Data Structures for Genome Annotation, Alternative Splicing, and Validation

2006 ◽  
pp. 114-123
Author(s):  
Sven Mielordt ◽  
Ivo Grosse ◽  
Jürgen Kleffe
Keyword(s):  
Alternative Splicing ◽  
Data Structures ◽  
Genome Annotation

scholarly journals ECgene: genome annotation for alternative splicing

2004 ◽  
Vol 33 (Database issue) ◽  
pp. D75-D79 ◽  
Author(s):  
P. Kim
Keyword(s):  
Alternative Splicing ◽  
Genome Annotation

scholarly journals PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes

2021 ◽  
Vol 12 ◽  
Author(s):  
Ali Ali ◽  
Gary H. Thorgaard ◽  
Mohamed Salem
Keyword(s):  
Rainbow Trout ◽  
Alternative Splicing ◽  
Single Molecule ◽  
Genome Annotation ◽  
Reference Genome ◽  
Cold Water ◽  
Intron Retention ◽  
Transcriptome Assembly ◽  
Model Organism ◽  
Fish Growth

Rainbow trout is an important model organism that has received concerted international efforts to study the transcriptome. For this purpose, short-read sequencing has been primarily used over the past decade. However, these sequences are too short of resolving the transcriptome complexity. This study reported a first full-length transcriptome assembly of the rainbow trout using single-molecule long-read isoform sequencing (Iso-Seq). Extensive computational approaches were used to refine and validate the reconstructed transcriptome. The study identified 10,640 high-confidence transcripts not previously annotated, in addition to 1,479 isoforms not mapped to the current Swanson reference genome. Most of the identified lncRNAs were non-coding variants of coding transcripts. The majority of genes had multiple transcript isoforms (average ∼3 isoforms/locus). Intron retention (IR) and exon skipping (ES) accounted for 56% of alternative splicing (AS) events. Iso-Seq improved the reference genome annotation, which allowed identification of characteristic AS associated with fish growth, muscle accretion, disease resistance, stress response, and fish migration. For instance, an ES in GVIN1 gene existed in fish susceptible to bacterial cold-water disease (BCWD). Besides, under five stress conditions, there was a commonly regulated exon in prolyl 4-hydroxylase subunit alpha-2 (P4HA2) gene. The reconstructed gene models and their posttranscriptional processing in rainbow trout provide invaluable resources that could be further used for future genetics and genomics studies. Additionally, the study identified characteristic transcription events associated with economically important phenotypes, which could be applied in selective breeding.

Profiling novel alternative splicing within multiple tissues puts insight into the porcine genome annotation

2019 ◽  
Author(s):  
Jian-Feng Liu ◽  
Wen Feng ◽  
Pengju Zhao ◽  
Xianrui Zheng
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
Genome Annotation ◽  
Donor Site ◽  
The Novel ◽  
Rna Seq ◽  
Novel Proteins ◽  
Genome Wide ◽  
Alternative Donor ◽  
Mrna Precursor

Abstract Background Alternative splicing (AS) is a process that mRNA precursor splices intron to form the mature mRNA. AS plays important roles in contributing to transcriptome and proteome divert. However, to date there is no research about pig AS in genome-wide level by RNA sequencing. Results To characterize the AS in pigs, herein we detected genome-wide transcripts and events by RNA sequencing technology (RNA-seq) 34 different tissues in Duroc pigs. In total, we identified 138, 403 AS events and 29, 270 expressed genes. We found alternative donor site was the most common AS form, which is accounted for 44% of the total AS events. The percentage of the other 3 AS forms are all around 19%. The results showed that the most common AS events (alternative donor site) can produce different transcripts or different proteins which affect the biological process. Among these AS events, 109, 483 were novel AS events, and the number of alternative donor splice site has increased the most (Accounting for 44% of the novel AS events).Conclusions The expression of gene with tissue specific AS events showed that the functions of these genes were consistent with the tissue function. AS increased proteome diversity and resulted in novel proteins that gained and lost important functional domains. In summary, these findings extend genome annotation and highlight roles that AS acts in tissue identity in pig.Key words: Alternative splicing; transcript; protein; SNP

scholarly journals Improved reference genome annotation of Brassica rapa by PacBio RNA sequencing

2021 ◽  
Author(s):  
Zhicheng Zhang ◽  
Jing Guo ◽  
Xu Cai ◽  
Yufang Li ◽  
Xi Xi ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Brassica Rapa ◽  
Genome Annotation ◽  
Reference Genome ◽  
Genomic Analysis ◽  
Genomic Research ◽  
Vegetable Crops ◽  
Structural Variations ◽  
Protein Coding ◽  
Genome Annotations

The species Brassica rapa includes several important vegetable crops. The draft reference genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated twice. The pangenome with structural variations of 18 B. rapa accessions was published in 2021. Although extensive genomic analysis has been conducted on B. rapa, a comprehensive genome annotation including gene structure, alternative splicing events, and non-coding genes is still lacking. Therefore, we used the Pacific Biosciences (PacBio) single-molecular long-read technology to improve gene models and produced the annotated genome version 3.5. In total, we obtained 753,041 full-length non-chimeric (FLNC) reads and collapsed these into 92,810 non-redundant consensus isoforms, capturing 48% of the genes annotated in the B. rapa reference genome annotation v3.1. Based on the isoform data, we identified 830 novel protein-coding genes that were missed in previous genome annotations, defined the UTR regions of 20,340 annotated genes and corrected 886 wrongly-spliced genes. We also identified 28,564 alternative splicing (AS) events and 1,480 long non-coding RNAs (lncRNAs). We produced a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.

scholarly journals The importance of identifying alternative splicing in vertebrate genome annotation

Database ◽  
2012 ◽  
Vol 2012 ◽  
Author(s):  
Adam Frankish ◽  
Jonathan M. Mudge ◽  
Mark Thomas ◽  
Jennifer Harrow
Keyword(s):  
Alternative Splicing ◽  
Genome Annotation ◽  
Vertebrate Genome

scholarly journals Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1405
Author(s):  
Wen Feng ◽  
Pengju Zhao ◽  
Xianrui Zheng ◽  
Zhengzheng Hu ◽  
Jianfeng Liu
Keyword(s):  
Alternative Splicing ◽  
Genome Annotation ◽  
Intron Retention ◽  
Single Gene ◽  
Donor Site ◽  
Exon Skipping ◽  
Acceptor Site ◽  
Porcine Genome ◽  
Expression Of Genes ◽  
Alternative Donor

Alternative splicing (AS) is a process during gene expression that results in a single gene coding for different protein variants. AS contributes to transcriptome and proteome diversity. In order to characterize AS in pigs, genome-wide transcripts and AS events were detected using RNA sequencing of 34 different tissues in Duroc pigs. In total, 138,403 AS events and 29,270 expressed genes were identified. An alternative donor site was the most common AS form and accounted for 44% of the total AS events. The percentage of the other three AS forms (exon skipping, alternative acceptor site, and intron retention) was approximately 19%. The results showed that the most common AS events involving alternative donor sites could produce different transcripts or proteins that affect the biological processes. The expression of genes with tissue-specific AS events showed that gene functions were consistent with tissue functions. AS increased proteome diversity and resulted in novel proteins that gained or lost important functional domains. In summary, these findings extend porcine genome annotation and highlight roles that AS could play in determining tissue identity.

scholarly journals Profiling novel alternative splicing within multiple tissues puts insight into the porcine genome annotation

2019 ◽  
Author(s):  
Wen Feng ◽  
Pengju Zhao ◽  
Xianrui Zheng ◽  
Jian-Feng Liu
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
Genome Annotation ◽  
Intron Retention ◽  
Donor Site ◽  
Exon Skipping ◽  
Acceptor Site ◽  
Novel Proteins ◽  
Genome Wide ◽  
Alternative Donor

Abstract Background Alternative splicing (AS) is a process that mRNA precursor splices intron to form the mature mRNA. AS plays important roles in contributing to transcriptome and proteome divert. However, to date there is no research about pig AS in genome-wide level by RNA sequencing. Results To characterize the AS in pigs, herein we detected genome-wide transcripts and events by RNA sequencing technology (RNA-seq) 34 different tissues in Duroc pigs. In total, we identified 138, 403 AS events and 29, 270 expressed genes. We found alternative donor site was the most common AS form, which is accounted for 44% of the total AS events. The percentage of the other 3 AS forms (Exon skipping, Alternative acceptor site and Intron retention) are all around 19%. The results showed that the most common AS events (alternative donor site) can produce different transcripts or different proteins which affect the biological process. Among these AS events, 109, 483 were novel AS events, and the number of alternative donor splice site has increased the most (Accounting for 44% of the novel AS events). Conclusions The expression of gene with tissue specific AS events showed that the functions of these genes were consistent with the tissue function. AS increased proteome diversity and resulted in novel proteins that gained and lost important functional domains. In summary, these findings extend genome annotation and highlight roles that AS acts in tissue identity in pig.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

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