Deep sequencing of the zebrafish transcriptome response to mycobacterium infection
Open accessAbstract
Novel high-throughput deep sequencing technology has dramatically changed the way that the functional complexity of transcriptomes can be studied. Here we report on the first use of this technology to gain insight into the wide range of transcriptional responses that are associated with an infectious disease process. Using Solexa/Illumina's digital gene expression (DGE) system, a tag-based transcriptome sequencing method, we investigated mycobacterium-induced transcriptome changes in a model vertebrate species, the zebrafish. We obtained a sequencing depth of over 5 million tags per sample with strong correlation between replicates. Tag mapping indicated that healthy and infected adult zebrafish express over 70% of all genes represented in transcript databases. Comparison of the data with a previous multi-platform microarray analysis showed that both types of technologies identified regulation of similar functional groups of genes. However, the unbiased nature of DGE analysis provided insights that microarray analysis could not have achieved. In particular, we show that DGE data sets are instrumental for verification of predicted gene models and allowed us to detect mycobacterium-regulated switching between different transcript isoforms. Moreover, genomic mapping of infection-induced DGE tags revealed novel transcript forms for which any previous EST-based evidence of expression was lacking. In conclusion, our deep sequencing analysis revealed in depth the high degree of transcriptional complexity of the host response to mycobacterial infection and resulted in the discovery and validation of new gene products with induced expression in infected individuals.
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Over the last two years, Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model and non-model organisms.
“Over the last two years, with the further confirmation that the relatively short reads can be effectively assembled [15], especially with the great advantage of paired-end sequencing [54], the Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model [12,16,55-58]and non-model organisms [25-27,59].”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [55]
The Abstract identifies this as a successful Solexa/Illumina transcriptome-sequencing study in zebrafish, a model organism. But the Methods (section 2.5, page unavailable) describe mapping short tags to existing transcript databases and the zebrafish genome, not de novo assembly; the cited paper therefore supports the sequencing example but not that part of the claim. (LLM, conf=0.87)
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Self-citation
- Authors
- Hegedűs, Z., Zakrzewska, A., Ágoston, V. C., Ordas, A., Rácz, P., Mink, M., Spaink, H. P., & Meijer, A. H.
- Affiliations
- Leiden University (NL)
- University of Szeged (HU)
- Corresponding author
- Meijer, Annemarie H.
- Venue
- Molecular Immunology
- Publisher
- Elsevier BV
- Published
- 2009-09
- Volume
- 46
- Issue
- 15
- Pages
- 2918-2930
- ISSN
- 0161-5890 (ISSN-L)
- OpenAlex
- W1966486838
- Cited by
- 216
- References
- 58
- Citations by year
- 2025: 2 · 2024: 1 · 2023: 4 · 2022: 1 · 2021: 6 · 2020: 13 · 2019: 16 · 2018: 5 · 2017: 6 · 2016: 15 · 2015: 19 · 2014: 26 · 2013: 25 · 2012: 30
- FWCI
- 10.29
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Immunology (publishedVersion)
- PubMed (publishedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- Funders
- European Commission
- Universiteit Leiden
- Leids Universitair Medisch Centrum
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Keywords
- zebrafish, mycobacterial infection, transcriptome, digital gene expression, gene expression profiling, alternative splicing, isoform switching, novel transcripts, microarray comparison
- MeSH terms
- Animals, Disease Models, Animal, Humans, Male, Mycobacterium Infections, Zebrafish, Transcriptional Activation, Sequence Analysis, RNA, Mycobacterium marinum, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Host-Pathogen Interactions
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