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

Overview of attention for article published in G3: Genes, Genomes, Genetics, May 2015
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Title
Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
Published in
G3: Genes, Genomes, Genetics, May 2015
DOI 10.1534/g3.114.015966
Pubmed ID
Authors

Wilson Leung, Christopher D. Shaffer, Laura K. Reed, Sheryl T. Smith, William Barshop, William Dirkes, Matthew Dothager, Paul Lee, Jeannette Wong, David Xiong, Han Yuan, James E. J. Bedard, Joshua F. Machone, Seantay D. Patterson, Amber L. Price, Bryce A. Turner, Srebrenka Robic, Erin K. Luippold, Shannon R. McCartha, Tezin A. Walji, Chelsea A. Walker, Kenneth Saville, Marita K. Abrams, Andrew R. Armstrong, William Armstrong, Robert J. Bailey, Chelsea R. Barberi, Lauren R. Beck, Amanda L. Blaker, Christopher E. Blunden, Jordan P. Brand, Ethan J. Brock, Dana W. Brooks, Marie Brown, Sarah C. Butzler, Eric M. Clark, Nicole B. Clark, Ashley A. Collins, Rebecca J. Cotteleer, Peterson R. Cullimore, Seth G. Dawson, Carter T. Docking, Sasha L. Dorsett, Grace A. Dougherty, Kaitlyn A. Downey, Andrew P. Drake, Erica K. Earl, Trevor G. Floyd, Joshua D. Forsyth, Jonathan D. Foust, Spencer L. Franchi, James F. Geary, Cynthia K. Hanson, Taylor S. Harding, Cameron B. Harris, Jonathan M. Heckman, Heather L. Holderness, Nicole A. Howey, Dontae A. Jacobs, Elizabeth S. Jewell, Maria Kaisler, Elizabeth A. Karaska, James L. Kehoe, Hannah C. Koaches, Jessica Koehler, Dana Koenig, Alexander J. Kujawski, Jordan E. Kus, Jennifer A. Lammers, Rachel R. Leads, Emily C. Leatherman, Rachel N. Lippert, Gregory S. Messenger, Adam T. Morrow, Victoria Newcomb, Haley J. Plasman, Stephanie J. Potocny, Michelle K. Powers, Rachel M. Reem, Jonathan P. Rennhack, Katherine R. Reynolds, Lyndsey A. Reynolds, Dong K. Rhee, Allyson B. Rivard, Adam J. Ronk, Meghan B. Rooney, Lainey S. Rubin, Luke R. Salbert, Rasleen K. Saluja, Taylor Schauder, Allison R. Schneiter, Robert W. Schulz, Karl E. Smith, Sarah Spencer, Bryant R. Swanson, Melissa A. Tache, Ashley A. Tewilliager, Amanda K. Tilot, Eve VanEck, Matthew M. Villerot, Megan B. Vylonis, David T. Watson, Juliana A. Wurzler, Lauren M. Wysocki, Monica Yalamanchili, Matthew A. Zaborowicz, Julia A. Emerson, Carlos Ortiz, Frederic J. 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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 Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

X Demographics

X Demographics

The data shown below were collected from the profiles of 167 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 259 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 7 3%
Brazil 3 1%
Germany 2 <1%
Italy 1 <1%
South Africa 1 <1%
France 1 <1%
Czechia 1 <1%
India 1 <1%
Singapore 1 <1%
Other 1 <1%
Unknown 240 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 54 21%
Researcher 42 16%
Professor > Associate Professor 24 9%
Student > Bachelor 24 9%
Student > Master 20 8%
Other 65 25%
Unknown 30 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 98 38%
Biochemistry, Genetics and Molecular Biology 50 19%
Medicine and Dentistry 19 7%
Neuroscience 10 4%
Psychology 7 3%
Other 40 15%
Unknown 35 14%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 239. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 21 December 2023.
All research outputs
#158,145
of 25,537,395 outputs
Outputs from G3: Genes, Genomes, Genetics
#8
of 3,436 outputs
Outputs of similar age
#1,595
of 279,274 outputs
Outputs of similar age from G3: Genes, Genomes, Genetics
#2
of 63 outputs
Altmetric has tracked 25,537,395 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 99th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,436 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 7.8. This one has done particularly well, scoring higher than 99% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 279,274 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 99% of its contemporaries.
We're also able to compare this research output to 63 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 98% of its contemporaries.