Large-Scale Coding Sequence Change Underlies the Evolution of Postdevelopmental Novelty in Honey Bees Article Swipe
W. Cameron Jasper
,
Timothy A. Linksvayer
,
Joel Atallah
,
Daniel Friedman
,
Joanna C. Chiu
,
Brian R. Johnson
·
YOU?
·
· 2016
· Open Access
·
· DOI: https://doi.org/10.1093/molbev/msw022
YOU?
·
· 2016
· Open Access
·
· DOI: https://doi.org/10.1093/molbev/msw022
During a subsequent analysis of the RNA-Seq data sets in Jasper et al. (2015), we discovered an error in the script we used to generate gene counts.The recommended HTSeq -i option initially did not work with the Apis melliera gff3 file.After examination of the gff3 file, we decided to use "-i Dbxref," as Dbxref seemed to show the same pattern as the recommend identifiers.We checked expression levels for many genes and found that this option worked well.However, in a recent reanalyses of this data, we discovered that this option does not work for all genes and some genes with high expression showed zero expression in our original analyses.To correct this problem, we created a GTF file with the gffread script from Cufflinks for the most recent Apis mellifera gff3 file and reanalyzed our data using STAR with the built-in HTSeq option (--quantMode GeneCounts).None of the conclusions drawn in Jasper et al. ( 2015) change with the new analysis, but expression levels change for many genes.Because researchers may use expression values in later work, we have published corrected gene counts (supplementary table S1, see Supplementary Data online in doi:10.1093/molbev/msu292).We also updated supplementary table S3 as the follow up analysis found many more differentially expressed genes in addition to those we identified in the initial analysis (supplementary table S2, see Supplementary Data
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- Type
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- Language
- en
- Landing Page
- https://doi.org/10.1093/molbev/msw022
- https://academic.oup.com/mbe/article-pdf/33/5/1379/9593371/msw022.pdf
- OA Status
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- Cited By
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- OpenAlex ID
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https://openalex.org/W3173063009Canonical identifier for this work in OpenAlex
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https://doi.org/10.1093/molbev/msw022Digital Object Identifier
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Large-Scale Coding Sequence Change Underlies the Evolution of Postdevelopmental Novelty in Honey BeesWork title
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erratumOpenAlex work type
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enPrimary language
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2016Year of publication
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2016-02-23Full publication date if available
- Authors
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W. Cameron Jasper, Timothy A. Linksvayer, Joel Atallah, Daniel Friedman, Joanna C. Chiu, Brian R. JohnsonList of authors in order
- Landing page
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https://doi.org/10.1093/molbev/msw022Publisher landing page
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https://academic.oup.com/mbe/article-pdf/33/5/1379/9593371/msw022.pdfDirect link to full text PDF
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bronzeOpen access status per OpenAlex
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https://academic.oup.com/mbe/article-pdf/33/5/1379/9593371/msw022.pdfDirect OA link when available
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Biology, Novelty, Honey Bees, Evolutionary biology, Sequence (biology), Scale (ratio), Genetics, Ecology, Cartography, Philosophy, Geography, TheologyTop concepts (fields/topics) attached by OpenAlex
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9Total citation count in OpenAlex
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2022: 1, 2021: 2, 2020: 1, 2019: 1, 2018: 1Per-year citation counts (last 5 years)
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