Dataset Information

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

ABSTRACT: Motivation:Sequencing studies on non-model organisms often interrogate both genomes and transcriptomes with massive amounts of short sequences. Such studies require de novo analysis tools and techniques, when the species and closely related species lack high quality reference resources. For certain applications such as de novo annotation, information on putative exons and alternative splicing may be desirable. Results:Here we present ChopStitch, a new method for finding putative exons de novo and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-Seq data with the help of a Bloom filter that represents the k-mer spectrum of WGSS reads. The algorithm also accounts for base substitutions in transcript sequences that may be derived from sequencing or assembly errors, haplotype variations, or putative RNA editing events. The primary output of our tool is a FASTA file containing putative exons. Further, exon edges are interrogated for alternative exon-exon boundaries to detect transcript isoforms, which are represented as splice graphs in DOT output format. Availability and implementation:ChopStitch is written in Python and C++ and is released under the GPL license. It is freely available at https://github.com/bcgsc/ChopStitch. Contact:hkhan@bcgsc.ca or ibirol@bcgsc.ca. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Khan H

PROVIDER: S-EPMC5946899 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

Khan Hamza H Mohamadi Hamid H Vandervalk Benjamin P BP Warren Rene L RL Chu Justin J Birol Inanc I

Bioinformatics (Oxford, England) 20180501 10

<h4>Motivation</h4>Sequencing studies on non-model organisms often interrogate both genomes and transcriptomes with massive amounts of short sequences. Such studies require de novo analysis tools and techniques, when the species and closely related species lack high quality reference resources. For certain applications such as de novo annotation, information on putative exons and alternative splicing may be desirable.<h4>Results</h4>Here we present ChopStitch, a new method for finding putative e ...[more]

PMID: 29300846

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Project description:BACKGROUND:The investigation of transcriptome profiles using short reads in non-model organisms, which lack of well-annotated genomes, is limited by partial gene reconstruction and isoform detection. In contrast, long-reads sequencing techniques revealed their potential to generate complete transcript assemblies even when a reference genome is lacking. Cynara cardunculus var. altilis (DC) (cultivated cardoon) is a perennial hardy crop adapted to dry environments with many industrial and nutraceutical applications due to the richness of secondary metabolites mostly produced in flower heads. The investigation of this species benefited from the recent release of a draft genome, but the transcriptome profile during the capitula formation still remains unexplored. In the present study we show a transcriptome analysis of vegetative and inflorescence organs of cultivated cardoon through a novel hybrid RNA-seq assembly approach utilizing both long and short RNA-seq reads. RESULTS:The inclusion of a single Nanopore flow-cell output in a hybrid sequencing approach determined an increase of 15% complete assembled genes and 18% transcript isoforms respect to short reads alone. Among 25,463 assembled unigenes, we identified 578 new genes and updated 13,039 gene models, 11,169 of which were alternatively spliced isoforms. During capitulum development, 3424 genes were differentially expressed and approximately two-thirds were identified as transcription factors including bHLH, MYB, NAC, C2H2 and MADS-box which were highly expressed especially after capitulum opening. We also show the expression dynamics of key genes involved in the production of valuable secondary metabolites of which capitulum is rich such as phenylpropanoids, flavonoids and sesquiterpene lactones. Most of their biosynthetic genes were strongly transcribed in the flower heads with alternative isoforms exhibiting differentially expression levels across the tissues. CONCLUSIONS:This novel hybrid sequencing approach allowed to improve the transcriptome assembly, to update more than half of annotated genes and to identify many novel genes and different alternatively spliced isoforms. This study provides new insights on the flowering cycle in an Asteraceae plant, a valuable resource for plant biology and breeding in Cynara and an effective method for improving gene annotation.

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Dataset Information

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

Publications

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

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