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PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map

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.

Aims and scope

For almost a century, Hereditas has published original cutting-edge research and reviews. As the Official journal of the Mendelian Society of Lund, the journal welcomes research from across all areas of genetics and genomics. Topics of interest include human and medical genetics, animal and plant genetics, microbial genetics, agriculture and bioinformatics. Articles covering novel viral sequences or the use of new technology and software in genomic research are also welcomed.

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Previous content

Hereditas launched with BioMed Central in 2015, transferring from its previous publisher Wiley. All back content is available in the archive.

As a result of the significant disruption that is being caused by the COVID-19 pandemic we are very aware that many researchers will have difficulty in meeting the timelines associated with our peer review process during normal times.  Please do let us know if you need additional time. Our systems will continue to remind you of the original timelines but we intend to be highly flexible at this time.

Editors-in-Chief

Stefan Baumgartner, Lund University
Yongyong Shi, Shanghai Jiao Tong University



Call for Papers: Arthropod Genomics

New Content ItemRecent reductions in sequencing costs and the introduction of new long-read sequencing technologies have led to a resurgence in genome sequencing projects. This abundance of new genome information has facilitated various genetic and genomic studies in a wide variety of species, including in arthropods.

Genome Biology and Hereditas are partnering on a thematic series focused on arthropod genomics. Topics of interest include but are not limited to: gene drive and gene editing in relation to vector or pest control, functional genomics, population genomics, comparative genomes and genetics.  Additionally, wetlab and/or computational techniques that have been developed to overcome the unique challenges of working with arthropods are of interest.

Guest Editor: Scott Geib, USDA ARS

Submission deadline: September 30, 2021

Society information

The Mendelian Society of Lund was founded in 1910 and except for a short break during 1912-1916 has been active ever since. In 1920, the Society started to publish Hereditas, a scientific journal in genetics. In the post-genomic era, the scope of Hereditas has evolved to include any research on genomic analysis.

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