Intron exclusion and the mystery of intron loss

Hu, Kejin

doi:10.1016/j.febslet.2006.10.048

Cited by 25 publications

(20 citation statements)

References 33 publications

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“…An increased rate of intron loss might thus be facilitated by the extraordinarily high rate of DNA repair by homologous recombination in P. patens . This hypothesis is based on models proposing a prominent role of gene conversion and DNA repair in intron loss [84,85]. …”

Section: Resultsmentioning

confidence: 99%

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

et al. 2013

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BackgroundThe moss Physcomitrella patens as a model species provides an important reference for early-diverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies. The usability of a reference genome greatly depends on the quality of the annotation and the availability of centralized community resources. Therefore, in the light of accumulating evidence for missing genes, fragmentary gene structures, false annotations and a low rate of functional annotations on the original release, we decided to improve the moss genome annotation.ResultsHere, we report the complete moss genome re-annotation (designated V1.6) incorporating the increased transcript availability from a multitude of developmental stages and tissue types. We demonstrate the utility of the improved P. patens genome annotation for comparative genomics and new extensions to the cosmoss.org resource as a central repository for this plant “flagship” genome. The structural annotation of 32,275 protein-coding genes results in 8387 additional loci including 1456 loci with known protein domains or homologs in Plantae. This is the first release to include information on transcript isoforms, suggesting alternative splicing events for at least 10.8% of the loci. Furthermore, this release now also provides information on non-protein-coding loci. Functional annotations were improved regarding quality and coverage, resulting in 58% annotated loci (previously: 41%) that comprise also 7200 additional loci with GO annotations. Access and manual curation of the functional and structural genome annotation is provided via the http://www.cosmoss.org model organism database.ConclusionsComparative analysis of gene structure evolution along the green plant lineage provides novel insights, such as a comparatively high number of loci with 5’-UTR introns in the moss. Comparative analysis of functional annotations reveals expansions of moss house-keeping and metabolic genes and further possibly adaptive, lineage-specific expansions and gains including at least 13% orphan genes.

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Section: Resultsmentioning

confidence: 99%

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

et al. 2013

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“…4). Intron length variation probably is an outcome of recombination46. Variable introns would increase genome diversity by permitting different recombination arrangements and would accelerate the proteome evolution by differential splicing4748, which could benefit organism fitness and contribute not only to gene family divergence but also to species diversity and differentiation47.…”

Section: Resultsmentioning

confidence: 99%

Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes

Huang

Chen

Huang

et al. 2016

Sci Rep

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Gene duplication could be beneficial by functional division but might increase the risk of genetic load. The dynamics of duplicated paralogs number could involve recombination, positive selection, and functional divergence. Duplication of DIHYDROFLAVONOL 4-REDUCTASE (DFR) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm DFR gene focusing on a diversified genus Scutellaria to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of DFR was before the divergence of Scutellaria. Asymmetric positive selective pressures resulted in different evolutionary rates between the duplicates. Different numbers of regulatory elements, differential codon usages, radical amino acid changes, and differential gene expressions provide evidences of functional divergence between the two DFR duplicates in Scutellaria, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one DFR paralogous gene suggested possibly leading to “loss of function” due to dosage imbalance after the transient adaptive subfunctionalization in the early stage of duplication. Notwithstanding, episodic gene duplication and functional divergence may be relevant to the diversification of ecological function of DFR gene in Scutellaria.

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“…Because these losses were adjacent and appear to have occurred simultaneously, we assume these introns were deleted by RTMIL. The exact mechanism by which RTMIL may remove internal or 5' intron(s) but conserve 3' intron(s) has proved elusive but received considerable attention [9,11,13,44,51,52]. The most commonly proposed mechanism to account for internal or 5' intron loss(es) by RTMIL is the formation of a double stranded mRNA secondary structure upstream from the 3' conserved intron position(s).…”

Section: Resultsmentioning

confidence: 99%

“…By identifying orthologs, aligning gene sequences, and coupling intron absences/presences with known species phylogenies, numerous studies have identified the number of intron gains and losses that have occurred among species throughout evolution [1-11]. However, very little is known about the molecular mechanisms underlying these changes [12,13]. …”

Section: Introductionmentioning

confidence: 99%

Mechanisms of intron gain and loss in Drosophila

2011

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BackgroundIt is widely accepted that orthologous genes have lost or gained introns throughout evolution. However, the specific mechanisms that generate these changes have proved elusive. Introns are known to affect nearly every level of gene expression. Therefore, understanding their mechanism of evolution after their initial fixation in eukaryotes is pertinent to understanding the means by which organisms develop greater regulation and complexity.ResultsTo investigate possible mechanisms of intron gain and loss, we identified 189 intron gain and 297 intron loss events among 11 Drosophila species. We then investigated these events for signatures of previously proposed mechanisms of intron gain and loss. This work constitutes the first comprehensive study into the specific mechanisms that may generate intron gains and losses in Drosophila. We report evidence of intron gain via transposon insertion; the first intron loss that may have occurred via non-homologous end joining; intron gains via the repair of a double strand break; evidence of intron sliding; and evidence that internal or 5' introns may not frequently be deleted via the self-priming of reverse transcription during mRNA-mediated intron loss. Our data also suggest that the transcription process may promote or result in intron gain.ConclusionOur findings support the occurrence of intron gain via transposon insertion, repair of double strand breaks, as well as intron loss via non-homologous end joining. Furthermore, our data suggest that intron gain may be enabled by or due to transcription, and we shed further light on the exact mechanism of mRNA-mediated intron loss.

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Intron exclusion and the mystery of intron loss

Cited by 25 publications

References 33 publications

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes

Mechanisms of intron gain and loss in Drosophila

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