Extensive Divergence in Alternative Splicing Patterns after Gene and Genome Duplication During the Evolutionary History of Arabidopsis

Zhang, Peter G.; Huang, S.Z.; Pin, Anne-Laure; Adams, Keith L.

doi:10.1093/molbev/msq054

Cited by 59 publications

(45 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Zhang et al (2010c) used RT-PCR to look at 104 whole-genome gene duplicates in six organ types and in plants grown under abiotic stress. In a large majority of the duplicated pairs, they found differences in splicing patterns between the genes in one or more organs or under stress conditions, indicating AS divergence after genome duplication.…”

Section: Genome Duplication and Asmentioning

confidence: 99%

Complexity of the Alternative Splicing Landscape in Plants

et al. 2013

View full text Add to dashboard Cite

Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.

show abstract

Section: Genome Duplication and Asmentioning

confidence: 99%

Complexity of the Alternative Splicing Landscape in Plants

et al. 2013

View full text Add to dashboard Cite

show abstract

“…Changes in the AS patterns are important for the evolution of GD pairs. The majority of studies have reported that GD decreases the AS frequency, as the number of AS isoforms per locus in singleton genes is higher than in duplicated genes and small gene families have a larger average number of AS isoforms per locus than the large gene families (Kopelman et al, 2005;Su et al, 2006;Talavera et al, 2007;P.G. Zhang et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

et al. 2014

View full text Add to dashboard Cite

Alternative splicing (AS) is common in higher eukaryotes and plays an important role in gene posttranscriptional regulation. It has been suggested that AS varies dramatically among species, tissues, and duplicated gene families of different sizes. However, the genomic forces that govern AS variation remain poorly understood. Here, through genome-wide identification of AS events in the soybean (Glycine max) genome using high-throughput RNA sequencing of 28 samples from different developmental stages, we found that more than 63% of multiexonic genes underwent AS. More AS events occurred in the younger developmental stages than in the older developmental stages for the same type of tissue, and the four main AS types, exon skipping, intron retention, alternative donor sites, and alternative acceptor sites, exhibited different characteristics. Global computational analysis demonstrated that the variations of AS frequency and AS types were significantly correlated with the changes of gene features and gene transcriptional level. Further investigation suggested that the decrease of AS within the genome-wide duplicated genes were due to the diminution of intron length, exon number, and transcriptional level. Altogether, our study revealed that a large number of genes were alternatively spliced in the soybean genome and that variations in gene structure and transcriptional level may play important roles in regulating AS.

show abstract

“…Genome-wide identification and physiological implications of AS have been reported in plant species including A. thaliana (Filichkin et al, 2010;Zhang et al, 2010;Marquez et al, 2012;Syed et al, 2012), Oryza sativa (Wang and Brendel, 2006), Nelumbo nucifera (sacred lotus) (VanBuren et al, 2013), Vitis vinifera (Vitulo et al, 2014), Brachypodium distachyon (Sablok et al, 2011;Walters et al, 2013), Zea mays (maize), and Sorghum bicolor (sorghum) (Thatcher et al, 2014;Min et al, 2015). Approximately 60 -75% of AS events occur within the protein coding regions of mRNAs, resulting changes in binding properties, intracellular localization, protein stability, enzymatic, and signaling activities (Stamm et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Cataloging and Analysis of Alternative Splicing in Maize

Min

2017

cmb

View full text Add to dashboard Cite

Gene expression is a key step in developmental regulation and responses in changing environments in plants. Alternative splicing (AS) is a process generating multiple RNA isoforms from a single gene pre-mRNA transcript that increases the diversity of functional proteins and RNAs. Identification and analysis of alternatively splicing events are critical for crop improvement and understanding regulatory mechanisms. In maize large numbers of transcripts generated by RNA-seq technology are available, we incorporated these data with data assembled with ESTs and mRNAs to comprehensively catalog all genes having pre-mRNAs undergoing AS. A total of 192 624 AS events were detected and classified, including 103 566 (53.8%) basic events and 89 058 (46.2%) complex events which were formed by combination of various types of basic events. Intron retention was the dominant type of basic AS event, accounting for 24.1%. These AS events were identified from 91 128 transcripts which were generated from 26 669 genomic loci, of which consisted of 20 860 gene models. It was estimated that 55.3% maize genes may be subjected to AS. The transcripts mapping information can be used to improve the predicted gene models in maize. The data can be accessed at Plant Alternative Splicing Database

show abstract

Extensive Divergence in Alternative Splicing Patterns after Gene and Genome Duplication During the Evolutionary History of Arabidopsis

Cited by 59 publications

References 47 publications

Complexity of the Alternative Splicing Landscape in Plants

Complexity of the Alternative Splicing Landscape in Plants

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

Comprehensive Cataloging and Analysis of Alternative Splicing in Maize

Contact Info

Product

Resources

About