Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.

Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked diffe...

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Autores principales:	Jean-Luc Da Lage, Frédérique Maczkowiak, Marie-Louise Cariou
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/04bf551afac94b0ea323a2715a9c7a8e
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spelling	oai:doaj.org-article:04bf551afac94b0ea323a2715a9c7a8e2021-11-18T06:53:52ZPhylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.1932-620310.1371/journal.pone.0019673https://doaj.org/article/04bf551afac94b0ea323a2715a9c7a8e2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21611157/?tool=EBIhttps://doaj.org/toc/1932-6203Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked differences between phyla. The question of the rates of intron gains and loss in the course of evolution and factors influencing them remains controversial. We have investigated a single gene family, alpha-amylase, in 55 species covering a variety of animal phyla. Comparison of intron positions across phyla suggests a complex history, with a likely ancestral intronless gene undergoing frequent intron loss and gain, leading to extant intron/exon structures that are highly variable, even among species from the same phylum. Because introns are known to play no regulatory role in this gene and there is no alternative splicing, the structural differences may be interpreted more easily: intron positions, sizes, losses or gains may be more likely related to factors linked to splicing mechanisms and requirements, and to recognition of introns and exons, or to more extrinsic factors, such as life cycle and population size. We have shown that intron losses outnumbered gains in recent periods, but that "resets" of intron positions occurred at the origin of several phyla, including vertebrates. Rates of gain and loss appear to be positively correlated. No phase preference was found. We also found evidence for parallel gains and for intron sliding. Presence of introns at given positions was correlated to a strong protosplice consensus sequence AG/G, which was much weaker in the absence of intron. In contrast, recent intron insertions were not associated with a specific sequence. In animal Amy genes, population size and generation time seem to have played only minor roles in shaping gene structures.Jean-Luc Da LageFrédérique MaczkowiakMarie-Louise CariouPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 5, p e19673 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jean-Luc Da Lage Frédérique Maczkowiak Marie-Louise Cariou Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.
description	Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked differences between phyla. The question of the rates of intron gains and loss in the course of evolution and factors influencing them remains controversial. We have investigated a single gene family, alpha-amylase, in 55 species covering a variety of animal phyla. Comparison of intron positions across phyla suggests a complex history, with a likely ancestral intronless gene undergoing frequent intron loss and gain, leading to extant intron/exon structures that are highly variable, even among species from the same phylum. Because introns are known to play no regulatory role in this gene and there is no alternative splicing, the structural differences may be interpreted more easily: intron positions, sizes, losses or gains may be more likely related to factors linked to splicing mechanisms and requirements, and to recognition of introns and exons, or to more extrinsic factors, such as life cycle and population size. We have shown that intron losses outnumbered gains in recent periods, but that "resets" of intron positions occurred at the origin of several phyla, including vertebrates. Rates of gain and loss appear to be positively correlated. No phase preference was found. We also found evidence for parallel gains and for intron sliding. Presence of introns at given positions was correlated to a strong protosplice consensus sequence AG/G, which was much weaker in the absence of intron. In contrast, recent intron insertions were not associated with a specific sequence. In animal Amy genes, population size and generation time seem to have played only minor roles in shaping gene structures.
format	article
author	Jean-Luc Da Lage Frédérique Maczkowiak Marie-Louise Cariou
author_facet	Jean-Luc Da Lage Frédérique Maczkowiak Marie-Louise Cariou
author_sort	Jean-Luc Da Lage
title	Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.
title_short	Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.
title_full	Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.
title_fullStr	Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.
title_full_unstemmed	Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.
title_sort	phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/04bf551afac94b0ea323a2715a9c7a8e
work_keys_str_mv	AT jeanlucdalage phylogeneticdistributionofintronpositionsinalphaamylasegenesofbilateriasuggestsnumerousgainsandlosses AT frederiquemaczkowiak phylogeneticdistributionofintronpositionsinalphaamylasegenesofbilateriasuggestsnumerousgainsandlosses AT marielouisecariou phylogeneticdistributionofintronpositionsinalphaamylasegenesofbilateriasuggestsnumerousgainsandlosses
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Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.

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