Ronald J Nowling1, Susanta K Behura2, Marc S Halfon3, Scott J Emrich4, Molly Duman-Scheel5,6. 1. Electrical Engineering and Computer Science, Milwaukee School of Engineering, 1025 North Broadway, Milwaukee, WI, 53202, USA. nowling@msoe.edu. 2. Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. 3. Department of Biochemistry, State University of New York at Buffalo, NY, 14203, Buffalo, USA. 4. Min H. Kao Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, 37996, USA. 5. Department of Medical and Molecular Genetics, Indiana University School of Medicine, South Bend, IN, 46617, USA. 6. Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.
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.
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.
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Authors: Benjamin J Matthews; Olga Dudchenko; Sarah B Kingan; Sergey Koren; Igor Antoshechkin; Jacob E Crawford; William J Glassford; Margaret Herre; Seth N Redmond; Noah H Rose; Gareth D Weedall; Yang Wu; Sanjit S Batra; Carlos A Brito-Sierra; Steven D Buckingham; Corey L Campbell; Saki Chan; Eric Cox; Benjamin R Evans; Thanyalak Fansiri; Igor Filipović; Albin Fontaine; Andrea Gloria-Soria; Richard Hall; Vinita S Joardar; Andrew K Jones; Raissa G G Kay; Vamsi K Kodali; Joyce Lee; Gareth J Lycett; Sara N Mitchell; Jill Muehling; Michael R Murphy; Arina D Omer; Frederick A Partridge; Paul Peluso; Aviva Presser Aiden; Vidya Ramasamy; Gordana Rašić; Sourav Roy; Karla Saavedra-Rodriguez; Shruti Sharan; Atashi Sharma; Melissa Laird Smith; Joe Turner; Allison M Weakley; Zhilei Zhao; Omar S Akbari; William C Black; Han Cao; Alistair C Darby; Catherine A Hill; J Spencer Johnston; Terence D Murphy; Alexander S Raikhel; David B Sattelle; Igor V Sharakhov; Bradley J White; Li Zhao; Erez Lieberman Aiden; Richard S Mann; Louis Lambrechts; Jeffrey R Powell; Maria V Sharakhova; Zhijian Tu; Hugh M Robertson; Carolyn S McBride; Alex R Hastie; Jonas Korlach; Daniel E Neafsey; Adam M Phillippy; Leslie B Vosshall Journal: Nature Date: 2018-11-14 Impact factor: 49.962
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