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The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes.

ABSTRACT: BACKGROUND:Whole genome sequences have allowed us to have an overview of the evolution of gene repertoires. The target of the present study, the TGFbeta superfamily, contains many genes involved in vertebrate development, and provides an ideal system to explore the relationships between evolution of gene repertoires and that of developmental programs. RESULTS:As a result of a bioinformatic survey of sequenced vertebrate genomes, we identified an uncharacterized member of the TGFbeta superfamily, designated bmp16, which is confined to teleost fish species. Our molecular phylogenetic study revealed a high affinity of bmp16 to the Bmp2/4 subfamily. Importantly, further analyses based on the maximum-likelihood method unambiguously ruled out the possibility that this teleost-specific gene is a product of teleost-specific genome duplication. This suggests that the absence of a bmp16 ortholog in tetrapods is due to a secondary loss. In situ hybridization showed embryonic expression of the zebrafish bmp16 in the developing swim bladder, heart, tail bud, and ectoderm of pectoral and median fin folds in pharyngula stages, as well as gut-associated expression in 5-day embryos. CONCLUSION:Comparisons of expression patterns revealed (1) the redundancy of bmp16 expression with its homologs in presumably plesiomorphic expression domains, such as the fin fold, heart, and tail bud, which might have permitted its loss in the tetrapod lineage, and (2) the loss of craniofacial expression and gain of swim bladder expression of bmp16 after the gene duplication between Bmp2, -4 and -16. Our findings highlight the importance of documenting secondary changes of gene repertoires and expression patterns in other gene families.

SUBMITTER: Feiner N

PROVIDER: S-EPMC2801517 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes.

Feiner Nathalie N Begemann Gerrit G Renz Adina J AJ Meyer Axel A Kuraku Shigehiro S

BMC evolutionary biology 20091201

<h4>Background</h4>Whole genome sequences have allowed us to have an overview of the evolution of gene repertoires. The target of the present study, the TGFbeta superfamily, contains many genes involved in vertebrate development, and provides an ideal system to explore the relationships between evolution of gene repertoires and that of developmental programs.<h4>Results</h4>As a result of a bioinformatic survey of sequenced vertebrate genomes, we identified an uncharacterized member of the TGFbe ...[more]

PMID: 19951429

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Project description:BackgroundTeleost fish genome size has been repeatedly demonstrated to positively correlate with the proportion of transposable elements (TEs). This finding might have far-reaching implications for our understanding of the evolution of nucleotide composition across vertebrates. Genomes of fish and amphibians are GC homogenous, with non-teleost gars being the single exception identified to date, whereas birds and mammals are AT/GC heterogeneous. The exact reason for this phenomenon remains controversial. Since TEs make up significant proportions of genomes and can quickly accumulate across genomes, they can potentially influence the host genome with their own GC content (GC%). However, the GC% of fish TEs has so far been neglected.ResultsThe genomic proportion of TEs indeed correlates with genome size, although not as linearly as previously shown with fewer genomes, and GC% negatively correlates with genome size in the 33 fish genome assemblies analysed here (excluding salmonids). GC% of fish TE consensus sequences positively correlates with the corresponding genomic GC% in 29 species tested. Likewise, the GC contents of the entire repetitive vs. non-repetitive genomic fractions correlate positively in 54 fish species in Ensembl. However, among these fish species, there is also a wide variation in GC% between the main groups of TEs. Class II DNA transposons, predominant TEs in fish genomes, are significantly GC-poorer than Class I retrotransposons. The AT/GC heterogeneous gar genome contains fewer Class II TEs, a situation similar to fugu with its extremely compact and also GC-enriched but AT/GC homogenous genome.ConclusionOur results reveal a previously overlooked correlation between GC% of fish genomes and their TEs. This applies to both TE consensus sequences as well as the entire repetitive genomic fraction. On the other hand, there is a wide variation in GC% across fish TE groups. These results raise the question whether GC% of TEs evolves independently of GC% of the host genome or whether it is driven by TE localization in the host genome. Answering these questions will help to understand how genomic GC% is shaped over time. Long-term accumulation of GC-poor(er) Class II DNA transposons might indeed have influenced AT/GC homogenization of fish genomes and requires further investigation.

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The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes.

Publications

The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes.

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