Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins.
Although large scale informatics studies on introns can be useful in making broad inferences concerning patterns of intron gain and loss, more specific questions about intron evolution at a finer scale can be addressed using a gene family where structure and function are well known. Genome wide surv...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2009-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2650405?pdf=render |
| _version_ | 1819066676857012224 |
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| author | Antonio Garcia-España Roso Mares Tung-Tien Sun Rob Desalle |
| author_facet | Antonio Garcia-España Roso Mares Tung-Tien Sun Rob Desalle |
| author_sort | Antonio Garcia-España |
| collection | DOAJ |
| description | Although large scale informatics studies on introns can be useful in making broad inferences concerning patterns of intron gain and loss, more specific questions about intron evolution at a finer scale can be addressed using a gene family where structure and function are well known. Genome wide surveys of tetraspanins from a broad array of organisms with fully sequenced genomes are an excellent means to understand specifics of intron evolution. Our approach incorporated several new fully sequenced genomes that cover the major lineages of the animal kingdom as well as plants, protists and fungi. The analysis of exon/intron gene structure in such an evolutionary broad set of genomes allowed us to identify ancestral intron structure in tetraspanins throughout the eukaryotic tree of life.We performed a phylogenomic analysis of the intron/exon structure of the tetraspanin protein family. In addition, to the already characterized tetraspanin introns numbered 1 through 6 found in animals, three additional ancient, phase 0 introns we call 4a, 4b and 4c were found. These three novel introns in combination with the ancestral introns 1 to 6, define three basic tetraspanin gene structures which have been conserved throughout the animal kingdom. Our phylogenomic approach also allows the estimation of the time at which the introns of the 33 human tetraspanin paralogs appeared, which in many cases coincides with the concomitant acquisition of new introns. On the other hand, we observed that new introns (introns other than 1-6, 4a, b and c) were not randomly inserted into the tetraspanin gene structure. The region of tetraspanin genes corresponding to the small extracellular loop (SEL) accounts for only 10.5% of the total sequence length but had 46% of the new animal intron insertions.Our results indicate that tests of intron evolution are strengthened by the phylogenomic approach with specific gene families like tetraspanins. These tests add to our understanding of genomic innovation coupled to major evolutionary divergence events, functional constraints and the timing of the appearance of evolutionary novelty. |
| first_indexed | 2024-12-21T16:06:09Z |
| format | Article |
| id | doaj.art-682d1549e8ba4e3896feba4efa2a5941 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T16:06:09Z |
| publishDate | 2009-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS ONE |
| spelling | doaj.art-682d1549e8ba4e3896feba4efa2a59412022-12-21T18:57:53ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-01-0143e468010.1371/journal.pone.0004680Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins.Antonio Garcia-EspañaRoso MaresTung-Tien SunRob DesalleAlthough large scale informatics studies on introns can be useful in making broad inferences concerning patterns of intron gain and loss, more specific questions about intron evolution at a finer scale can be addressed using a gene family where structure and function are well known. Genome wide surveys of tetraspanins from a broad array of organisms with fully sequenced genomes are an excellent means to understand specifics of intron evolution. Our approach incorporated several new fully sequenced genomes that cover the major lineages of the animal kingdom as well as plants, protists and fungi. The analysis of exon/intron gene structure in such an evolutionary broad set of genomes allowed us to identify ancestral intron structure in tetraspanins throughout the eukaryotic tree of life.We performed a phylogenomic analysis of the intron/exon structure of the tetraspanin protein family. In addition, to the already characterized tetraspanin introns numbered 1 through 6 found in animals, three additional ancient, phase 0 introns we call 4a, 4b and 4c were found. These three novel introns in combination with the ancestral introns 1 to 6, define three basic tetraspanin gene structures which have been conserved throughout the animal kingdom. Our phylogenomic approach also allows the estimation of the time at which the introns of the 33 human tetraspanin paralogs appeared, which in many cases coincides with the concomitant acquisition of new introns. On the other hand, we observed that new introns (introns other than 1-6, 4a, b and c) were not randomly inserted into the tetraspanin gene structure. The region of tetraspanin genes corresponding to the small extracellular loop (SEL) accounts for only 10.5% of the total sequence length but had 46% of the new animal intron insertions.Our results indicate that tests of intron evolution are strengthened by the phylogenomic approach with specific gene families like tetraspanins. These tests add to our understanding of genomic innovation coupled to major evolutionary divergence events, functional constraints and the timing of the appearance of evolutionary novelty.http://europepmc.org/articles/PMC2650405?pdf=render |
| spellingShingle | Antonio Garcia-España Roso Mares Tung-Tien Sun Rob Desalle Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins. PLoS ONE |
| title | Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins. |
| title_full | Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins. |
| title_fullStr | Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins. |
| title_full_unstemmed | Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins. |
| title_short | Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins. |
| title_sort | intron evolution testing hypotheses of intron evolution using the phylogenomics of tetraspanins |
| url | http://europepmc.org/articles/PMC2650405?pdf=render |
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