The Atlas Genome Assembly System

Havlak, Paul; Chen, Rui; Durbin, K. James; Egan, Amy; Ren, Yanru; Song, Xingzhi; Weinstock, George M.; Gibbs, Richard A.

doi:10.1101/gr.2264004

Cited by 145 publications

(105 citation statements)

References 42 publications

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“…We are tempted to conclude that differences in the assembler were responsible for the higher level of fragmentation in D. pseudoobscura. The Freeze 1 assembly of D. pseudoobscura was done with ATLAS (Havlak et al 2004), while the D. persimilis assembly was done as assisted assembly using an ARACHNE assembly of the D. pseudoobscura genome. The D. persimilis assembly appears to be less fragmented through a more aggressive joining of contigs, which led to mis-joins.…”

Section: Discussionmentioning

confidence: 99%

Polytene Chromosomal Maps of 11 Drosophila Species: The Order of Genomic Scaffolds Inferred From Genetic and Physical Maps

et al. 2008

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The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events. O NE of the primary strengths of the genus Drosophila as a model system has been the relative ease of generating detailed cytogenetic maps. Indeed, the first definitive mapping of genes to chromosomes Genetics 179: 1601-1655 ( July 2008) was performed in Drosophila melanogaster (Bridges 1916). The subsequent discovery of polytene chromosomes in the salivary glands in this same species (Painter 1934) and their codification into fine-structure genetic/ cytogenetic maps represents perhaps one of the first forays into ''genomics.'' Polytene maps (Bridges 1935;Lefevre 1976) provided an important genetic tool for mapping genes, for detecting genetic diversity within populations, and for inferring phylogenies among related species (Dobzhansky and Sturtevant 1938;Judd et al. 1972;Ashburner and Lemeunier 1976;Lemeunier and Ashburner 1976). Sturtevant and Tan (1937) laid the groundwork for comparative genomics when they established that genes within the chromosomal arms are conserved or syntenic among species. In an insightful melding of the gene mapping and evolutionary studies, H. J. Muller (1940) proposed that the genomes of Drosophila species were subdivided into a set of homologous elements represented by chromosome arms. What Muller (1940) noted, which was subsequently elaborated on by Sturtevant and Novitski (1941), was that the presumed homologs of identified mutant alleles within a chromosome arm of D. melanogaster were also confined to a single arm in other species within the genus where mapping data were available. Using D. melanogaster as a reference, Muller proposed that each of the five major chromosome arms plus the dot chromosome be given a letter designation (A-F) and that this nomenclature be used to identify equivalent linkage groups within the genus.The an...

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Section: Discussionmentioning

confidence: 99%

Polytene Chromosomal Maps of 11 Drosophila Species: The Order of Genomic Scaffolds Inferred From Genetic and Physical Maps

et al. 2008

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“…DNA sequencing reactions were performed using BigDye version 3.1 (Applied Biosystems), and analyzed on ABI 3700 sequencing machines. These reads were assembled using the Atlas suite of assembly tools (Havlak et al 2004). The Atlas suite identifies relatively small groups of reads that contain sequence overlap, assembles these groups individually, and uses paired-end information to join the resulting contigs into large scaffolds.…”

Section: Sequencing and Assemblymentioning

confidence: 99%

Comparative genome sequencing ofDrosophila pseudoobscura: Chromosomal, gene, andcis-element evolution

Richards¹,

Liu²,

Bettencourt³

et al. 2005

Genome Res.

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478

506

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We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species-but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

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“…Detection of copy-number losses, however, can be caused by a deletion in the test samples, by a gain in the control sample or by a combination of both. To determine whether some of the apparent deletion regions may be due to sequence duplications in the control sample from strain C67BL/6J rather than bona fide deletion in the test samples, we use an oligomer counting approach 3 (Supplementary Methods online) to analyze the copy-number variations across the genome of the C57BL/6J strain. We found that BAC clones showing loss were more frequently (P o 0.0023, w 2 test) located in regions with higher copy number in strain C57BL/6J, suggesting that the reduced copy number in the test strains may not be caused by real deletion.…”

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confidence: 99%