Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis

Makapedua, Daisy Monica; Barucca, Marco; Forconi, Marikò; Antonucci, N.; Bizzaro, Davide; Amici, Adolfo; Carradori, Maria Rita; Olmo, Ettore; Canapa, Adriana

doi:10.1016/j.margen.2011.04.001

Cited by 13 publications

(16 citation statements)

References 24 publications

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“…3A). These results indicate that the sequences of the exons of HOX cluster genes are probably unique in the coelacanth genome because the genome size estimated from the coverage of those exons was consistent with the size estimated from the weight of nuclear DNA content (~3 Gbp) (Makapedua et al, 2011).…”

Section: Repetitive Elements and Coveragesupporting

confidence: 75%

Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths

Higasa

Nikaido

Saito

et al. 2012

Gene

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Section: Repetitive Elements and Coveragesupporting

confidence: 75%

Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths

Higasa

Nikaido

Saito

et al. 2012

Gene

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“…The teleost (bony fish), which have 5mC and CGIs (Han and Zhao 2008), do not have a bimodal distribution of 8-mers suggesting that CG methylation in these genomes is not mutagenic and the T•G mismatches are repaired to C•G base pair. The bimodal distribution of 8-mers is initially observed in the coelacanth (Amemiya et al 2013) which also contains 5mC (Makapedua et al 2011) and has fewer CGs than expected (Iwasaki et al 2014) suggesting that at this time the efficient repair of T•G mismatch to a C•G base pair was lost (fig. 1 and supplementary fig.…”

Section: Resultsmentioning

confidence: 84%

Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution

Tillo

Vierstra

et al. 2015

Genome Biol Evol

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In mammals, the cytosine in CG dinucleotides is typically methylated producing 5-methylcytosine (5mC), a chemically less stable form of cytosine that can spontaneously deaminate to thymidine resulting in a T•G mismatched base pair. Unlike other eukaryotes that efficiently repair this mismatched base pair back to C•G, in mammals, 5mCG deamination is mutagenic, sometimes producing TG dinucleotides, explaining the depletion of CG dinucleotides in mammalian genomes. It was suggested that new TG dinucleotides generate genetic diversity that may be critical for evolutionary change. We tested this conjecture by examining the DNA sequence properties of regulatory sequences identified by DNase I hypersensitive sites (DHSs) in human and mouse genomes. We hypothesized that the new TG dinucleotides generate transcription factor binding sites (TFBS) that become tissue-specific DHSs (TS-DHSs). We find that 8-mers containing the CG dinucleotide are enriched in DHSs in both species. However, 8-mers containing a TG and no CG dinucleotide are preferentially enriched in TS-DHSs when compared with 8-mers with neither a TG nor a CG dinucleotide. The most enriched 8-mer with a TG and no CG dinucleotide in tissue-specific regulatory regions in both genomes is the AP-1 motif (TGAC/GTCAN), and we find evidence that TG dinucleotides in the AP-1 motif arose from CG dinucleotides. Additional TS-DHS-enriched TFBS containing the TG/CA dinucleotide are the E-Box motif (GCAGCTGC), the NF-1 motif (GGCA—TGCC), and the GR (glucocorticoid receptor) motif (G-ACA—TGT-C). Our results support the suggestion that cytosine methylation is mutagenic in tetrapods producing TG dinucleotides that create TFBS that drive evolution.

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“…Despite the high number of expected transposable elements responsible for the enormous size of the lungfish genomes (Metcalfe et al. 2012; Metcalfe and Casane 2013), which is about 38 fold of the coelacanth genome (Makapedua et al. 2011), transposable elements showed lower expression values in P. annectens than in coelacanths (Biscotti et al.…”

Section: Discussionmentioning

confidence: 99%

The Small Noncoding RNA Processing Machinery of Two Living Fossil Species, Lungfish and Coelacanth, Gives New Insights into the Evolution of the Argonaute Protein Family

Biscotti

Canapa

Forkoni

et al. 2017

Genome Biology and Evolution

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Argonaute (AGO) family proteins play many roles in epigenetic programming, genome rearrangement, mRNA breakdown, inhibition of translation, and transposon silencing. Despite being a hotspot in current scientific research, their evolutionary history is still poorly understood and consequently the identification of evolutionary conserved structural features should also generate useful information for better understanding their functions. We report here for the first time the transcript sets of the two subfamilies, Ago and Piwi, in the West African lungfish Protopterus annectens and in the Indonesian coelacanth Latimeria menadoensis, two key species in the evolutionary lineage leading to tetrapods. The phylogenetic analysis of 142 inferred protein sequences in 22 fully sequenced species and the analysis of microsynteny performed in the major vertebrate lineages indicate an intricate pattern for the evolution of both subfamilies that has been shaped by whole genome duplications and lineage specific gains and losses. The argonaute subfamily was additionally expanded by local gene duplications at the base of the jawed vertebrate lineage. The subfamily of Piwi proteins is involved in several processes such as spermatogenesis, piRNA biogenesis, and transposon repression. Expression assessment of AGO genes and genes coding for proteins involved in small RNA biogenesis suggests a limited activity of the Piwi pathway in lungfish in agreement with the lungfish genome containing mainly old and inactive transposons.

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Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis

Cited by 13 publications

References 24 publications

Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths

Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths

Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution

The Small Noncoding RNA Processing Machinery of Two Living Fossil Species, Lungfish and Coelacanth, Gives New Insights into the Evolution of the Argonaute Protein Family

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