The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes)

Imai, Satoshi; Sasaki, Takashi; Shimizu, Atsushi; Asakawa, Shuichi; Hori, Hiroshi; Shimizu, Nobuyoshi

doi:10.1266/ggs.82.135

Cited by 17 publications

(15 citation statements)

References 49 publications

(43 reference statements)

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“…An explanation for this may be found in the evolution of genome size. It has been shown that teleost genomes tend to accumulate most indels in intergenic or intronic regions leading towards large differences in genome size, while synteny of genes is conserved [47]. Thus one may conclude that the ratio of the maxima in the insert size distributions of BAC-clones equals the ratio of genome sizes.…”

Section: Discussionmentioning

confidence: 99%

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

et al. 2010

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BackgroundFood supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model.ResultsEnd sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome.ConclusionsThe BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.

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Section: Discussionmentioning

confidence: 99%

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

et al. 2010

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“…They have a lower percentage of repeated sequences (especially DNA transposons) and shorter intronic sequences. This situation would depend both on a high rate of intron and transposon loss and on a higher level of indels (insertions/ deletions) [Imai et al, 2007;Loh et al, 2008;Noleto et al, 2009;Guo et al, 2012].…”

Section: Deuterostomesmentioning

confidence: 99%

Transposons, Genome Size, and Evolutionary Insights in Animals

Canapa¹,

Barucca

Biscotti³

et al. 2015

Cytogenet Genome Res

135

124

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The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.

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“…In addition, teleost and tetrapod genomes are known to have markedly different transposable elements (TEs); teleost genome contains thousands of copies of several types of retrotransposon that are not present in tetrapod (Aparicio et al 2002). Such TEs are estimated to be responsible for more than 50% of genome-size difference between pufferfishes and medaka (Imai et al 2007). The proliferation and insertion of the TE into new genomic sites is implied to played a role in the evolution of brain development in mammals (Sasaki et al 2008).…”

Section: Genome Evolutionmentioning

confidence: 99%

Teleost fish with specific genome duplication as unique models of vertebrate evolution

Sato

Nishida

2010

Environ Biol Fish

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Whole-genome duplication (WGD) is believed to be one of the major evolutionary events that shaped the genome organization of vertebrates. Here, we review recent research on vertebrate genome evolution, specifically on WGD and its consequences for gene and genome evolution in teleost fishes. Recent genome analyses confirmed that all vertebrates experienced two rounds of WGD early in their evolution, and that teleosts experienced a subsequent additional third-round (3R)-WGD. The 3R-WGD was estimated to have occurred 320-400 million years ago in a teleost ancestor, but after its divergence from a common ancestor with living non-teleost actinopterygians (Bichir, Sturgeon, Bowfin, and Gar) based on the analyses of teleost-specific duplicate genes. This 3R-WGD was confirmed by synteny analysis and ancestral karyotype inference using the genome sequences of Tetraodon and medaka. Most of the tetrapods, on the other hand, have not experienced an additional WGD; however, they have experienced repeated chromosomal rearrangements throughout the whole genome. Therefore, different types of chromosomal events have characterized the genomes of teleosts and tetrapods, respectively. The 3R-WGD is useful to investigate the consequences of WGD because it is an evolutionarily recent WGD and thus teleost genomes retain many more WGD-derived duplicates and "traces" of their evolution. In addition, the remarkable morphological, physiological, and ecological diversity of teleosts may facilitate understanding of macrophenotypic evolution on the basis of genetic/genomic information. We highlight the teleosts with 3R-WGD as unique models for future studies on ecology and evolution taking advantage of emerging genomics technologies and systems biology environments.

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The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes)

Cited by 17 publications

References 49 publications

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

Transposons, Genome Size, and Evolutionary Insights in Animals

Teleost fish with specific genome duplication as unique models of vertebrate evolution

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