Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
SMC Affiliated Work
1
Status
Faculty
School
School of Science
Department
Biology
Document Type
Article
Publication Date
11-2017
Publication / Conference / Sponsorship
G3: GENES, GENOMES, GENETICS
Description/Abstract
The Muller F element (4.2 Mb, ~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 higher 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% versus 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 (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 versus 8.4-8.8 genes per block), indicating higher rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophilalineage, illuminating the constraints imposed by a heterochromatic milieu.
Keywords
CODON BIAS, EVOLUTION OF HETEROCHROMATIN, GENE SIZE, MELTING CHARACTERISTICS, TRANSPOSONS
Scholarly
yes
DOI
10.1534/g3.114.015966
Volume
7
Issue
11
Disciplines
Biology | Genetics and Genomics
Rights
Open Access journal
Original Citation
Vidya Chandrasekaran (Biology): “Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution,” with Wilson Leung (primary author) and Participating Students and Faulty of the Genomics Education Partnership, in G3 vol. 7 no. 11; Nov. 2017. https://doi.org/10.1534/g3.114.015966
Repository Citation
Leung, Wilson; Chandrasekaran, Vidya; Beck, Christopher; Hatfield, Kristen R.; Herrick, Douglas A.; Khoury, Christopher B.; Lea, Charlotte; Louie, Christopher A.; Lowell, Shannon M.; Reynolds, Thomas J.; Schibler, Jeanine; Scoma, Alexandra H.; Smith-Gee, Maxwell T.; and Tuberty, Sarah. Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution (2017). G3: GENES, GENOMES, GENETICS. 7 (11), 10.1534/g3.114.015966 [article]. https://digitalcommons.stmarys-ca.edu/school-science-faculty-works/41
Comments
Article written with participating students and faculty of the Genomics Education Partnership including the following Saint Mary’s students: Christopher Beck, Kristen R. Hatfield, Douglas A. Herrick, Christopher B. Khoury, Charlotte Lea, Christopher A. Louie, Shannon M. Lowell, Thomas J. Reynolds, Jeanine Schibler, Alexandra H. Scoma, Maxwell T. Smith-Gee, Sarah Tubert.