Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

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dc.contributor.authorParticipating Students Fac Genomic
dc.contributor.otherWashington University (WUSTL)
dc.contributor.otherUniversity of Alabama Tuscaloosa
dc.contributor.otherAlbion College
dc.contributor.otherAmherst College
dc.contributor.otherCalifornia Lutheran University
dc.contributor.otherCalifornia Polytechnic State University San Luis Obispo
dc.contributor.otherCalvin University
dc.contributor.otherCardinal Stritch University
dc.contributor.otherWilliam & Mary
dc.contributor.otherDenison University
dc.contributor.otherDuke University
dc.contributor.otherGeorgetown University
dc.contributor.otherGrand Valley State University
dc.contributor.otherHofstra University
dc.contributor.otherJohnson C Smith University
dc.contributor.otherLongwood University
dc.contributor.otherLoyola Marymount University
dc.contributor.otherMacalester College
dc.contributor.otherMontclair State University
dc.contributor.otherUniversity of North Carolina
dc.contributor.otherNorth Carolina A&T State University
dc.contributor.otherNorth Carolina Central University
dc.contributor.otherOberlin College
dc.contributor.otherClaremont Colleges
dc.contributor.otherPomona College
dc.contributor.otherPrairie View A&M University
dc.contributor.otherSaint Joseph's University
dc.contributor.otherSaint Mary's College of California
dc.contributor.otherSan Francisco State University
dc.contributor.otherSimmons University
dc.contributor.otherCity College of New York (CUNY)
dc.contributor.otherGeorge Washington University
dc.contributor.otherUniversity of California San Diego
dc.contributor.otherUniversity of Evansville
dc.contributor.otherUniversity of Nebraska Lincoln
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dc.contributor.otherUniversity of Puerto Rico
dc.contributor.otherUniversity of Puerto Rico at Cayey
dc.contributor.otherUniversity of Puerto Rico Mayaguez
dc.contributor.otherUniversity Incarnate Word
dc.contributor.otherUniversity of West Florida
dc.contributor.otherUtah Valley University
dc.contributor.otherWebster University
dc.contributor.otherWidener University
dc.contributor.otherWilkes University
dc.contributor.otherWilliam Woods University
dc.contributor.otherWorcester State University
dc.contributor.otherYork College NY (CUNY)
dc.date.accessioned2023-09-28T22:05:24Z
dc.date.available2023-09-28T22:05:24Z
dc.date.issued2015
dc.description.abstractThe Muller F element (4.2 Mb, similar to 80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (similar to 90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.en_US
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dc.identifier.citationLeung, W., Shaffer, C. D., Reed, L. K., Smith, S. T., Barshop, W., Dirkes, W., Dothager, M., Lee, P., Wong, J., Xiong, D., Yuan, H., Bedard, J. E. J., Machone, J. F., Patterson, S. D., Price, A. L., Turner, B. A., Robic, S., Luippold, E. K., McCartha, S. R., … Elgin, S. C. R. (2015). Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution. In G3 Genes|Genomes|Genetics (Vol. 5, Issue 5, pp. 719–740). Oxford University Press (OUP). https://doi.org/10.1534/g3.114.015966
dc.identifier.doi10.1534/g3.114.015966
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dc.identifier.urihttps://ir.ua.edu/handle/123456789/12330
dc.languageEnglish
dc.language.isoen_US
dc.publisherOxford University Press
dc.rights.licenseAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectcodon bias
dc.subjectevolution of heterochromatin
dc.subjectgene size
dc.subjectmelting characteristics
dc.subjecttransposons
dc.subjectCODON USAGE BIAS
dc.subjectDINE-1 TRANSPOSABLE ELEMENTS
dc.subjectRNA INTERFERENCE
dc.subjectHETEROCHROMATIN FORMATION
dc.subjectHIGHLY ABUNDANT
dc.subjectTANDEM REPEATS
dc.subjectDOT CHROMOSOME
dc.subjectMELANOGASTER
dc.subjectDNA
dc.subjectREVEALS
dc.subjectGenetics & Heredity
dc.titleDrosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolutionen_US
dc.typeArticle
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