Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum
Bin-Bin Xie,Dan Li,Wei-Ling Shi,Qi-Long Qin,Xiao-Wei Wang,Jin-Cheng Rong,Cai-Yun Sun,Feng Huang,Xi-Ying Zhang,Xiao-Wei Dong,Xiu-Lan Chen,Bai-Cheng Zhou,Yu-Zhong Zhang,Xiao-Yan Song +13 more
Reads0
Chats0
TLDR
A comprehensive analysis of the alternative splicing landscape in the filamentous fungus T. longibrachiatum was performed in this article, which revealed an unexpectedly high ratio of alternative splice events and provided new insights into transcriptome diversity in fungi.Abstract:
Alternative splicing is crucial for proteome diversity and functional complexity in higher organisms. However, the alternative splicing landscape in fungi is still elusive. The 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. This 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.read more
Citations
More filters
Journal ArticleDOI
Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi.
Krisztina Krizsán,Éva Almási,Zsolt Merényi,Neha Sahu,Máté Virágh,Tamás Kószó,Stephen J. Mondo,Brigitta Kiss,Balázs Bálint,Ursula Kües,Kerrie Barry,Judit Cseklye,Botond Hegedüs,Bernard Henrissat,Bernard Henrissat,Jenifer Johnson,Anna Lipzen,Robin A. Ohm,István Nagy,Jasmyn Pangilinan,Juying Yan,Yi Xiong,Igor V. Grigoriev,Igor V. Grigoriev,David S. Hibbett,László Nagy +25 more
TL;DR: A reference atlas of mushroom formation is constructed based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes).
Journal ArticleDOI
Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae
TL;DR: Functional enrichment analysis showed that AS genes are involved in most known biological functions and enriched in ATP biosynthesis, sexual/asexual reproduction, morphogenesis, signal transduction etc., predicting that the AS regulation modulates mRNA isoform output and shapes the V. dahliae proteome plasticity of the pathogen in response to the environmental and developmental changes.
Journal ArticleDOI
Intron retention-dependent gene regulation in Cryptococcus neoformans.
Sara Gonzalez-Hilarion,Damien Paulet,Kyung-Tae Lee,Chung-Chau Hon,Pierre Lechat,Estelle Mogensen,Frédérique Moyrand,Caroline Proux,Rony Barboux,Giovanni Bussotti,Jungwook Hwang,Jean Yves Coppée,Yong Sun Bahn,Guilhem Janbon +13 more
TL;DR: The re-annotated genome of C. neoformans suggests the existence of an intron retention-dependent mechanism of gene expression regulation that is not dependent on NMD and provides a mechanism to tune gene expression levels in response to any environmental modification.
Journal ArticleDOI
Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant.
Yeyun Li,Xiaozeng Mi,Shiqi Zhao,Junyan Zhu,Rui Guo,Xiaobo Xia,Lu Liu,Shengrui Liu,Chaoling Wei +8 more
TL;DR: It is demonstrated that changes in AS numbers and transcript expression may contribute to rapid changes in gene expression and metabolite profile during cold acclimation, suggesting that AS events play an important regulatory role in response to cold Acclimation in tea plant.
Journal ArticleDOI
Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects of Trichoderma.
TL;DR: This review highlights the associated bottlenecks and use of state-of-the-art procedures in addressing the gap to accelerate future accomplishment of biocontrol mechanisms.
References
More filters
Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell,Cole Trapnell,Brian A. Williams,Geo Pertea,Ali Mortazavi,Gordon Kwan,Marijke J. van Baren,Steven L. Salzberg,Barbara J. Wold,Lior Pachter +9 more
TL;DR: The results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.
Journal ArticleDOI
TopHat: discovering splice junctions with RNA-Seq
TL;DR: The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer.
Journal ArticleDOI
WebLogo: A Sequence Logo Generator
TL;DR: WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment that provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive.
Journal ArticleDOI
Alternative Isoform Regulation in Human Tissue Transcriptomes
Eric T. Wang,Rickard Sandberg,Rickard Sandberg,Shujun Luo,Irina Khrebtukova,Lu Zhang,Christine Mayr,Stephen F. Kingsmore,Gary P. Schroth,Christopher B. Burge +9 more
TL;DR: An in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments yielding a digital inventory of gene and mRNA isoform expression suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.