ORCID Profile
0000-0002-3619-7533
Current Organisations
Wageningen University
,
Wageningen Universiteit
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Publisher: Springer Science and Business Media LLC
Date: 25-01-2016
DOI: 10.1038/NCOMMS10474
Abstract: For over 50 years, the great tit ( Parus major ) has been a model species for research in evolutionary, ecological and behavioural research in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 in iduals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species.
Publisher: Public Library of Science (PLoS)
Date: 07-09-2010
Publisher: Springer Science and Business Media LLC
Date: 11-2012
DOI: 10.1038/NATURE11622
Publisher: Oxford University Press (OUP)
Date: 28-12-2022
DOI: 10.1093/GIGASCIENCE/GIAD051
Abstract: The domesticated turkey (Meleagris gallopavo) is a species of significant agricultural importance and is the second largest contributor, behind broiler chickens, to world poultry meat production. The previous genome is of draft quality and partly based on the chicken (Gallus gallus) genome. A high-quality reference genome of M. gallopavo is essential for turkey genomics and genetics research and the breeding industry. By adopting the trio-binning approach, we were able to assemble a high-quality chromosome-level F1 assembly and 2 parental haplotype assemblies, leveraging long-read technologies and genome-wide chromatin interaction data (Hi-C). From a total of 40 chromosomes (2n = 80), we captured 35 chromosomes in a single scaffold, showing much improved genome completeness and continuity compared to the old assembly build. The 3 assemblies are of higher quality than the previous draft quality assembly and comparable to the chicken assemblies (GRCg7) shown by the largest contig N50 (26.6 Mb) and comparable BUSCO gene set completeness scores (96–97%). Comparative analyses confirm a previously identified large inversion of around 19 Mbp on the Z chromosome not found in other Galliformes. Structural variation between the parent haplotypes was identified, which poses potential new target genes for breeding. We contribute a new high-quality turkey genome at the chromosome level, benefiting turkey genetics and other avian genomics research as well as the turkey breeding industry.
Publisher: Oxford University Press (OUP)
Date: 22-11-2012
No related grants have been discovered for Hendrik-Jan Megens.