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 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.

journal_name

Hereditas

journal_title

Hereditas

authors

Nowling RJ,Behura SK,Halfon MS,Emrich SJ,Duman-Scheel M

doi

10.1186/s41065-021-00172-2

subject

Has Abstract

pub_date

2021-01-28 00:00:00

pages

7

issue

1

eissn

0018-0661

issn

1601-5223

pii

10.1186/s41065-021-00172-2

journal_volume

158

pub_type

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