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What Can Domesticated Genes Tell Us about the Intron Gain in Mammals?

Kordiš D, Kokošar J - Int J Evol Biol (2012)

Bottom Line: A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified.In the coding regions of some domesticated genes up to 8 de novo gained introns have been found.This paper summarizes the current understanding of intron gain in mammals.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Biomedical Sciences, Josef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.

ABSTRACT
Domesticated genes, originating from retroelements or from DNA-transposons, constitute an ideal system for testing the hypothesis on the absence of intron gain in mammals. Since single-copy domesticated genes originated from the intronless multicopy transposable elements, the ancestral intron state for domesticated genes is zero. A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5' UTR and coding regions, while 3' UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Surprisingly, the majority of intron gains have occurred in the ancestor of placental mammals. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain. This paper summarizes the current understanding of intron gain in mammals.

No MeSH data available.


Related in: MedlinePlus

Numbers of transposable element-derived gene domestication events and intron gains mapped on the chordate phylogenetic tree. In the superorder Boreoeutheria some additional intron gains have occurred.
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fig1: Numbers of transposable element-derived gene domestication events and intron gains mapped on the chordate phylogenetic tree. In the superorder Boreoeutheria some additional intron gains have occurred.

Mentions: The analysis of all domesticated genes in chordates and mammals has shown that by far the greatest amount of intron gain occurred in the ancestor of placentals [19] (Figure 1). Twenty intron-containing domesticated genes originated in the ancestor of placentals, 18 of them being retroelement-derived and only two DNA transposon-derived genes. Interestingly, a recent study reported that 11 retrogenes with newly gained 5′ UTR introns also originated in the ancestor of placentals [20]. In the case of retrogenes they found 18 intron gains, 17 into the 5′ UTR, and a single gain in the 3′ UTR. In the case of domesticated genes 49 to 57 cases of de novo gained introns were found in the ancestor of placentals (Figure 1). In retroelement-derived genes 42 to 50 cases of intron gain have been found, while in DNA transposon-derived genes only 7 cases were found. Collectively, the 20 domesticated genes and 11 retrogenes provide evidence for at least 50 to 70 cases of intron gain in the ancestor of placentals [19]. This finding contrasts strongly with previous studies [17, 18], in which no intron gain could be found in mammals.


What Can Domesticated Genes Tell Us about the Intron Gain in Mammals?

Kordiš D, Kokošar J - Int J Evol Biol (2012)

Numbers of transposable element-derived gene domestication events and intron gains mapped on the chordate phylogenetic tree. In the superorder Boreoeutheria some additional intron gains have occurred.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3369469&req=5

fig1: Numbers of transposable element-derived gene domestication events and intron gains mapped on the chordate phylogenetic tree. In the superorder Boreoeutheria some additional intron gains have occurred.
Mentions: The analysis of all domesticated genes in chordates and mammals has shown that by far the greatest amount of intron gain occurred in the ancestor of placentals [19] (Figure 1). Twenty intron-containing domesticated genes originated in the ancestor of placentals, 18 of them being retroelement-derived and only two DNA transposon-derived genes. Interestingly, a recent study reported that 11 retrogenes with newly gained 5′ UTR introns also originated in the ancestor of placentals [20]. In the case of retrogenes they found 18 intron gains, 17 into the 5′ UTR, and a single gain in the 3′ UTR. In the case of domesticated genes 49 to 57 cases of de novo gained introns were found in the ancestor of placentals (Figure 1). In retroelement-derived genes 42 to 50 cases of intron gain have been found, while in DNA transposon-derived genes only 7 cases were found. Collectively, the 20 domesticated genes and 11 retrogenes provide evidence for at least 50 to 70 cases of intron gain in the ancestor of placentals [19]. This finding contrasts strongly with previous studies [17, 18], in which no intron gain could be found in mammals.

Bottom Line: A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified.In the coding regions of some domesticated genes up to 8 de novo gained introns have been found.This paper summarizes the current understanding of intron gain in mammals.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Biomedical Sciences, Josef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.

ABSTRACT
Domesticated genes, originating from retroelements or from DNA-transposons, constitute an ideal system for testing the hypothesis on the absence of intron gain in mammals. Since single-copy domesticated genes originated from the intronless multicopy transposable elements, the ancestral intron state for domesticated genes is zero. A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5' UTR and coding regions, while 3' UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Surprisingly, the majority of intron gains have occurred in the ancestor of placental mammals. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain. This paper summarizes the current understanding of intron gain in mammals.

No MeSH data available.


Related in: MedlinePlus