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Spliceosomal introns as tools for genomic and evolutionary analysis.

Irimia M, Roy SW - Nucleic Acids Res. (2008)

Bottom Line: First, we discuss uses of intron length distributions and positions in sequence assembly and annotation, and for improving alignment of homologous regions.Second, we review uses of introns in evolutionary studies, including the utility of introns as indicators of rates of sequence evolution, for inferences about molecular evolution, as signatures of orthology and paralogy, and for estimating rates of nucleotide substitution.We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions.

View Article: PubMed Central - PubMed

Affiliation: Departament de Genètica, Universitat de Barcelona, Barcelona, Spain.

ABSTRACT
Over the past 5 years, the availability of dozens of whole genomic sequences from a wide variety of eukaryotic lineages has revealed a very large amount of information about the dynamics of intron loss and gain through eukaryotic history, as well as the evolution of intron sequences. Implicit in these advances is a great deal of information about the structure and evolution of surrounding sequences. Here, we review the wealth of ways in which structures of spliceosomal introns as well as their conservation and change through evolution may be harnessed for evolutionary and genomic analysis. First, we discuss uses of intron length distributions and positions in sequence assembly and annotation, and for improving alignment of homologous regions. Second, we review uses of introns in evolutionary studies, including the utility of introns as indicators of rates of sequence evolution, for inferences about molecular evolution, as signatures of orthology and paralogy, and for estimating rates of nucleotide substitution. We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions.

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Intron positions are often conserved over long evolutionary times. Protein-level alignments of the translation initiation factor 4A gene (TIF4A) from a variety of metazoan species are shown. Intron positions are indicated by digits corresponding to the phase of the intron relative to the surrounding codons (phases 0, 1 and 2 introns fall before the first, second and third bases of a codon, respectively). Most intron positions are conserved at the exact homologous position and phase over all of animal history within these species, all the way from the placozoan Trichoplax adhaerens to chordates. Abbreviations: Hsa, Homo sapiens; Mmu, Mus musculus; Cin, Ciona intestinalis; Bfl, Branchiostoma floridae; Cap, Capitella sp; Lgi, Lottia gigantea; Nve, Nematostella vectensis; Tad, Trichoplax adhaerens.
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Figure 1: Intron positions are often conserved over long evolutionary times. Protein-level alignments of the translation initiation factor 4A gene (TIF4A) from a variety of metazoan species are shown. Intron positions are indicated by digits corresponding to the phase of the intron relative to the surrounding codons (phases 0, 1 and 2 introns fall before the first, second and third bases of a codon, respectively). Most intron positions are conserved at the exact homologous position and phase over all of animal history within these species, all the way from the placozoan Trichoplax adhaerens to chordates. Abbreviations: Hsa, Homo sapiens; Mmu, Mus musculus; Cin, Ciona intestinalis; Bfl, Branchiostoma floridae; Cap, Capitella sp; Lgi, Lottia gigantea; Nve, Nematostella vectensis; Tad, Trichoplax adhaerens.

Mentions: Over the past 5 years, the focus has shifted away from the question of the ultimate origin of introns to attempts to track the history of intron loss/gain and intron sequence evolution during eukaryotic history. We can now be confident that large numbers of introns were present by early eukaryotic history (14,34–40) and that many or even most modern introns date to the times of early eukaryotic ancestors. Over at least recent eukaryotic evolution (say, the last ∼100 My), intron gain has been a very rare event, with most lineages experiencing rates of gain corresponding to <0.0002 gains per gene per million years (7,8,41–46). Rates of intron loss have been more variable: in some lineages, rates of loss are perhaps 10% per 100 My, whereas other lineages have experienced almost no intron loss over tens or hundreds of millions of years (2,6,7,42,44–48). Figure 1 shows the example of metazoans, where the majority of intron positions have been retained between vertebrates and basal animals.Figure 1.


Spliceosomal introns as tools for genomic and evolutionary analysis.

Irimia M, Roy SW - Nucleic Acids Res. (2008)

Intron positions are often conserved over long evolutionary times. Protein-level alignments of the translation initiation factor 4A gene (TIF4A) from a variety of metazoan species are shown. Intron positions are indicated by digits corresponding to the phase of the intron relative to the surrounding codons (phases 0, 1 and 2 introns fall before the first, second and third bases of a codon, respectively). Most intron positions are conserved at the exact homologous position and phase over all of animal history within these species, all the way from the placozoan Trichoplax adhaerens to chordates. Abbreviations: Hsa, Homo sapiens; Mmu, Mus musculus; Cin, Ciona intestinalis; Bfl, Branchiostoma floridae; Cap, Capitella sp; Lgi, Lottia gigantea; Nve, Nematostella vectensis; Tad, Trichoplax adhaerens.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC2275149&req=5

Figure 1: Intron positions are often conserved over long evolutionary times. Protein-level alignments of the translation initiation factor 4A gene (TIF4A) from a variety of metazoan species are shown. Intron positions are indicated by digits corresponding to the phase of the intron relative to the surrounding codons (phases 0, 1 and 2 introns fall before the first, second and third bases of a codon, respectively). Most intron positions are conserved at the exact homologous position and phase over all of animal history within these species, all the way from the placozoan Trichoplax adhaerens to chordates. Abbreviations: Hsa, Homo sapiens; Mmu, Mus musculus; Cin, Ciona intestinalis; Bfl, Branchiostoma floridae; Cap, Capitella sp; Lgi, Lottia gigantea; Nve, Nematostella vectensis; Tad, Trichoplax adhaerens.
Mentions: Over the past 5 years, the focus has shifted away from the question of the ultimate origin of introns to attempts to track the history of intron loss/gain and intron sequence evolution during eukaryotic history. We can now be confident that large numbers of introns were present by early eukaryotic history (14,34–40) and that many or even most modern introns date to the times of early eukaryotic ancestors. Over at least recent eukaryotic evolution (say, the last ∼100 My), intron gain has been a very rare event, with most lineages experiencing rates of gain corresponding to <0.0002 gains per gene per million years (7,8,41–46). Rates of intron loss have been more variable: in some lineages, rates of loss are perhaps 10% per 100 My, whereas other lineages have experienced almost no intron loss over tens or hundreds of millions of years (2,6,7,42,44–48). Figure 1 shows the example of metazoans, where the majority of intron positions have been retained between vertebrates and basal animals.Figure 1.

Bottom Line: First, we discuss uses of intron length distributions and positions in sequence assembly and annotation, and for improving alignment of homologous regions.Second, we review uses of introns in evolutionary studies, including the utility of introns as indicators of rates of sequence evolution, for inferences about molecular evolution, as signatures of orthology and paralogy, and for estimating rates of nucleotide substitution.We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions.

View Article: PubMed Central - PubMed

Affiliation: Departament de Genètica, Universitat de Barcelona, Barcelona, Spain.

ABSTRACT
Over the past 5 years, the availability of dozens of whole genomic sequences from a wide variety of eukaryotic lineages has revealed a very large amount of information about the dynamics of intron loss and gain through eukaryotic history, as well as the evolution of intron sequences. Implicit in these advances is a great deal of information about the structure and evolution of surrounding sequences. Here, we review the wealth of ways in which structures of spliceosomal introns as well as their conservation and change through evolution may be harnessed for evolutionary and genomic analysis. First, we discuss uses of intron length distributions and positions in sequence assembly and annotation, and for improving alignment of homologous regions. Second, we review uses of introns in evolutionary studies, including the utility of introns as indicators of rates of sequence evolution, for inferences about molecular evolution, as signatures of orthology and paralogy, and for estimating rates of nucleotide substitution. We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions.

Show MeSH