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Ultraconserved Non-coding DNA Within Diptera and Hymenoptera
Ultraconserved Non-coding DNA Within Diptera and Hymenoptera
- Source :
- G3: Genes|Genomes|Genetics, G3: Genes, Genomes, Genetics, Vol 10, Iss 9, Pp 3015-3024 (2020)
- Publication Year :
- 2020
- Publisher :
- Oxford University Press (OUP), 2020.
-
Abstract
- This study has taken advantage of the availability of the assembled genomic sequence of flies, mosquitos, ants and bees to explore the presence of ultraconserved sequence elements in these phylogenetic groups. We compared non-coding sequences found within and flanking Drosophila developmental genes to homologous sequences in Ceratitis capitata and Musca domestica. Many of the conserved sequence blocks (CSBs) that constitute Drosophila cis-regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca. Also conserved is the position but not necessarily the orientation of many of these ultraconserved CSBs (uCSBs) with respect to flanking genes. Using the mosquito EvoPrint algorithm, we have also identified uCSBs shared among distantly related mosquito species. Side by side comparison of bee and ant EvoPrints of selected developmental genes identify uCSBs shared between these two Hymenoptera, as well as less conserved CSBs in either one or the other taxon but not in both. Analysis of uCSBs in these dipterans and Hymenoptera will lead to a greater understanding of their evolutionary origin and function of their conserved non-coding sequences and aid in discovery of core elements of enhancers. This study applies the phylogenetic footprinting program EvoPrinter to detection of ultraconserved non-coding sequence elements in Diptera, including flies and mosquitos, and Hymenoptera, including ants and bees. EvoPrinter outputs an interspecies comparison as a single sequence in terms of the input reference sequence. Ultraconserved sequences flanking known developmental genes were detected in Ceratitis and Musca when compared with Drosophila species, in Aedes and Culex when compared with Anopheles, and between ants and bees. Our methods are useful in detecting and understanding the core evolutionarily hardened sequences required for gene regulation.
- Subjects :
- animal structures
QH426-470
Software and Data Resources
Phylogenetic footprinting
Conserved sequence
03 medical and health sciences
Ultraconserved non-coding sequences
0302 clinical medicine
Enhancers
Genetics
Animals
Ceratitis
Molecular Biology
Drosophila
Gene
Conserved Sequence
Phylogeny
Genetics (clinical)
030304 developmental biology
0303 health sciences
biology
Phylogenetic tree
Diptera
fungi
DNA
Bees
biology.organism_classification
Hymenoptera
Noncoding DNA
EvoPrinter
Evolutionary biology
030217 neurology & neurosurgery
Reference genome
Subjects
Details
- ISSN :
- 21601836
- Volume :
- 10
- Database :
- OpenAIRE
- Journal :
- G3 Genes|Genomes|Genetics
- Accession number :
- edsair.doi.dedup.....191e64873490f340da0591bb1b83a3cc
- Full Text :
- https://doi.org/10.1534/g3.120.401502