Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatumReport as inadecuate

Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 16:54

First Online: 06 February 2015Received: 08 February 2014Accepted: 15 January 2015DOI: 10.1186-s12864-015-1251-8

Cite this article as: Xie, BB., Li, D., Shi, WL. et al. BMC Genomics 2015 16: 54. doi:10.1186-s12864-015-1251-8


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.

KeywordsAlternative splicing Fungi RNA-Seq Intron retention Transcriptome Trichoderma longibrachiatum AbbreviationsA3SSAlternative 3’ splice site

A5SSAlternative 5’ splice site

ASAlternative splicing

FPKMNumbers of fragments per kilobase of exon per million fragments mapped

IA-IRAlternatively spliced introns except retained introns

ICConstitutive introns

IRIntron retention

IRRIntron retention ratio

MA3SSMultiple-alternative 3’ splice site

MA5SSMultiple-alternative 5’ splice site

MSMModified mineral salt medium

PDBPotato Dextrose Broth

RNA-SeqTranscriptome sequencing using high-throughput sequencing technology

SJSplice junction

TlTrichoderma longibrachiatum

5’ss5’ splice site

3’ss3’ splice site

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-1251-8 contains supplementary material, which is available to authorized users.

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Author: Bin-Bin Xie - Dan Li - Wei-Ling Shi - Qi-Long Qin - Xiao-Wei Wang - Jin-Cheng Rong - Cai-Yun Sun - Feng Huang - Xi-Ying Z


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