ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera
Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq) annotation of regulatory eleme...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2016-09-01
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| Series: | Cell Reports |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124716311068 |
| _version_ | 1819152128039452672 |
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| author | James J. Lewis Karin R.L. van der Burg Anyi Mazo-Vargas Robert D. Reed |
| author_facet | James J. Lewis Karin R.L. van der Burg Anyi Mazo-Vargas Robert D. Reed |
| author_sort | James J. Lewis |
| collection | DOAJ |
| description | Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq) annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution. |
| first_indexed | 2024-12-22T14:44:22Z |
| format | Article |
| id | doaj.art-0541c3c744b541d1bc42e9ccfed89b9e |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-12-22T14:44:22Z |
| publishDate | 2016-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-0541c3c744b541d1bc42e9ccfed89b9e2022-12-21T18:22:28ZengElsevierCell Reports2211-12472016-09-0116112855286310.1016/j.celrep.2016.08.042ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in LepidopteraJames J. Lewis0Karin R.L. van der Burg1Anyi Mazo-Vargas2Robert D. Reed3Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853-7202, USADepartment of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853-7202, USADepartment of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853-7202, USADepartment of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853-7202, USAUncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq) annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution.http://www.sciencedirect.com/science/article/pii/S2211124716311068 |
| spellingShingle | James J. Lewis Karin R.L. van der Burg Anyi Mazo-Vargas Robert D. Reed ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera Cell Reports |
| title | ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera |
| title_full | ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera |
| title_fullStr | ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera |
| title_full_unstemmed | ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera |
| title_short | ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera |
| title_sort | chip seq annotated heliconius erato genome highlights patterns of cis regulatory evolution in lepidoptera |
| url | http://www.sciencedirect.com/science/article/pii/S2211124716311068 |
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