Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

Hegedűs, Zoltán; Zakrzewska, Anna; Ágoston, Vilmos; Ordas, Anita; Rácz, Péter; Mink, Mátyás; Spaink, Herman P.; Meijer, Annemarie H.

doi:10.1016/j.molimm.2009.07.002

Cited by 192 publications

(159 citation statements)

References 57 publications

Supporting

Mentioning

142

Contrasting

Order By: Relevance

“…These studies show a modest but complex host response in the early stages of infection (Meijer et al 2005;Hegedus et al 2009). Detailed analysis of immune factors involved in mycobacterial disease depends on the generation of more knockout zebrafish and development of specific antibodies directed against immune cells and chemokines/cytokines.…”

Section: Animal Models Of Tuberculosis: Zebrafishmentioning

confidence: 96%

“…Cite this article as Cold Spring Harb Perspect Med 2015;5:a018580 www.perspectivesinmedicine.org quencing studies (Meijer et al 2005;Hegedus et al 2009;Meijer and Spaink 2011;van der Vaart et al 2012). These studies show a modest but complex host response in the early stages of infection (Meijer et al 2005;Hegedus et al 2009).…”

Section: Animal Models Of Tuberculosis: Zebrafishmentioning

confidence: 99%

See 1 more Smart Citation

Animal Models of Tuberculosis: Zebrafish

Leeuwen

Sar

Bitter

2014

Cold Spring Harbor Perspectives in Medicine

View full text Add to dashboard Cite

Correspondence: a.vandersar@vumc.nl Over the past decade the zebrafish (Danio rerio) has become an attractive new vertebrate model organism for studying mycobacterial pathogenesis. The combination of mediumthroughput screening and real-time in vivo visualization has allowed new ways to dissect host pathogenic interaction in a vertebrate host. Furthermore, genetic screens on the host and bacterial sides have elucidated new mechanisms involved in the initiation of granuloma formation and the importance of a balanced immune response for control of mycobacterial pathogens. This article will highlight the unique features of the zebrafish-Mycobacterium marinum infection model and its added value for tuberculosis research.

show abstract

Section: Animal Models Of Tuberculosis: Zebrafishmentioning

confidence: 96%

Section: Animal Models Of Tuberculosis: Zebrafishmentioning

confidence: 99%

Animal Models of Tuberculosis: Zebrafish

Leeuwen

Sar

Bitter

2014

Cold Spring Harbor Perspectives in Medicine

View full text Add to dashboard Cite

show abstract

“…Over the past several years, NGS technologies have emerged as powerful tools for high-throughput sequence analysis and dramatically improved the speed and efficiency of gene discovery (Schuster 2008;Metzker, 2010). Moreover, these technologies have shown great potential for expanding sequence databases of not only model species (Hegedűs et al, 2009;Hillier et al, 2009;, but also non-model organisms (Collins et al, 2008;Wang et al, 2010a;Gao et al, 2012). Recently, the development of high-throughput DNA sequencing strategies has provided a new means of both mapping and quantifying transcriptomes, which is the complete set of all transcripts for certain types of cells or tissues in a specific developmental stage or physiological condition.…”

Section: Introductionmentioning

confidence: 99%

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

Wang

et al. 2013

J. Zhejiang Univ. Sci. B

View full text Add to dashboard Cite

Abstract:The soft-shelled turtle Pelodiscus sinensis is a high-profile turtle species because of its nutritional and medicinal value in Asian countries. However, little is known about the genes that are involved in formation of their nutritional quality traits, especially the molecular mechanisms responsible for unsaturated fatty acid and collagen biosynthesis. In the present study, the transcriptomes from six tissues from Pelodiscus sinensis were sequenced using an Illumina paired-end sequencing platform. We obtained more than 47 million sequencing reads and 73 954 unigenes with an average size of 754 bp by de-novo assembly. In total, 55.19% of the unigenes (40 814) had significant similarity with proteins in the National Center of Biotechnology Information (NCBI) non-redundant protein database and Swiss-Prot database (E-value <10 −5 ). Of these annotated unigenes, 9 156 and 11 947 unigenes were assigned to 52 gene ontology categories (GO) and 25 clusters of orthologous groups (COG), respectively. In total, 26 496 (35.83%) unigenes were assigned to 242 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we found a number of highly expressed genes involved in the regulation of P. sinensis unsaturated fatty acid biosynthesis and collagen formation, including desaturases, growth factors, transcription factors, and extracellular matrix components. Our data represent the most comprehensive sequence resource available for the Chinese soft-shelled turtle and could provide a basis for new research on this turtle as well as the molecular genetics and functional genomics of other terrapins. To our knowledge, we report for the first time, the large-scale RNA sequencing (RNA-Seq) of terrapin animals and would enrich the knowledge of turtles for future research.

show abstract

“…The sequencing platforms, such as the Illumina/Solexa Genome Analyzer, GS FLX Titanium System and ABI/SOLiD Gene Sequencer, can sequence in parallel massive amounts of cDNAs [10]. They have been successfully used to investigate the transcriptomes of a wide range of organisms including Pseudosciaena crocea, zebrafish, Aspergillus oryzae, rice, mouse and human [11][12][13][14][15][16]. The next-generation sequencing technologies have also been used in other functional genomics researches including genome annotation, small ncRNA profiling and aberrant transcript detection, which are areas previously covered by microarrays [17].…”

mentioning

confidence: 99%

Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology

et al. 2011

View full text Add to dashboard Cite

With high-throughput Solexa sequencing technology, we profiled Porphyra yezoensis transcriptomes from 8 different samples. More than 1200 megabases from 13333334 quality paired-end reads were generated, which were assembled into 31538 unigenes. Blast analysis showed that 56.7% unigenes were novel, which represented the specific genes of Porphyra and/or rhodophytes. Several hundreds of unigenes related to stress tolerance were discovered, including genes related to desiccation-(211) and high light-tolerance (31), flavonoid biosynthesis (10), reactive oxygen scavenging (48) and other stress-tolerance processes (208), which indicated there existed complex and diversity modes of stress tolerance in this species. A complete set of essential genes involved in the C3-(57) and C4-(44) carbon fixation pathway (except pyruvate phosphate dikinase) were discovered, which not only proved that they were actively transcribed but also clearly outlined the panoptic view of carbon fixation in Porphyra. Moreover, by statistically analyzing the types, proportions and frequencies of the interspersed repeats (TEs) and simple sequence repeats (SSRs), we discovered that the top three types of TEs were all retrotransposons and the trinucleotide was the absolute predominant type among SSRs, promoting our understanding of structural characteristics of the transcriptome. This study substantially improved the global view of the Porphyra genome and provided a valuable resource for future research.Porphyra yezoensis, red algae, transcriptome, Solexa sequencing technology, expressed sequence tags, functional analysis, transposable elements, microsatellites Citation:

show abstract

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

Cited by 192 publications

References 57 publications

Animal Models of Tuberculosis: Zebrafish

Animal Models of Tuberculosis: Zebrafish

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology

Contact Info

Product

Resources

About