The Genome of the Western Clawed Frog
            <i>Xenopus tropicalis</i>

Hellsten, Uffe; Harland, Richard M.; Gilchrist, Michael J.; Hendrix, David A.; Jurka, Jerzy; Kapitonov, Vladimir V.; Ovcharenko, Ivan; Putnam, Nicholas H.; Shu, Shengqiang; Taher, Leila; Blitz, Ira L.; Blumberg, Bruce; Dichmann, Darwin S.; Dubchak, Inna; Amaya, Enrique; Detter, John C.; Fletcher, Russell B.; Gerhard, Daniela S.; Goodstein, David; Graves, Tina; Grigoriev, Igor V.; Grimwood, Jane; Kawashima, Takeshi; Lindquist, Erika; Lucas, Susan; Mead, Paul E.; Mitros, Therese; Ogino, Hitoshi; Ohta, Yuko; Poliakov, Alexander; Pollet, Nicolas; Robert, Jacques; Salamov, Asaf; Sater, Amy K.; Schmutz, Jeremy; Terry, Astrid; Vize, Peter D.; Warren, Wesley C.; Wells, Dan E.; Wills, Andrea E.; Wilson, Richard K.; Zimmerman, Lyle B.; Zorn, Aaron M.; Grainger, Robert M.; Grammer, Timothy C.; Khokha, Mustafa K.; Richardson, Paul M.; Rokhsar, Daniel S.

doi:10.1126/science.1183670

Cited by 701 publications

(701 citation statements)

References 26 publications

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“…As an amphibian model species, the Western clawed frog, Xenopus tropicalis, is a widely used experimental subject for biotechnology, developmental genetics, and comparative immunology (Hellsten et al, 2010). In this study, we proved that intronless and intron-containing type I IFNs coexist in X. tropicalis, supporting our hypothesis that a retroposition event occurred in amphibians, resulting in the generation of intronless type I IFNs, which shared same genomic structure with modern type I IFNs in amniotes.…”

Section: Introductionsupporting

confidence: 74%

Intronless and intron-containing type I IFN genes coexist in amphibian Xenopus tropicalis : Insights into the origin and evolution of type I IFNs in vertebrates

Gan

Chen

Huang

et al. 2017

Developmental & Comparative Immunology

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Section: Introductionsupporting

confidence: 74%

Intronless and intron-containing type I IFN genes coexist in amphibian Xenopus tropicalis : Insights into the origin and evolution of type I IFNs in vertebrates

Gan

Chen

Huang

et al. 2017

Developmental & Comparative Immunology

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“…There are dozens of diverse families and subfamilies as well as nonautonomous elements related to the Harbinger superfamily. Although Harbinger elements are also found in other vertebrates such as fishes and frogs (Kapitonov and Jurka 2004;Hellsten et al 2010), their high level of diversity, as well as their high number in the coelacanth genome is unique (see Supplemental Information 5 for details).…”

Section: Tes In the Coelacanth Genomementioning

confidence: 99%

“…17; International Human Genome Sequencing Consortium 2001; Hillier et al 2004;Mikkelsen et al 2007;Piskurek et al 2009;Hellsten et al 2010; UCSC Genome Bioinformatics, http://genome.ucsc.edu/). Interestingly, a comparison of LINE distribution among vertebrates reveals the loss of diversity of LINE families in tetrapods (Fig.…”

Section: Comparison Of Tes Among Vertebratesmentioning

confidence: 99%

Coelacanth genomes reveal signatures for evolutionary transition from water to land

et al. 2013

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Coelacanths are known as ''living fossils,'' as they show remarkable morphological resemblance to the fossil record and belong to the most primitive lineage of living Sarcopterygii (lobe-finned fishes and tetrapods). Coelacanths may be key to elucidating the tempo and mode of evolution from fish to tetrapods. Here, we report the genome sequences of five coelacanths, including four Latimeria chalumnae individuals (three specimens from Tanzania and one from Comoros) and one L. menadoensis individual from Indonesia. These sequences cover two African breeding populations and two known extant coelacanth species. The genome is~2.74 Gbp and contains a high proportion (~60%) of repetitive elements. The genetic diversity among the individuals was extremely low, suggesting a small population size and/or a slow rate of evolution. We found a substantial number of genes that encode olfactory and pheromone receptors with features characteristic of tetrapod receptors for the detection of airborne ligands. We also found that limb enhancers of bmp7 and gli3, both of which are essential for limb formation, are conserved between coelacanth and tetrapods, but not ray-finned fishes. We expect that some tetrapod-like genes may have existed early in the evolution of primitive Sarcopterygii and were later co-opted to adapt to terrestrial environments. These coelacanth genomes will provide a cornerstone for studies to elucidate how ancestral aquatic vertebrates evolved into terrestrial animals.

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“…DNA methylation of repetitive sequences is a common phenomenon observed in plants, fungi, and mammals (Selker 2004;Schulz et al 2006;Zilberman et al 2007). Almost 35% of the Xenopus genome corresponds to transposable elements, mostly DNA transposons (72% of all transposable elements), which constitute 25% of the genome (Hellsten et al 2010). To gain insight into the nature of DNA methylation in these gene-distant regions and repetitive DNA, the repetitive DNA Fig.…”

Section: Methylation Of Repetitive Elementsmentioning

confidence: 99%

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

Bogdanović

Long²,

Heeringen³

et al. 2011

Genome Res.

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DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated DNA obtained from early Xenopus tropicalis embryos demonstrates that this genome is heavily methylated during blastula and gastrula stages. Although DNA methylation is largely absent from transcriptional start sites marked with histone H3 lysine 4 trimethylation (H3K4me3), we find both promoters and gene bodies of active genes robustly methylated. In contrast, DNA methylation is absent in large H3K27me3 domains, indicating that these two repression pathways have different roles. Comparison with chromatin state maps of human ES cells reveals strong conservation of epigenetic makeup and gene regulation between the two systems. Strikingly, genes that are highly expressed in pluripotent cells and in Xenopus embryos but not in differentiated cells exhibit relatively high DNA methylation. Therefore, we tested the repressive potential of DNA methylation using transient and transgenic approaches and show that methylated promoters are robustly transcribed in blastula-and gastrula-stage embryos, but not in oocytes or late embryos. These findings have implications for reprogramming and the epigenetic regulation of pluripotency and differentiation and suggest a relatively open, pliable chromatin state in early embryos followed by reestablished methylation-dependent transcriptional repression during organogenesis and differentiation.

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The Genome of the Western Clawed Frog Xenopus tropicalis

Cited by 701 publications

References 26 publications

Intronless and intron-containing type I IFN genes coexist in amphibian Xenopus tropicalis : Insights into the origin and evolution of type I IFNs in vertebrates

Intronless and intron-containing type I IFN genes coexist in amphibian Xenopus tropicalis : Insights into the origin and evolution of type I IFNs in vertebrates

Coelacanth genomes reveal signatures for evolutionary transition from water to land

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

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