Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Chromosomal rearrangements as a source of new gene formation in
  Drosophila yakuba   The origins of new genes are among the most fundamental questions in
evolutionary biology. Our understanding of the ways that new genetic material
appears and how that genetic material shapes population variation remains
incomplete. De novo genes and duplicate genes are a key source of new genetic
material on which selection acts. To better understand the origins of these new
gene sequences, we explored the ways that structural variation might alter
expression patterns and form novel transcripts. We provide evidence that
chromosomal rearrangements are a source of novel genetic variation that
facilitates the formation of de novo genes in Drosophila. We identify 52 cases
of de novo gene formation created by chromosomal rearrangements in 14 strains
of D. yakuba. These new genes inherit transcription start signals and open
reading frames when the 5' end of existing genes are combined with previously
untranscribed regions. Such new genes would appear with novel peptide
sequences, without the necessity for secondary transitions from non-coding RNA
to protein. This mechanism of new peptide formations contrasts with canonical
theory of de novo gene progression requiring non-coding intermediaries that
must acquire new mutations prior to loss via pseudogenization. Hence, these
mutations offer a means to de novo gene creation and protein sequence formation
in a single mutational step, answering a long standing open question concerning
new gene formation. We further identify gene expression changes to 134 existing
genes, indicating that these mutations can alter gene regulation. Population
variability for chromosomal rearrangements is considerable, with 2368
rearrangements observed across 14 inbred lines. More rearrangements were
identified on the X chromosome than any of the autosomes, suggesting the X is
more susceptible to chromosome alterations.

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The categories of this paper are: alg-geom
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The categories of this paper are: solv-int
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The categories of this paper are: astro-ph
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The categories of this paper are: supr-con
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The categories of this paper are: patt-sol
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The categories of this paper are: chao-dyn
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The categories of this paper are: ao-sci
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The categories of this paper are: math
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The categories of this paper are: funct-an
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The categories of this paper are: dg-ga
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The categories of this paper are: nucl-th
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The categories of this paper are: nucl-ex
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The categories of this paper are: atom-ph
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The categories of this paper are: chem-ph
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The categories of this paper are: mtrl-th
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The categories of this paper are: acc-phys