Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes)

Elgar, Greg; Sandford, Richard; Aparicio, Samuel; Macrae, Alexander D.; Venkatesh, Byrappa; Brenner, Sydney

doi:10.1016/0168-9525(96)10018-4

Cited by 144 publications

(63 citation statements)

References 34 publications

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“…The degree of compaction most probably depends on the degree of AT-richness of the corresponding human chromosomal location (Villard et al, 1998). However, in fETV6, the introns 1 (2.1 kb), 2 (8.1 kb) and 3 (2.3 kb) are much larger than the average size of 150 bp reported for the Fugu genome (Elgar et al, 1996). No major repeated element such as Alu-like and LINE sequences was found in these introns or in the whole fETV6 gene.…”

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confidence: 79%

Comparative analysis of the ETV6 gene in vertebrate genomes from pufferfish to human

Montpetit

Sinnett

2001

Oncogene

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The ETV6 gene encodes an Ets-like transcription factor that is frequently rearranged in leukemias. While some of the functions of ETV6 have been uncovered recently, little is known about the key structural elements involved. Comparative genome analysis may provide novel insights into gene evolution and functions. In this study, we cloned and sequenced the homologue of ETV6 from the compact genome of the pu er®sh Fugu rubripes (fETV6). The genomic structure of the fETV6 gene was investigated by sequence analysis of a contig of genomic clones. The fETV6 gene, composed of eight exons, spans about 15 kb and is 16 times smaller than its human counterpart mainly because of the reduced intron size. Three of the seven introns of fETV are unusually large (more than 2 kb), including the 8.2 kb intron 2. The gene codes for a protein of 465 amino acids that is highly related to its human homologue, exhibiting an overall identity of 58% (72% similarity). To investigate the functional and evolutionary aspects of ETV6, we undertook a comparative analysis of this gene from various vertebrates (human, mouse, chicken, zebra®sh and Fugu). As expected, the PNT and ETS domains were highly conserved, with on average 81 and 95% peptide sequence identity, respectively. In addition, we found several new highly conserved regions within the central section of the protein that are likely to represent further functional or structural domains, which may be associated with the transcription repression capacity of this protein. We also found conserved putative regulatory elements in the promoter as well as in the large intron 2 of fETV6. The information derived from this comparative analysis will serve as the basis for more precise functional studies of ETV6 gene regulation and function. Oncogene (2001) 20, 3437 ± 3442.

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confidence: 79%

Comparative analysis of the ETV6 gene in vertebrate genomes from pufferfish to human

Montpetit

Sinnett

2001

Oncogene

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“…This idea was based on the observation that organism complexity has been increasing together with intron number and size, a possible indication of positive selection. Given the small size of most Fugu intervening sequences (Elgar et al 1996), it has been speculated that not all introns should necessarily be relevant in terms of information content, and the pufferfish was indicated as "an uncluttered system for the identification of and analysis of those introns important for vertebrate gene regu- Simple, simple repeats and low complexity DNA; species-specific, repeated elements specific for either the human or mouse genome; mammalian, mammalian-wide repeated elements; matching, mammalian-wide intersepersed repeats matching in global human-mouse genomic alignments.…”

Section: Discussionmentioning

confidence: 99%

Comparative Analysis of Vertebrate Dystrophin Loci Indicate Intron Gigantism as a Common Feature

Pozzoli

Elgar²,

Cagliani

et al. 2003

Genome Res.

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The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes (pufferfish) genomic DNA corresponding to the complete dystrophin gene (FrDMD) and provide the first report of gene structure and sequence comparison among dystrophin genomic sequences from different vertebrate organisms. Almost all intron positions and phases are conserved between FrDMD and its mammalian counterparts, and the predicted protein product of the Fugu gene displays 55% identity and 71% similarity to human dystrophin. In analogy to the human gene, FrDMD presents several-fold longer than average intronic regions. Analysis of intron sequences of the human and murine genes revealed that they are extremely conserved in size and that a similar fraction of total intron length is represented by repetitive elements; moreover, our data indicate that intron expansion through repeat accumulation in the two orthologs is the result of independent insertional events. The hypothesis that intron length might be functionally relevant to the DMD gene regulation is proposed and substantiated by the finding that dystrophin intron gigantism is common to the three vertebrate genes.

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“…The pufferfishes are a morphologically derived group of teleosts with numerous reductive characteristics, including a lack of pelvic fins, ribs, and lower pharyngeal jaws, a reduced number of vertebrae, and absence of various cranial bones (6)(7)(8)(9). Moreover, members of the family Tetraodontidae possess some of the most concise vertebrate genomes known (10)(11)(12)(13). In the present study, we focused on the southern Asian freshwater pufferfish genus Monotrete and examined embryos of several closely related species (M. abei, M. cochinchinensis, M. leiurus, and M. suvattii) (Fig.…”

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confidence: 99%

Replacing the first-generation dentition in pufferfish with a unique beak

Fraser

Britz

Hall

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Teleost fishes comprise approximately half of all living vertebrates. The extreme range of diversity in teleosts is remarkable, especially, extensive morphological variation in their jaws and dentition. Some of the most unusual dentitions are found among members of the highly derived teleost order Tetraodontiformes, which includes triggerfishes, boxfishes, ocean sunfishes, and pufferfishes. Adult pufferfishes (Tetraodontidae) exhibit a distinctive parrot-like beaked jaw, forming a cutting edge, unlike in any other group of teleosts. Here we show that despite novelty in the structure and development of this "beak," it is initiated by formation of separate first-generation teeth that line the embryonic pufferfish jaw, with timing of development and gene expression patterns conserved from the last common ancestor of osteichthyans. Most of these first-generation larval teeth are lost in development. Continuous tooth replacement proceeds in only four parasymphyseal teeth, as sequentially stacked, multigenerational, jaw-length dentine bands, before development of the functional beak. These data suggest that dental novelties, such as the pufferfish beak, can develop later in ontogeny through modified continuous tooth addition and replacement. We conclude that even highly derived morphological structures like the pufferfish beak form via a conserved developmental bauplan capable of modification during ontogeny by subtle respecification of the developmental module.evolutionary developmental biology | morphological novelty | tooth development | replacement dentition | phenotypic diversity

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Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes)

Cited by 144 publications

References 34 publications

Comparative analysis of the ETV6 gene in vertebrate genomes from pufferfish to human

Comparative analysis of the ETV6 gene in vertebrate genomes from pufferfish to human

Comparative Analysis of Vertebrate Dystrophin Loci Indicate Intron Gigantism as a Common Feature

Replacing the first-generation dentition in pufferfish with a unique beak

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