ArticleBMC genomics2015
Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 39 citations in OpenAlex.
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- The golden genome annotation of Ganoderma lingzhi reveals a more complex scenario of eukaryotic gene structure and transcription activity.BMC biology · 2024Article
- Organization and Unconventional Integration of the Mating-Type Loci inJournal of fungi (Basel, Switzerland) · 2022Article
- Intron retention coupled with nonsense-mediated decay is involved in cellulase biosynthesis in cellulolytic fungi.Biotechnology for biofuels and bioproducts · 2022Article
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- Evidence of a New MoYpd1p Phosphotransferase Isoform in the Multistep Phosphorelay System ofJournal of fungi (Basel, Switzerland) · 2021Article
- Production of tailor-made enzymes to facilitate lipid extraction from the oleaginous yeast Schwanniomyces occidentalis.AMB Express · 2020Article
- Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant.BMC genomics · 2020Article
- Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves.PloS one · 2020Article
- The Putative MethyltransferaseFrontiers in microbiology · 2020Article
- A spliceosomal twin intron (stwintron) participates in both exon skipping and evolutionary exon loss.Scientific reports · 2019Article
- Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- A novel splice mutation induces exon skipping of the EXT1 gene in patients with hereditary multiple exostoses.International journal of oncology · 2019Article
- Transcriptome analysis reveals the host selection fitness mechanisms of the Rhizoctonia solani AG1IA pathogen.Scientific reports · 2017Article
- Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae.BMC genomics · 2017Article
- Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects ofFrontiers in microbiology · 2017Review
- Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses.Frontiers in plant science · 2017Review
- Distinct Transcriptional and Alternative Splicing Signatures of Decidual CD4Frontiers in immunology · 2017Article
- Identification of Three Novel Splicing Variants and Expression Analysis of Chicken GPR1 Gene.BioMed research international · 2017Article
- Schizophyllum commune has an extensive and functional alternative splicing repertoire.Scientific reports · 2016Article
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Authors and funding
14 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative splicing is crucial for proteome diversity and functional complexity in higher organisms. However, the alternative splicing landscape in fungi is still elusive.
resultsThe transcriptome of the filamentous fungus Trichoderma longibrachiatum was deep sequenced using Illumina Solexa technology. A total of 14305 splice junctions were discovered. Analyses of alternative splicing events revealed that the number of all alternative splicing events (10034), intron retentions (IR, 9369), alternative 5' splice sites (A5SS, 167), and alternative 3' splice sites (A3SS, 302) is 7.3, 7.4, 5.1, and 5.9-fold higher, respectively, than those observed in the fungus Aspergillus oryzae using Illumina Solexa technology. This unexpectedly high ratio of alternative splicing suggests that alternative splicing is important to the transcriptome diversity of T. longibrachiatum. Alternatively spliced introns had longer lengths, higher GC contents, and lower splice site scores than constitutive introns. Further analysis demonstrated that the isoform relative frequencies were correlated with the splice site scores of the isoforms. Moreover, comparative transcriptomics determined that most enzymes related to glycolysis and the citrate cycle and glyoxylate cycle as well as a few carbohydrate-active enzymes are transcriptionally regulated.
conclusionsThis study, consisting of a comprehensive analysis of the alternative splicing landscape in the filamentous fungus T. longibrachiatum, revealed an unexpectedly high ratio of alternative splicing events and provided new insights into transcriptome diversity in fungi.
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