Dataset Information

The tendency to recreate ancestral CG dinucleotides in the human genome.

ABSTRACT: BACKGROUND: The CG dinucleotides are known to be deficient in the human genome, due to a high mutation rate from 5-methylated CG to TG and its complementary pair CA. Meanwhile, many cellular functions rely on these CG dinucleotides, such as gene expression controlled by cytosine methylation status. Thus, CG dinucleotides that provide essential functional substrates should be retained in genomes. How these two conflicting processes regarding the fate of CG dinucleotides - i.e., high mutation rate destroying CG dinucleotides, vs. functional processes that require their preservation remains an unsolved question. RESULTS: By analyzing the mutation and frequency spectrum of newly derived alleles in the human genome, a tendency towards generating more CGs was observed, which was mainly contributed by an excess number of mutations from CA/TG to CG. Simultaneously, we found a fixation preference for CGs derived from TG/CA rather than CGs generated by other dinucleotides. These tendencies were observed both in intergenic and genic regions. An analysis of Integrated Extended Haplotype Homozygosity provided no evidence of selection for newly derived CGs. CONCLUSIONS: Ancestral CG dinucleotides that were subsequently lost by mutation tend to be recreated in the human genome, as indicated by a biased mutation and fixation pattern favoring new CGs that derived from TG/CA.

SUBMITTER: Li M

PROVIDER: S-EPMC3025853 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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The tendency to recreate ancestral CG dinucleotides in the human genome.

Li Mingkun M Chen Su-Shing SS

BMC evolutionary biology 20110105

<h4>Background</h4>The CG dinucleotides are known to be deficient in the human genome, due to a high mutation rate from 5-methylated CG to TG and its complementary pair CA. Meanwhile, many cellular functions rely on these CG dinucleotides, such as gene expression controlled by cytosine methylation status. Thus, CG dinucleotides that provide essential functional substrates should be retained in genomes. How these two conflicting processes regarding the fate of CG dinucleotides - i.e., high mutati ...[more]

PMID: 21208429

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Project description:BackgroundTraditionally, the evolution of terrestrial reproduction in anurans from ancestors that bred in water has been accepted in the literature. Still, the existence of intermediate stages of water dependency, such as species that lay eggs close to water (e.g., in burrows) instead of in bodies of water, supports the hypothesis of an ordered and gradual evolution in the direction of a more terrestrial form of reproduction. However, this conventional view has recently been challenged for some anurans groups. Leptodactylinae frogs are a remarkable example of anurans with an outstanding diversity in terms of reproductive features, with distinct water dependency among lineages. Here, we tested the hypothesis of a gradual and ordered tendency towards terrestriality in Leptodactylinae, including the existence of obligatory intermediate stages, such as semi-terrestrial reproductive strategies. We also addressed the association between reproductive modes and the morphological and ecological features.ResultsAn ancestral reconstruction analysis indicated that even though shifts from aquatic to terrestrial breeding occurred throughout the history of Leptodactylus and Adenomera, shifts from terrestrial to aquatic reproduction happened at almost the same frequency. Our results also demonstrated that reproductive modes for semi-terrestrial tadpoles were not necessarily an intermediate form between aquatic and terrestrial breeds. Correlations among reproductive modes and other life-history traits suggested that tadpole environment, clutch size, nuptial spines, and egg pigmentation were co-evolving and driven by water dependency.ConclusionsOur results found no evidence of evolutionary tendencies toward terrestriality in Leptodactylinae. We found reversals from terrestrial to aquatic tadpole development and no evidence of obligatory intermediate stages, such as semi-terrestrial reproductive strategies. We also found correlations between reproductive modes and other life-history traits driven by water dependence. Aquatic reproductive modes are associated with higher clutch sizes, lentic waters, and the presence of nuptial spines and egg pigmentation.

Dataset Information

The tendency to recreate ancestral CG dinucleotides in the human genome.

Publications

The tendency to recreate ancestral CG dinucleotides in the human genome.

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