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

Abstract

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...

Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes

“…Synpipe (Bhutkar et al 2006) output helped to assign assembly scaffolds to one of six Muller elements and join contiguous scaffolds together. The inferred ordered scaffolds were largely 1658 A. Bhutkar et al consistent with the genetic and physical map data (Schaeffer et al 2008). The assembled and ordered scaffolds provided a unique opportunity to study how gene order changes among species of Drosophila by the processes of inversion and transposition, using the study of adjacency information at conserved linkage breakpoints.…”

“…Synpipe accommodates for contig and scaffold gaps in the assembly by identifying homologous elements that might either fall in unsequenced assembly gaps or lie on the edges of sequenced segments or on small assembly fragments. The resulting Synpipe Drosophila data set has been used for breakpoint analysis, a comparative study of chromosomal rearrangements between species, multispecies alignment and orthology refinement, and for mapping and orienting scaffolds onto the Drosophila Muller elements or chromosome arms (Schaeffer et al 2008).One protein isoform, that with the 59-most translation start site annotation, was chosen for each predicted gene in the reference set. Syntenic blocks were computed as segments of the assembly where orthologs shared the gene order of the reference species while allowing for gaps and localized scrambling due to micro-inversions.…”

“…These scaffold assignments were used in conjunction with synteny information to infer scaffold order and orientation along chromosome arms in a candidate assembly. This information supplemented experimental analysis using known markers, especially for the order and orientation of small scaffolds without markers (Schaeffer et al 2008).Analysis of syntenic block boundaries: The breakpoints between identified syntenic blocks harbor information about the past inversion history between two species. We define a breakpoint as the nucleotide sequence between two conserved linkage blocks whose adjacent genes are not adjacent in the reference species.…”

“…For example, the four species of the melanogaster subgroup have an average of ,4 such cases compared to D. grimshawi's 351 and D. willistoni's 383 same-arm singletons. Between 50 and 75% of the genome assembly sequence mapped to various Muller elements (Schaeffer et al 2008) in each species was inferred to be in syntenic segments (Table 1).Muller element dot plots using synteny data show phylogenetic correspondence of syntenic blocks (Figure 5). In addition to the D. melanogaster protein set, we used the D. virilis GLEAN-R consensus annotation protein set (Drosophila 12 Genomes Consortium 2007) (rana.lbl.gov/drosophila) as an additional reference set to undertake synteny analysis.…”

A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints

“…Cytological studies as well as comparative studies of the genome sequences from related species revealed that genome reorganization is widespread among taxa (for example, Krimbas and Powell, 1992;Newman et al, 2005;Clark et al, 2007;Ferguson-Smith and Trifonov, 2007;Schaeffer et al, 2008). Structural variation ranging from chromosome fusions to paracentric inversions underlies the detected reorganization.…”