Limits...
Recurrent loss of specific introns during angiosperm evolution.

Wang H, Devos KM, Bennetzen JL - PLoS Genet. (2014)

Bottom Line: The two larger genomes, maize and sorghum, were found to have a higher rate of both recurrent loss and overall loss and/or gain than foxtail millet, rice or Brachypodium.Adjacent introns and small introns were found to be preferentially lost.This last result suggests that epigenetic status, as evidenced by a loss of methylated CG dinucleotides, may play a role in the process of intron loss.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, Georgia, United States of America.

ABSTRACT
Numerous instances of presence/absence variations for introns have been documented in eukaryotes, and some cases of recurrent loss of the same intron have been suggested. However, there has been no comprehensive or phylogenetically deep analysis of recurrent intron loss. Of 883 cases of intron presence/absence variation that we detected in five sequenced grass genomes, 93 were confirmed as recurrent losses and the rest could be explained by single losses (652) or single gains (118). No case of recurrent intron gain was observed. Deep phylogenetic analysis often indicated that apparent intron gains were actually numerous independent losses of the same intron. Recurrent loss exhibited extreme non-randomness, in that some introns were removed independently in many lineages. The two larger genomes, maize and sorghum, were found to have a higher rate of both recurrent loss and overall loss and/or gain than foxtail millet, rice or Brachypodium. Adjacent introns and small introns were found to be preferentially lost. Intron loss genes exhibited a high frequency of germ line or early embryogenesis expression. In addition, flanking exon A+T-richness and intron TG/CG ratios were higher in retained introns. This last result suggests that epigenetic status, as evidenced by a loss of methylated CG dinucleotides, may play a role in the process of intron loss. This study provides the first comprehensive analysis of recurrent intron loss, makes a series of novel findings on the patterns of recurrent intron loss during the evolution of the grass family, and provides insight into the molecular mechanism(s) underlying intron loss.

No MeSH data available.


Related in: MedlinePlus

Patterns of intron loss and gain.The history of intron loss and/or gain is inferred by comparing the observed pattern of intron presence-absence with the phylogeny of the conserved genes exhibiting intron presence/absence variation using the parsimony principle. “*” denotes reconstructed loss or gain event. Bottom right example: intron exists in all genes studied, and no loss or gain has occurred. Middle left: the presence of an intron in the outgroup and two apparent losses in two lineages. Any other reconstruction requires at least 3 events. Applying the same logic, the other three patterns located at top left, top right, and middle right can be reconstructed.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4256211&req=5

pgen-1004843-g001: Patterns of intron loss and gain.The history of intron loss and/or gain is inferred by comparing the observed pattern of intron presence-absence with the phylogeny of the conserved genes exhibiting intron presence/absence variation using the parsimony principle. “*” denotes reconstructed loss or gain event. Bottom right example: intron exists in all genes studied, and no loss or gain has occurred. Middle left: the presence of an intron in the outgroup and two apparent losses in two lineages. Any other reconstruction requires at least 3 events. Applying the same logic, the other three patterns located at top left, top right, and middle right can be reconstructed.

Mentions: Patterns of intron loss and gain have been investigated extensively in numerous subclades of the eukaryotic tree of life with different levels of taxon sampling (see review in [3]). To date, vast numbers of single loss and gain events (events inferred as occurring only once in the phylogeny investigated (Fig. 1, top) have been well-documented. Some studies also document cases of recurrent loss [9]–[11] and/or recurrent gain (otherwise called parallel gain) [12]–[14], terms describing introns that are independently removed from or inserted into the identical sites more than once in an investigated phylogeny (Fig. 1, middle).


Recurrent loss of specific introns during angiosperm evolution.

Wang H, Devos KM, Bennetzen JL - PLoS Genet. (2014)

Patterns of intron loss and gain.The history of intron loss and/or gain is inferred by comparing the observed pattern of intron presence-absence with the phylogeny of the conserved genes exhibiting intron presence/absence variation using the parsimony principle. “*” denotes reconstructed loss or gain event. Bottom right example: intron exists in all genes studied, and no loss or gain has occurred. Middle left: the presence of an intron in the outgroup and two apparent losses in two lineages. Any other reconstruction requires at least 3 events. Applying the same logic, the other three patterns located at top left, top right, and middle right can be reconstructed.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4256211&req=5

pgen-1004843-g001: Patterns of intron loss and gain.The history of intron loss and/or gain is inferred by comparing the observed pattern of intron presence-absence with the phylogeny of the conserved genes exhibiting intron presence/absence variation using the parsimony principle. “*” denotes reconstructed loss or gain event. Bottom right example: intron exists in all genes studied, and no loss or gain has occurred. Middle left: the presence of an intron in the outgroup and two apparent losses in two lineages. Any other reconstruction requires at least 3 events. Applying the same logic, the other three patterns located at top left, top right, and middle right can be reconstructed.
Mentions: Patterns of intron loss and gain have been investigated extensively in numerous subclades of the eukaryotic tree of life with different levels of taxon sampling (see review in [3]). To date, vast numbers of single loss and gain events (events inferred as occurring only once in the phylogeny investigated (Fig. 1, top) have been well-documented. Some studies also document cases of recurrent loss [9]–[11] and/or recurrent gain (otherwise called parallel gain) [12]–[14], terms describing introns that are independently removed from or inserted into the identical sites more than once in an investigated phylogeny (Fig. 1, middle).

Bottom Line: The two larger genomes, maize and sorghum, were found to have a higher rate of both recurrent loss and overall loss and/or gain than foxtail millet, rice or Brachypodium.Adjacent introns and small introns were found to be preferentially lost.This last result suggests that epigenetic status, as evidenced by a loss of methylated CG dinucleotides, may play a role in the process of intron loss.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, Georgia, United States of America.

ABSTRACT
Numerous instances of presence/absence variations for introns have been documented in eukaryotes, and some cases of recurrent loss of the same intron have been suggested. However, there has been no comprehensive or phylogenetically deep analysis of recurrent intron loss. Of 883 cases of intron presence/absence variation that we detected in five sequenced grass genomes, 93 were confirmed as recurrent losses and the rest could be explained by single losses (652) or single gains (118). No case of recurrent intron gain was observed. Deep phylogenetic analysis often indicated that apparent intron gains were actually numerous independent losses of the same intron. Recurrent loss exhibited extreme non-randomness, in that some introns were removed independently in many lineages. The two larger genomes, maize and sorghum, were found to have a higher rate of both recurrent loss and overall loss and/or gain than foxtail millet, rice or Brachypodium. Adjacent introns and small introns were found to be preferentially lost. Intron loss genes exhibited a high frequency of germ line or early embryogenesis expression. In addition, flanking exon A+T-richness and intron TG/CG ratios were higher in retained introns. This last result suggests that epigenetic status, as evidenced by a loss of methylated CG dinucleotides, may play a role in the process of intron loss. This study provides the first comprehensive analysis of recurrent intron loss, makes a series of novel findings on the patterns of recurrent intron loss during the evolution of the grass family, and provides insight into the molecular mechanism(s) underlying intron loss.

No MeSH data available.


Related in: MedlinePlus