Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element

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dc.contributor.authorParticipating Students Fac
dc.contributor.otherWashington University (WUSTL)
dc.contributor.otherSaint Joseph's University
dc.contributor.otherIllinois State University
dc.contributor.otherUniversity of Alabama Tuscaloosa
dc.contributor.otherAlbion College
dc.contributor.otherCalifornia Lutheran University
dc.contributor.otherCalifornia Polytechnic State University San Luis Obispo
dc.contributor.otherCalifornia State University Stanislaus
dc.contributor.otherCardinal Stritch University
dc.contributor.otherDuke University
dc.contributor.otherGrand Valley State University
dc.contributor.otherHofstra University
dc.contributor.otherLongwood University
dc.contributor.otherUniversity of North Carolina
dc.contributor.otherNorth Carolina Central University
dc.contributor.otherOberlin College
dc.contributor.otherRochester Institute of Technology
dc.contributor.otherSimmons University
dc.contributor.otherGeorge Washington University
dc.contributor.otherUniversity of Evansville
dc.contributor.otherUniversity of Northern Colorado
dc.contributor.otherUniversity of Puerto Rico
dc.contributor.otherUniversity of Puerto Rico at Cayey
dc.contributor.otherUniversity of the Cumberlands
dc.contributor.otherYork College NY (CUNY)
dc.contributor.otherPennsylvania State University
dc.contributor.otherUniversity of San Diego
dc.contributor.otherNanjing Agricultural University
dc.contributor.otherOhio State University
dc.contributor.otherNationwide Childrens Hospital
dc.contributor.otherResearch Institute at Nationwide Children's Hospital
dc.date.accessioned2023-09-28T22:05:19Z
dc.date.available2023-09-28T22:05:19Z
dc.date.issued2017
dc.description.abstractThe discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (similar to 5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae. Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 59 ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.en_US
dc.format.mediumelectronic
dc.format.mimetypeapplication/pdf
dc.identifier.citationLeung, W., Shaffer, C. D., Chen, E. J., Quisenberry, T. J., Ko, K., Braverman, J. M., Giarla, T. C., Mortimer, N. T., Reed, L. K., Smith, S. T., Robic, S., McCartha, S. R., Perry, D. R., Prescod, L. M., Sheppard, Z. A., Saville, K. J., McClish, A., Morlock, E. A., Sochor, V. R., … Elgin, S. C. R. (2017). Retrotransposons Are the Major Contributors to the Expansion of theDrosophila ananassaeMuller F Element. In G3 Genes|Genomes|Genetics (Vol. 7, Issue 8, pp. 2439–2460). Oxford University Press (OUP). https://doi.org/10.1534/g3.117.040907
dc.identifier.doi10.1534/g3.117.040907
dc.identifier.orcidhttps://orcid.org/0000-0001-7162-7925
dc.identifier.orcidhttps://orcid.org/0000-0002-1789-603X
dc.identifier.orcidhttps://orcid.org/0000-0002-1789-603X
dc.identifier.orcidhttps://orcid.org/0000-0002-6725-8650
dc.identifier.orcidhttps://orcid.org/0000-0002-5176-2510
dc.identifier.orcidhttps://orcid.org/0000-0002-6694-4333
dc.identifier.orcidhttps://orcid.org/0000-0003-2754-4895
dc.identifier.orcidhttps://orcid.org/0000-0003-3787-9445
dc.identifier.orcidhttps://orcid.org/0000-0003-0000-0513
dc.identifier.orcidhttps://orcid.org/0000-0002-7377-0845
dc.identifier.orcidhttps://orcid.org/0000-0002-0799-3549
dc.identifier.orcidhttps://orcid.org/0000-0001-5800-5339
dc.identifier.orcidhttps://orcid.org/0000-0002-8573-1376
dc.identifier.orcidhttps://orcid.org/0000-0003-2686-765X
dc.identifier.orcidhttps://orcid.org/0000-0003-1190-1122
dc.identifier.orcidhttps://orcid.org/0000-0001-9517-2339
dc.identifier.orcidhttps://orcid.org/0000-0001-7818-6552
dc.identifier.orcidhttps://orcid.org/0000-0003-4990-8063
dc.identifier.orcidhttps://orcid.org/0000-0003-3372-9175
dc.identifier.orcidhttps://orcid.org/0000-0001-6622-9922
dc.identifier.orcidhttps://orcid.org/0000-0003-2211-3930
dc.identifier.orcidhttps://orcid.org/0000-0003-0596-3300
dc.identifier.orcidhttps://orcid.org/0000-0003-3219-6266
dc.identifier.orcidhttps://orcid.org/0000-0001-8629-0958
dc.identifier.orcidhttps://orcid.org/0000-0001-6859-3461
dc.identifier.orcidhttps://orcid.org/0000-0002-1480-6107
dc.identifier.orcidhttps://orcid.org/0000-0001-8052-9163
dc.identifier.orcidhttps://orcid.org/0000-0002-7187-3138
dc.identifier.orcidhttps://orcid.org/0000-0002-6592-3741
dc.identifier.urihttps://ir.ua.edu/handle/123456789/12327
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.subjectDrosophila
dc.subjectgenome size
dc.subjectheterochromatin
dc.subjectretrotransposons
dc.subjectWolbachia
dc.subjectCODON USAGE BIAS
dc.subjectGENOME SIZE
dc.subjectTRANSPOSABLE ELEMENTS
dc.subjectHETEROCHROMATIC GENES
dc.subjectPOLYCOMB GROUP
dc.subjectDNA-CONTENT
dc.subjectWOLBACHIA
dc.subjectMELANOGASTER
dc.subjectEVOLUTION
dc.subjectEXPRESSION
dc.subjectGenetics & Heredity
dc.titleRetrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Elementen_US
dc.typeArticle
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