Zebrafish
            <i>hox</i>
            Clusters and Vertebrate Genome Evolution

Amores, Angel; Force, Allan; Yan, Yi; Joly, Lucille; Amemiya, Chris T.; Fritz, Andreas; Ho, Ruoya; Langeland, James A.; Prince, Victoria; Wang, Yan Ling; Westerfield, Monte; Ekker, Marc; Postlethwait, John H.

doi:10.1126/science.282.5394.1711

Cited by 1,595 publications

(1,251 citation statements)

References 33 publications

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“…In accordance with previous reports, phylogenetic analysis in this study clearly revealed three major groups: mammalian MSTNs, avian MSTNs, and two copies of fish MSTNs (MSTN-1/2), respectively. These results confirm that there is an early genome duplication event prior to the teleost radiation but after the divergence of ray-and lobe-finned fishes [24,25]. The clades MSTN-1a, MSTN-1b, MSTN-2a and MSTN-2b appeared in some fish showed that the additional duplication had occurred more recently than the MSTN-1/2 duplication.…”

Section: Discussionsupporting

confidence: 76%

Molecular characterization of myostatin (MSTN) gene and association analysis with growth traits in the bighead carp (Aristichthys nobilis)

Liu

Tong

2012

Mol Biol Rep

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Myostatin (MSTN) is a member of the transforming growth factor-b superfamily and functions as a negative regulator of skeletal muscle development and growth. In this study, the bighead carp MSTN gene (AnMSTN for short) was cloned and characterized. The 3,769 bp genomic sequence of AnMSTN consisted of three exons and two introns, and the full length cDNA (2,141 bp) of the gene had an open reading frame encoding a polypeptide of 375 amino acids. The deduced amino acid sequence of AnMSTN showed 67.1-98.7 % homology with MSTNs of avian, mammalian and teleostean species. Sequence comparison and phylogenetic analysis confirmed the MSTNs were conserved throughout the vertebrates and AnMSTN belonged to MSNT-1 isoform. AnMSTN was expressed in various tissues with the highest expression in muscle. Two single nucleotide polymorphisms, g.1668T [ C in intron 2 and g.2770C [ A in 3 0 UTR, were identified in AnMSTN by sequencing PCR fragments, and genotyped by SSCP. Association analysis showed that g.2770C [ A genotypes were significantly associated with total length, body length and body weight (P \ 0.01). These results suggest that AnMSTN involves in the regulation of growth, and this polymorphism would be informative for further studies on selective breeding in bighead carp.

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Section: Discussionsupporting

confidence: 76%

Molecular characterization of myostatin (MSTN) gene and association analysis with growth traits in the bighead carp (Aristichthys nobilis)

Liu

Tong

2012

Mol Biol Rep

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“…The number and identity of genes in the most recent common ancestor of bony fish is based on the maximal parsimony reconstruction in [1]. For instance, the ancestor of bony fish has 11 paralog group members in HoxA while zebrafish HoxAa and HoxAb only have a total of 9 paralog groups represented.…”

Section: A Model For the Amount Of Structural Loss Of Pfcsmentioning

confidence: 99%

“…Most notably there is a tendency for gene loss after duplication [1] which can have a direct, "structural" rather than functional, influence on the retention of PFCs. To assess whether the loss of sequence conservation can be explained in its entirety by gene loss we propose a simple probabilistic model for the rate of PFC loss due to gene loss and stochastic resolution of genetic redundancy (structural causes).…”

Section: Introductionmentioning

confidence: 99%

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications

Prohaska

Fried

Flamm

et al. 2004

Molecular Phylogenetics and Evolution

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Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. Since these elements are subject to stabilizing selection they evolve much slower than adjacent non-functional DNA. These so-called phylogenetic footprints can be detected by comparison of the sequences surrounding orthologous genes in different species. In this paper we present a new method and an efficient software tool for the identification of corresponding footprints in long sequences from multiple species. This allows the evolutionary study of the origin and loss of phylogenetic footprints if sufficient number and appropriately placed species are included. We apply this method to the published sequences of HoxA clusters of shark, human, and the duplicated zebrafish and Takifugu clusters as well as the published HoxB cluster sequences. We find that there is a massive loss of sequence conservation in the intergenic region of the HoxA clusters, consistent with the finding in [Chiu et al., PNAS 99, 5492-5497 (2002)]. We further propose a simple model to estimate the loss of sequence conservation that can be attributed to gene loss and other structural reasons. We find that the loss of conservation after cluster duplication is more extensive than expected by this model. This suggests that binding site turnover and/or adaptive modification may also contribute to the loss of sequence conservation. We conclude that this method is suitable for the large scale study of the evolution of (putative) cis-regulatory elements.

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“…These three families are characterized by numerous paralog miRNA genes at dispersed genomic locations and an additional expansion of families in teleosts. This points at a close association of the miRNA expansion with the genome duplications at the root of vertebrate tree [ 261,99] and early in the evolution of the actinopterygian lineage [8].…”

Section: Micrornasmentioning

confidence: 97%

“…In the case of E2 they separated before the advent of the tetrapods; the split between the two E3 groups predates the last common ancestor of the eutherian mammals. The six copies of E3 in the zebrafish apparently arose after the teleost-specific genome duplication [8].…”

Section: Small Nucleolar Rnas (Snornas)mentioning

confidence: 99%

Evolutionary patterns of non-coding RNAs

Bompfünewerer

Flamm

Fried

et al. 2005

Theory in Biosciences

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A plethora of new functions of non-coding RNAs have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and Manuscript January 2005RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this "Modern RNA World" and its components. In this contribution we attempt to provide at least a cursory overview of the diversity of non-coding RNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates, studies of the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution of microRNAs in metazoans, which suggests an explosive increase in the microRNA repertoire in vertebrates. The analysis of the transcription of non-coding RNAs (ncRNAs) suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from introns of a mRNA) can change on evolutionary time scales. The let-7 family demonstrates, that even the mode of transcription (as intron or as exon) can change among paralogous ncRNA.

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Zebrafish hox Clusters and Vertebrate Genome Evolution

Cited by 1,595 publications

References 33 publications

Molecular characterization of myostatin (MSTN) gene and association analysis with growth traits in the bighead carp (Aristichthys nobilis)

Molecular characterization of myostatin (MSTN) gene and association analysis with growth traits in the bighead carp (Aristichthys nobilis)

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications

Evolutionary patterns of non-coding RNAs

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