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

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Leung, Wilson

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Shaffer, Christopher D

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Reed, Laura K

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Smith, Sheryl T

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Barshop, William

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Dirkes, William

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Dothager, Matthew

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Lee, Paul

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Wong, Jeannette

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Xiong, David

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Yuan, Han

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Bedard, James EJ

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Machone, Joshua F

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Patterson, Seantay D

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Price, Amber L

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Robic, Srebrenka

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McCartha, Shannon R

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George, Eunice

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Haltaufderhyde, Kirk

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Haye, Joanna

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Semon, Max

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Serjanov, Dmitri

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Toorie, Anika

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Elgin, Sarah CR

dc.date.accessioned

2021-09-03T12:56:37Z

dc.date.available

2021-09-03T12:56:37Z

dc.date.issued

2015-03-04

dc.date.updated

2021-09-03T12:56:33Z

dc.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 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.

dc.identifier

g3.114.015966

dc.identifier.issn

2160-1836

dc.identifier.issn

2160-1836

dc.identifier.uri

https://hdl.handle.net/10161/23707

dc.language

eng

dc.publisher

Oxford University Press (OUP)

dc.relation.ispartof

G3 (Bethesda, Md.)

dc.relation.isversionof

10.1534/g3.114.015966

dc.subject

Heterochromatin

dc.subject

Animals

dc.subject

Drosophila

dc.subject

Drosophila melanogaster

dc.subject

Drosophila Proteins

dc.subject

DNA Transposable Elements

dc.subject

Codon

dc.subject

Computational Biology

dc.subject

Genomics

dc.subject

Evolution, Molecular

dc.subject

Species Specificity

dc.subject

Gene Rearrangement

dc.subject

Repetitive Sequences, Nucleic Acid

dc.subject

Genome

dc.subject

Introns

dc.subject

Exons

dc.subject

Selection, Genetic

dc.subject

Molecular Sequence Annotation

dc.subject

Polytene Chromosomes

dc.title

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

dc.type

Journal article

duke.contributor.orcid

Spana, Eric P|0000-0002-2057-8278

duke.contributor.orcid

Waldman, Leah|0000-0001-9100-3482

pubs.begin-page

719

pubs.end-page

740

pubs.issue

5

pubs.organisational-group

Trinity College of Arts & Sciences

pubs.organisational-group

Biology

pubs.organisational-group

Duke

pubs.organisational-group

Faculty

pubs.organisational-group

School of Medicine

pubs.organisational-group

Radiology, Musculoskeletal Imaging

pubs.organisational-group

Radiology

pubs.organisational-group

Clinical Science Departments

pubs.publication-status

Published

pubs.volume

5

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