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Genome survey sequencing of giraffe

ABSTRACT: Multi-locus Analyses Reveal Four Giraffe Species Instead of One

PROVIDER: PRJEB12634 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1248124_1.fastq.gz	Fastqsanger.gz
	ERR1248124_2.fastq.gz	Fastqsanger.gz

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Project description:The current study was designed to examine the potential role of environmental epigenetics (DNA methylation) in the phenotypic variation between two species of giraffe and a related species okapi (Okapi johnstoni). The Angolan giraffe (Giraffa giraffa angolensis), subspecies of the southern giraffe (G. giraffa), has a longer neck, and is more muscular and larger in size than the Kordofan giraffe (Giraffa camelopardalis antiquorum), subspecies of the northern giraffe (G. camelopardalis). Epigenetic changes generally have orders of magnitude higher frequency compared to genetic mutations and have been shown to regulate physiological traits in all species examined, from insects to humans. Observations obtained identify differences in the DNA methylation between the two giraffe species. The related okapi (Okapi johnstoni) is also epigenetically distinct from the giraffes. A role for environmental epigenetics in the speciation of giraffes is suggested and supporting data presented. Although genetic mutation change will also have a role, it occurs less frequently than epigenetic change. Genetic single nucleotide polymorphisms (SNPs) were found to have significantly lower frequency than epigenetic differences. Conclusions that environmental induced change in epigenetics will have a significant role in the evolution and speciation of these giraffes is consistent to the observations made in other species such as Darwin’s finches. Observations further support the Unified Theory of Evolution and Extended Evolutionary Synthesis, which integrates neo-Lamarckian and neo-Darwinian concepts.

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Project description:The aim of our study was to characterize the genotypic and phenotypic extent of multi-locus imprinting disturbances. Therefore, we analyzed the DNA methylation pattern of 37 individuals with different DNA methylation disturbances. Of these 37 individuals 17 were previously diagnosed with a multi-locus methylation disturbance (MLID) and the remaing 20 were diagnosed with a typical single locus imprinting disorder (SLID). We compared the DNA methylation of these 37 individuals to the DNA methylation of 38 evaluable individuals born small for gestational age. Our analysis revealed 21/37 individuals with a multi-locus methylation disturbances, characterzied by an aberrant DNA methylation in more than one imprintend gene region. Validation analyses were performed by bisulfite-pyrosequencing in the two imprinted gene regions ZDBF2 and FAM50B. Our analyses revealed each one patient previously diagnosed with Temple- and Angelman syndrome to have MLID. Furthermore, we showed that many of the aberrantly methylated imprinted gene regions in patients with MLID are not associated with the so far known typical imprinting disorders.

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