gelbart, B. Oliver, T. A. Markow, T. C. Kaufman and M. Kellis. D. R. Smith served as primary coordinator for the assemblies. The remaining authors contributed either through their efforts in sequence production, assembly and annotation, or in the analysis of specific topics that served as the focus of more than 40 companion papers.

Author information

Correspondence to Andrew G. Clark or Michael B. Eisen or Douglas R. Smith or Casey M. Bergman or Brian Oliver or Therese A. Markow or Thomas C. Kaufman or Manolis Kellis or William Gelbart or Venky N. Iyer or Daniel A. Pollard or Timothy B. Sackton or Amanda M. Larracuente or Nadia D. Singh or Michael Kleber.

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The author declare no competing financial interests.

Additional information

A list of participants and affiliations appears at the end of the paper.

Supplementary information

Supplementary Information

The file contains all methods for the project as well as further detail on certain sections. Also contains Supplementary Tables 1-10 and 13-20, and Supplementary Figures 1-10 with Legends. This document has a detailed table of contents. (PDF 1381 kb)

Supplementary Table 11

The file contains Supplementary Table 11 which is a list of 44 lineage-specific genes arising in the melanogaster group or some subset of the melanogaster group phylogeny. (XLS 22 kb)

Supplementary Table 12

The file contains Supplementary Table 12 which shows median value of ω, the negative log of the P-value from the test of positive selection and dN for each of the 115 GO (XLS 58 kb)

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