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Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.

Publication ,  Journal Article
Leung, W; Shaffer, CD; Reed, LK; Smith, ST; Barshop, W; Dirkes, W; Dothager, M; Lee, P; Wong, J; Xiong, D; Yuan, H; Bedard, JEJ; Machone, JF ...
Published in: G3 (Bethesda)
March 4, 2015

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 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 (~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.

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Published In

G3 (Bethesda)

DOI

EISSN

2160-1836

Publication Date

March 4, 2015

Volume

5

Issue

5

Start / End Page

719 / 740

Location

England

Related Subject Headings

  • Species Specificity
  • Selection, Genetic
  • Repetitive Sequences, Nucleic Acid
  • Polytene Chromosomes
  • Molecular Sequence Annotation
  • Introns
  • Heterochromatin
  • Genomics
  • Genome
  • Gene Rearrangement
 

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Leung, W., Shaffer, C. D., Reed, L. K., Smith, S. T., Barshop, W., Dirkes, W., … Aso, S. (2015). Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. G3 (Bethesda), 5(5), 719–740. https://doi.org/10.1534/g3.114.015966
Leung, Wilson, Christopher D. Shaffer, Laura K. Reed, Sheryl T. Smith, William Barshop, William Dirkes, Matthew Dothager, et al. “Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.G3 (Bethesda) 5, no. 5 (March 4, 2015): 719–40. https://doi.org/10.1534/g3.114.015966.
Leung W, Shaffer CD, Reed LK, Smith ST, Barshop W, Dirkes W, et al. Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. G3 (Bethesda). 2015 Mar 4;5(5):719–40.
Leung, Wilson, et al. “Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.G3 (Bethesda), vol. 5, no. 5, Mar. 2015, pp. 719–40. Pubmed, doi:10.1534/g3.114.015966.
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R, Tirasawasdichai T, Undem B, Urick D, Vondy K, Yarrington B, Eckdahl TT, Poet JL, Allen AB, Anderson JE, Barnett JM, Baumgardner JS, Brown AD, Carney JE, Chavez RA, Christgen SL, Christie JS, Clary AN, Conn MA, Cooper KM, Crowley MJ, Crowley ST, Doty JS, Dow BA, Edwards CR, Elder DD, Fanning JP, Janssen BM, Lambright AK, Lane CE, Limle AB, Mazur T, McCracken MR, McDonough AM, Melton AD, Minnick PJ, Musick AE, Newhart WH, Noynaert JW, Ogden BJ, Sandusky MW, Schmuecker SM, Shipman AL, Smith AL, Thomsen KM, Unzicker MR, Vernon WB, Winn WW, Woyski DS, Zhu X, Du C, Ament C, Aso S. Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. G3 (Bethesda). 2015 Mar 4;5(5):719–740.

Published In

G3 (Bethesda)

DOI

EISSN

2160-1836

Publication Date

March 4, 2015

Volume

5

Issue

5

Start / End Page

719 / 740

Location

England

Related Subject Headings

  • Species Specificity
  • Selection, Genetic
  • Repetitive Sequences, Nucleic Acid
  • Polytene Chromosomes
  • Molecular Sequence Annotation
  • Introns
  • Heterochromatin
  • Genomics
  • Genome
  • Gene Rearrangement