<i>Oases:</i>robust<i>de novo</i>RNA-seq assembly across the dynamic range of expression levels

Schulz, Marcel H.; Zerbino, Daniel R.; Vingron, Martin; Birney, Ewan

doi:10.1093/bioinformatics/bts094

Cited by 1,369 publications

(1,271 citation statements)

References 33 publications

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“…The data were used to assemble the viral genomes. Velvet (1.2.10) (Zerbino, 2010) and Oases (0.2.8) (Schulz et al, 2012) with a multi K-mer approach were used for this purpose (Zhao et al, 2011).…”

Section: Bioinformatics Analysismentioning

confidence: 99%

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi

Nerva¹,

et al. 2016

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Highlights• First report of mycoviruses isolated from fungi from marine environment.• Survey of mycoviruses using multiple approaches for both DNA and RNA genomes.• RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses.• Twelve new virus species were characterized molecularly.• Expression of a viral RNA from an endogenized cDNA segment. AbstractThe number of reported mycoviruses is increasing exponentially due to the current ability to detect mycoviruses using next-generation sequencing (NGS) approaches, with a large number of viral genomes built in-silico using data from fungal transcriptome projects. We decided to screen a collection of fungi originating from a specific marine environment (associated with the seagrass Posidonia oceanica) for the presence of mycoviruses: our findings reveal a wealth of diversity among these symbionts and this complexity will require further studies to address their specific role in this ecological niche. In specific, we identified twelve new virus species belonging to nine distinct lineages: they are members of megabirnavirus, totivirus, chrysovirus, partitivirus and five still undefined clades. We showed evidence of an endogenized virus ORF, and evidence of accumulation of dsRNA from metaviridae retroviral elements. We applied different techniques for detecting the presence of mycoviruses including (i) dsRNA extraction and cDNA cloning, (ii) small and total RNA sequencing through NGS techniques, (iii) rolling circle amplification (RCA) and total DNA extraction analyses, (iv) virus purifications and electron microscopy. We tried also to critically evaluate the intrinsic value and limitations of each of these techniques. Based on the samples we could compare directly, RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses. To our knowledge this is the first report on the virome of fungi isolated from marine environment.

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Section: Bioinformatics Analysismentioning

confidence: 99%

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi

Nerva¹,

et al. 2016

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“…The software applications Velvet version 1.1.04 (Zerbino and Birney, 2008) and Oases version 0.1 (Schulz et al, 2012) were used for de novo transcriptome assembly, with a k-mer size of 53. Oases was used to cluster the Velvet-assembled contigs to construct transcript isoforms.…”

Section: De Novo Short Read Assemblymentioning

confidence: 99%

Unfolding the secrets of coral–algal symbiosis

et al. 2014

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Dinoflagellates from the genus Symbiodinium form a mutualistic symbiotic relationship with reefbuilding corals. Here we applied massively parallel Illumina sequencing to assess genetic similarity and diversity among four phylogenetically diverse dinoflagellate clades (A, B, C and D) that are commonly associated with corals. We obtained more than 30 000 predicted genes for each Symbiodinium clade, with a majority of the aligned transcripts corresponding to sequence data sets of symbiotic dinoflagellates and o2% of sequences having bacterial or other foreign origin. We report 1053 genes, orthologous among four Symbiodinium clades, that share a high level of sequence identity to known proteins from the SwissProt (SP) database. Approximately 80% of the transcripts aligning to the 1053 SP genes were unique to Symbiodinium species and did not align to other dinoflagellates and unrelated eukaryotic transcriptomes/genomes. Six pathways were common to all four Symbiodinium clades including the phosphatidylinositol signaling system and inositol phosphate metabolism pathways. The list of Symbiodinium transcripts common to all four clades included conserved genes such as heat shock proteins (Hsp70 and Hsp90), calmodulin, actin and tubulin, several ribosomal, photosynthetic and cytochrome genes and chloroplast-based hemecontaining cytochrome P450, involved in the biosynthesis of xanthophylls. Antioxidant genes, which are important in stress responses, were also preserved, as were a number of calcium-dependent and calcium/calmodulin-dependent protein kinases that may play a role in the establishment of symbiosis. Our findings disclose new knowledge about the genetic uniqueness of symbiotic dinoflagellates and provide a list of homologous genes important for the foundation of coral-algal symbiosis.

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“…Firstly, RNA-seq reads are assembled using a de novo transcriptome assembler (such as Bridger (Chang et al, 2015), Trinity , Oases (Schulz et al, 2012), Trans-ABySS (Robertson et al, 2010) and etc.). Next, the assembled transcripts/contigs are mapped to the reference genome by employing an aligner for aligning long sequences (for example, Blat (Kent, 2002)).…”

Section: De Novo Transcriptome Reconstructionmentioning

confidence: 99%

Characterizing and annotating the genome using RNA-seq data

Chen

Shi

2016

Sci. China Life Sci.

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Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts (especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome-guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.RNA-seq, genome-guided transcriptome reconstruction, de novo assembly, long noncoding RNA, genetic variants

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Oases:robustde novoRNA-seq assembly across the dynamic range of expression levels

Cited by 1,369 publications

References 33 publications

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi

Unfolding the secrets of coral–algal symbiosis

Characterizing and annotating the genome using RNA-seq data

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