PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map
Abstract Background The Aedes aegypti mosquito is a threat to human health across the globe. The A. aegypti genome was recently re-sequenced and re-assembled. Due to a combination of long-read PacBio and Hi-C sequencing, the AaegL5 assembly is chromosome complete and significantly improves the assem...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-01-01
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| Series: | Hereditas |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s41065-021-00172-2 |
| _version_ | 1819168994887729152 |
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| author | Ronald J. Nowling Susanta K. Behura Marc S. Halfon Scott J. Emrich Molly Duman-Scheel |
| author_facet | Ronald J. Nowling Susanta K. Behura Marc S. Halfon Scott J. Emrich Molly Duman-Scheel |
| author_sort | Ronald J. Nowling |
| collection | DOAJ |
| description | Abstract Background The Aedes aegypti mosquito is a threat to human health across the globe. The A. aegypti genome was recently re-sequenced and re-assembled. Due to a combination of long-read PacBio and Hi-C sequencing, the AaegL5 assembly is chromosome complete and significantly improves the assembly in key areas such as the M/m sex-determining locus. Release of the updated genome assembly has precipitated the need to reprocess historical functional genomic data sets, including cis-regulatory element (CRE) maps that had previously been generated for A. aegypti. Results We re-processed and re-analyzed the A. aegypti whole embryo FAIRE seq data to create an updated embryonic CRE map for the AaegL5 genome. We validated that the new CRE map recapitulates key features of the original AaegL3 CRE map. Further, we built on the improved assembly in the M/m locus to analyze overlaps of open chromatin regions with genes. To support the validation, we created a new method (PeakMatcher) for matching peaks from the same experimental data set across genome assemblies. Conclusion Use of PeakMatcher software, which is available publicly under an open-source license, facilitated the release of an updated and validated CRE map, which is available through the NIH GEO. These findings demonstrate that PeakMatcher software will be a useful resource for validation and transferring of previous annotations to updated genome assemblies. |
| first_indexed | 2024-12-22T19:12:27Z |
| format | Article |
| id | doaj.art-1cab0454bb4741caa1e773a744b88c68 |
| institution | Directory Open Access Journal |
| issn | 1601-5223 |
| language | English |
| last_indexed | 2024-12-22T19:12:27Z |
| publishDate | 2021-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Hereditas |
| spelling | doaj.art-1cab0454bb4741caa1e773a744b88c682022-12-21T18:15:38ZengBMCHereditas1601-52232021-01-0115811810.1186/s41065-021-00172-2PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element mapRonald J. Nowling0Susanta K. Behura1Marc S. Halfon2Scott J. Emrich3Molly Duman-Scheel4Electrical Engineering and Computer Science, Milwaukee School of EngineeringDivision of Animal Sciences, University of MissouriDepartment of Biochemistry, State University of New York at BuffaloMin H. Kao Department of Electrical Engineering and Computer Science, University of TennesseeDepartment of Medical and Molecular Genetics, Indiana University School of MedicineAbstract Background The Aedes aegypti mosquito is a threat to human health across the globe. The A. aegypti genome was recently re-sequenced and re-assembled. Due to a combination of long-read PacBio and Hi-C sequencing, the AaegL5 assembly is chromosome complete and significantly improves the assembly in key areas such as the M/m sex-determining locus. Release of the updated genome assembly has precipitated the need to reprocess historical functional genomic data sets, including cis-regulatory element (CRE) maps that had previously been generated for A. aegypti. Results We re-processed and re-analyzed the A. aegypti whole embryo FAIRE seq data to create an updated embryonic CRE map for the AaegL5 genome. We validated that the new CRE map recapitulates key features of the original AaegL3 CRE map. Further, we built on the improved assembly in the M/m locus to analyze overlaps of open chromatin regions with genes. To support the validation, we created a new method (PeakMatcher) for matching peaks from the same experimental data set across genome assemblies. Conclusion Use of PeakMatcher software, which is available publicly under an open-source license, facilitated the release of an updated and validated CRE map, which is available through the NIH GEO. These findings demonstrate that PeakMatcher software will be a useful resource for validation and transferring of previous annotations to updated genome assemblies.https://doi.org/10.1186/s41065-021-00172-2Aedes aegyptiAaegL5Functional genomicsCis-regulatory elementsFAIRE-Seq |
| spellingShingle | Ronald J. Nowling Susanta K. Behura Marc S. Halfon Scott J. Emrich Molly Duman-Scheel PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map Hereditas Aedes aegypti AaegL5 Functional genomics Cis-regulatory elements FAIRE-Seq |
| title | PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map |
| title_full | PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map |
| title_fullStr | PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map |
| title_full_unstemmed | PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map |
| title_short | PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map |
| title_sort | peakmatcher facilitates updated aedes aegypti embryonic cis regulatory element map |
| topic | Aedes aegypti AaegL5 Functional genomics Cis-regulatory elements FAIRE-Seq |
| url | https://doi.org/10.1186/s41065-021-00172-2 |
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