Are all fishes ancient polyploids?

Peer, Yves Van de; Taylor, John S.; Meyer, Axel

doi:10.1007/978-94-010-0263-9_7

Cited by 32 publications

(44 citation statements)

References 52 publications

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“…Evidence for two rounds of genome duplication in stem vertebrates came from a whole-genome analysis of human, mouse, and fugu pufferfish using the urochordate Ciona intestinalis as an outgroup (Dehal and Boore 2005). Analysis of the Tetraodon nigroviridis (green spotted pufferfish) genome and the construction of a dense meiotic map for medaka supported earlier conclusions Postlethwait et al 1998;Woods et al 2000;Postlethwait et al 2002;Taylor et al 2003;Van de Peer et al 2003) that a third genome duplication had occurred in the teleost fish. Analysis of Tetraodon and medaka provided evidence for a 12-chromosome ancestral vertebrate genome by calculating conserved syntenic regions between the fish and human genomes ( Jaillon et al 2004;Naruse et al 2004).…”

mentioning

confidence: 68%

Automated identification of conserved synteny after whole-genome duplication

2009

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An important objective for inferring the evolutionary history of gene families is the determination of orthologies and paralogies. Lineage-specific paralog loss following whole-genome duplication events can cause anciently related homologs to appear in some assays as orthologs. Conserved synteny—the tendency of neighboring genes to retain their relative positions and orders on chromosomes over evolutionary time—can help resolve such errors. Several previous studies examined genome-wide syntenic conservation to infer the contents of ancestral chromosomes and provided insights into the architecture of ancestral genomes, but did not provide methods or tools applicable to the study of the evolution of individual gene families. We developed an automated system to identify conserved syntenic regions in a primary genome using as outgroup a genome that diverged from the investigated lineage before a whole-genome duplication event. The product of this automated analysis, the Synteny Database, allows a user to examine fully or partially assembled genomes. The Synteny Database is optimized for the investigation of individual gene families in multiple lineages and can detect chromosomal inversions and translocations as well as ohnologs (paralogs derived by whole-genome duplication) gone missing. To demonstrate the utility of the system, we present a case study of gene family evolution, investigating the ARNTL gene family in the genomes of Ciona intestinalis, amphioxus, zebrafish, and human.

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confidence: 68%

Automated identification of conserved synteny after whole-genome duplication

2009

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“…A third round of genome duplication (R3 in Fig. 2), also envisioned by Ohno, occurred at the base of the teleost radiation may be 350 Mya (Amores et al, '98;Postlethwait et al, '98;Wittbrodt et al, '98;Meyer and Schartl, '99;Postlethwait et al, 2000;Woods et al, 2000;Taylor et al, 2001;Postlethwait et al, 2002;Taylor et al, 2003;Van de Peer et al, 2003;Christoffels et al, 2004;Jaillon et al, 2004;Koopman et al, 2004;Naruse et al, 2004;Vandepoele et al, 2004;Volff, 2005;Woods et al, 2005). An additional genome duplication event (represented by R4 in Fig.…”

Section: Genome Duplication In Chordate Evolutionmentioning

confidence: 89%

The zebrafish genome in context: ohnologs gone missing

2006

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Some zebrafish genes appear to lack an ortholog in the human genome and researchers often call them ''novel'' genes. The origin of many so-called ''novel'' genes becomes apparent when considered in the context of genome duplication events that occurred during evolution of the phylum Chordata, including two rounds at about the origin of the subphylum Vertebrata (R1 and R2) and one round before the teleost radiation (R3). Ohnologs are paralogs stemming from such genome duplication events, and some zebrafish genes said to be ''novel'' are more appropriately interpreted as ''ohnologs gone missing'', cases in which ohnologs are preserved differentially in different evolutionary lineages. Here we consider ohnologs present in the zebrafish genome but absent from the human genome. Reasonable hypotheses are that lineage-specific loss of ohnologs can play a role in establishing lineage divergence and in the origin of developmental innovations. How does the evolution of ohnologs differ from the evolution of gene duplicates arising from other mechanisms, such as tandem duplication or retrotransposition? To what extent do different major vertebrate lineages or different teleost lineages differ in ohnolog content? What roles do differences in ohnolog content play in the origin of developmental mechanisms that differ among lineages? This review explores these questions.

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“…Whereas knockdown of isl1 produces no phenotype at the arterial pole in zebrafish (de Pater et al, 2009), the Isl1-null mouse has a dramatic arterial and venous pole phenotype (Cai et al, 2003). This suggests non-conservation of Isl1 function in zebrafish heart development or, alternatively, that another gene fulfills the same function but is yet to be recognized as a result of the ancient polyploidy event that took place in teleosts (Semon and Wolfe, 2007;Van de Peer et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

Zebrafish cardiac development requires a conserved secondary heart field

et al. 2011

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SUMMARYThe secondary heart field is a conserved developmental domain in avian and mammalian embryos that contributes myocardium and smooth muscle to the definitive cardiac arterial pole. This field is part of the overall heart field and its myocardial component has been fate mapped from the epiblast to the heart in both mammals and birds. In this study we show that the population that gives rise to the arterial pole of the zebrafish can be traced from the epiblast, is a discrete part of the mesodermal heart field, and contributes myocardium after initial heart tube formation, giving rise to both smooth muscle and myocardium. We also show that Isl1, a transcription factor associated with undifferentiated cells in the secondary heart field in other species, is active in this field. Furthermore, Bmp signaling promotes myocardial differentiation from the arterial pole progenitor population, whereas inhibiting Smad1/5/8 phosphorylation leads to reduced myocardial differentiation with subsequent increased smooth muscle differentiation. Molecular pathways required for secondary heart field development are conserved in teleosts, as we demonstrate that the transcription factor Tbx1 and the Sonic hedgehog pathway are necessary for normal development of the zebrafish arterial pole.

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Are all fishes ancient polyploids?

Cited by 32 publications

References 52 publications

Automated identification of conserved synteny after whole-genome duplication

Automated identification of conserved synteny after whole-genome duplication

The zebrafish genome in context: ohnologs gone missing

Zebrafish cardiac development requires a conserved secondary heart field

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