title: Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis.
abstract: The distal arm of the fourth ("dot") chromosome of Drosophila melanogaster is unusual in that it exhibits an amalgamation of heterochromatic properties (e.g., dense packaging, late replication) and euchromatic properties (e.g., gene density similar to euchromatic domains, replication during polytenization). To examine the evolution of this unusual domain, we undertook a comparative study by generating high-quality sequence data and manually curating gene models for the dot chromosome of D. virilis (Tucson strain 15010-1051.88). Our analysis shows that the dot chromosomes of D. melanogaster and D. virilis have higher repeat density, larger gene size, lower codon bias, and a higher rate of gene rearrangement compared to a reference euchromatic domain. Analysis of eight "wanderer" genes (present in a euchromatic chromosome arm in one species and on the dot chromosome in the other) shows that their characteristics are similar to other genes in the same domain, which suggests that these characteristics are features of the domain and are not required for these genes to function. Comparison of this strain of D. virilis with the strain sequenced by the Drosophila 12 Genomes Consortium (Tucson strain 15010-1051.87) indicates that most genes on the dot are under weak purifying selection. Collectively, despite the heterochromatin-like properties of this domain, genes on the dot evolve to maintain function while being responsive to changes in their local environment.
authors.affiliation: Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
authors.forename: Wilson
authors.initials: W
authors.lastname: Leung
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Shaffer
authors.forename: Taylor
authors.initials: T
authors.lastname: Cordonnier
authors.forename: Jeannette
authors.initials: J
authors.lastname: Wong
authors.forename: Michelle S
authors.initials: MS
authors.lastname: Itano
authors.forename: Elizabeth E
authors.initials: EE
authors.lastname: Slawson Tempel
authors.forename: Elmer
authors.initials: E
authors.lastname: Kellmann
authors.forename: David Michael
authors.initials: DM
authors.lastname: Desruisseau
authors.forename: Carolyn
authors.initials: C
authors.lastname: Cain
authors.forename: Robert
authors.initials: R
authors.lastname: Carrasquillo
authors.forename: Tien M
authors.initials: TM
authors.lastname: Chusak
authors.forename: Katazyna
authors.initials: K
authors.lastname: Falkowska
authors.forename: Kelli D
authors.initials: KD
authors.lastname: Grim
authors.forename: Rui
authors.initials: R
authors.lastname: Guan
authors.forename: Jacquelyn
authors.initials: J
authors.lastname: Honeybourne
authors.forename: Sana
authors.initials: S
authors.lastname: Khan
authors.forename: Louis
authors.initials: L
authors.lastname: Lo
authors.forename: Rebecca
authors.initials: R
authors.lastname: McGaha
authors.forename: Jevon
authors.initials: J
authors.lastname: Plunkett
authors.forename: Justin M
authors.initials: JM
authors.lastname: Richner
authors.forename: Ryan
authors.initials: R
authors.lastname: Richt
authors.forename: Leah
authors.initials: L
authors.lastname: Sabin
authors.forename: Anita
authors.initials: A
authors.lastname: Shah
authors.forename: Anushree
authors.initials: A
authors.lastname: Sharma
authors.forename: Sonal
authors.initials: S
authors.lastname: Singhal
authors.forename: Fine
authors.initials: F
authors.lastname: Song
authors.forename: Christopher
authors.initials: C
authors.lastname: Swope
authors.forename: Craig B
authors.initials: CB
authors.lastname: Wilen
authors.forename: Jeremy
authors.initials: J
authors.lastname: Buhler
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Sarah C R
authors.initials: SC
authors.lastname: Elgin
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D059006:Chromosomes, Insect / Q000235:genetics*; D004330:Drosophila / Q000145:classification / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D022041:Euchromatin / Q000235:genetics; D019143:Evolution, Molecular; D017344:Genes, Insect / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics*; D006570:Heterochromatin / Q000235:genetics; D054643:INDEL Mutation / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D013045:Species Specificity; D026801:Synteny; D020080:Tandem Repeat Sequences / Q000235:genetics
chemical_list: D029721:Drosophila Proteins; D022041:Euchromatin; D006570:Heterochromatin