title: Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum.
abstract: BACKGROUND
  Alternative splicing is crucial for proteome diversity and functional complexity in higher organisms. However, the alternative splicing landscape in fungi is still elusive.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. xbb@sdu.edu.cn.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. xbb@sdu.edu.cn.|Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China. xbb@sdu.edu.cn.
authors: Bin-Bin
authors: BB
authors: Xie
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. lidan0925@126.com.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. lidan0925@126.com.
authors: Dan
authors: D
authors: Li
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. Swl87930@163.com.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. Swl87930@163.com.
authors: Wei-Ling
authors: WL
authors: Shi
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. qinqilong@sdu.edu.cn.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. qinqilong@sdu.edu.cn.|Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China. qinqilong@sdu.edu.cn.
authors: Qi-Long
authors: QL
authors: Qin
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. wangxiaowei235@mail.sdu.edu.cn.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. wangxiaowei235@mail.sdu.edu.cn.
authors: Xiao-Wei
authors: XW
authors: Wang
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. jch100.cool@163.com.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. jch100.cool@163.com.
authors: Jin-Cheng
authors: JC
authors: Rong
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. suncy@sdu.edu.cn.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. suncy@sdu.edu.cn.
authors: Cai-Yun
authors: CY
authors: Sun
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. fhuang@sdu.edu.cn.
authors: Feng
authors: F
authors: Huang
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. zhangxiying@sdu.edu.cn.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. zhangxiying@sdu.edu.cn.|Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China. zhangxiying@sdu.edu.cn.
authors: Xi-Ying
authors: XY
authors: Zhang
authors: Technology Center, Shandong Tobacco Industry Corporation, Jinan, 250013, China. dongxiaowei1972@163.com.
authors: Xiao-Wei
authors: XW
authors: Dong
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. cxl0423@sdu.edu.cn.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. cxl0423@sdu.edu.cn.|Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China. cxl0423@sdu.edu.cn.
authors: Xiu-Lan
authors: XL
authors: Chen
authors: Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. bczhou@ms.qdio.ac.cn.
authors: Bai-Cheng
authors: BC
authors: Zhou
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. zhangyz@sdu.edu.cn.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. zhangyz@sdu.edu.cn.|Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China. zhangyz@sdu.edu.cn.
authors: Yu-Zhong
authors: YZ
authors: Zhang
authors: State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. xysong@sdu.edu.cn.|Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. xysong@sdu.edu.cn.|Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China. xysong@sdu.edu.cn.
authors: Xiao-Yan
authors: XY
authors: Song
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D001483:Base Sequence; D005091:Exons / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D007438:Introns / Q000235:genetics; D012313:RNA / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D012326:RNA Splicing / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014242:Trichoderma / Q000235:genetics*
chemical_list: D022821:RNA Splice Sites; D012313:RNA
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