Evolution of Alternative Splicing in Eudicots
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Zhihao Ling
- Thomas Brockmoeller
- Ian T Baldwin
- Shuqing Xu
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000471134000001&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.3389/fpls.2019.00707
- Externe Identifier
- Clarivate Analytics Document Solution ID: IC7DY
- PubMed Identifier: 31244865
- ISSN
- 1664-462X
- Zeitschrift
- FRONTIERS IN PLANT SCIENCE
- Schlüsselwörter
- alternative splicing
- evolution
- transcriptome
- splicing code
- deep learning
- nonsense-mediated decay
- Artikelnummer
- ARTN 707
- Datum der Veröffentlichung
- 2019
- Status
- Published
- Titel
- Evolution of Alternative Splicing in Eudicots
- Sub types
- Article
- Ausgabe der Zeitschrift
- 10
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Autoren
- Zhihao Ling
- Thomas Brockmöller
- Ian T Baldwin
- Shuqing Xu
- DOI
- 10.3389/fpls.2019.00707
- eISSN
- 1664-462X
- Zeitschrift
- Frontiers in Plant Science
- Online publication date
- 2019
- Status
- Published online
- Herausgeber
- Frontiers Media SA
- Herausgeber URL
- http://dx.doi.org/10.3389/fpls.2019.00707
- Datum der Datenerfassung
- 2019
- Titel
- Evolution of Alternative Splicing in Eudicots
- Ausgabe der Zeitschrift
- 10
Datenquelle: Crossref
- Abstract
- Alternative pre-mRNA splicing (AS) is prevalent in plants and is involved in many interactions between plants and environmental stresses. However, the patterns and underlying mechanisms of AS evolution in plants remain unclear. By analyzing the transcriptomes of four eudicot species, we revealed that the divergence of AS is largely due to the gains and losses of AS events among orthologous genes. Furthermore, based on a subset of AS, in which AS can be directly associated with specific transcripts, we found that AS that generates transcripts containing premature termination codons (PTC), are likely more conserved than those that generate non-PTC containing transcripts. This suggests that AS coupled with nonsense-mediated decay (NMD) might play an important role in affecting mRNA levels post-transcriptionally. To understand the mechanisms underlying the divergence of AS, we analyzed the key determinants of AS using a machine learning approach. We found that the presence/absence of alternative splice site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5' donor site and 3' acceptor site among the studied species, suggesting a relatively conserved AS mechanism. The comparative analysis further demonstrated that variations of the identified AS determinants significantly contributed to the AS divergence among closely related species in both Solanaceae and Brassicaceae taxa. Together, these results provide detailed insights into the evolution of AS in plants.
- Addresses
- Max Planck Institute for Chemical Ecology, Jena, Germany.
- Autoren
- Zhihao Ling
- Thomas Brockmöller
- Ian T Baldwin
- Shuqing Xu
- DOI
- 10.3389/fpls.2019.00707
- eISSN
- 1664-462X
- Externe Identifier
- PubMed Identifier: 31244865
- PubMed Central ID: PMC6581728
- Funding acknowledgements
- Swiss National Science Foundation:
- Swiss National Science Foundation: 142886
- European Research Council:
- European Research Council: 293926
- FP7 People: Marie-Curie Actions:
- Open access
- true
- ISSN
- 1664-462X
- Zeitschrift
- Frontiers in plant science
- Sprache
- eng
- Medium
- Electronic-eCollection
- Online publication date
- 2019
- Open access status
- Open Access
- Paginierung
- 707
- Datum der Veröffentlichung
- 2019
- Status
- Published
- Publisher licence
- CC BY
- Datum der Datenerfassung
- 2019
- Titel
- Evolution of Alternative Splicing in Eudicots.
- Sub types
- research-article
- Journal Article
- Ausgabe der Zeitschrift
- 10
Files
https://www.frontiersin.org/articles/10.3389/fpls.2019.00707/pdf https://europepmc.org/articles/PMC6581728?pdf=render
Datenquelle: Europe PubMed Central
- Abstract
- Alternative pre-mRNA splicing (AS) is prevalent in plants and is involved in many interactions between plants and environmental stresses. However, the patterns and underlying mechanisms of AS evolution in plants remain unclear. By analyzing the transcriptomes of four eudicot species, we revealed that the divergence of AS is largely due to the gains and losses of AS events among orthologous genes. Furthermore, based on a subset of AS, in which AS can be directly associated with specific transcripts, we found that AS that generates transcripts containing premature termination codons (PTC), are likely more conserved than those that generate non-PTC containing transcripts. This suggests that AS coupled with nonsense-mediated decay (NMD) might play an important role in affecting mRNA levels post-transcriptionally. To understand the mechanisms underlying the divergence of AS, we analyzed the key determinants of AS using a machine learning approach. We found that the presence/absence of alternative splice site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5' donor site and 3' acceptor site among the studied species, suggesting a relatively conserved AS mechanism. The comparative analysis further demonstrated that variations of the identified AS determinants significantly contributed to the AS divergence among closely related species in both Solanaceae and Brassicaceae taxa. Together, these results provide detailed insights into the evolution of AS in plants.
- Date of acceptance
- 2019
- Autoren
- Zhihao Ling
- Thomas Brockmöller
- Ian T Baldwin
- Shuqing Xu
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/31244865
- DOI
- 10.3389/fpls.2019.00707
- Externe Identifier
- PubMed Central ID: PMC6581728
- ISSN
- 1664-462X
- Zeitschrift
- Front Plant Sci
- Schlüsselwörter
- alternative splicing
- deep learning
- evolution
- nonsense-mediated decay
- splicing code
- transcriptome
- Sprache
- eng
- Country
- Switzerland
- Paginierung
- 707
- Datum der Veröffentlichung
- 2019
- Status
- Published online
- Titel
- Evolution of Alternative Splicing in Eudicots.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 10
Datenquelle: PubMed
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