ArticleNucleic acids research2007
EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Omics Application of Bio-Hydrogen Production Through Green AlgaFrontiers in bioengineering and biotechnology · 2019Review
- MicroRNAs modulate adaption to multiple abiotic stresses in Chlamydomonas reinhardtii.Scientific reports · 2016Article
- Do housekeeping genes exist?PloS one · 2015Article
- Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii.BMC genomics · 2011Article
- Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation.Photosynthesis research · 2010Article
- Critical role of 7,8-didemethyl-8-hydroxy-5-deazariboflavin for photoreactivation in Chlamydomonas reinhardtii.The Journal of biological chemistry · 2010Article
- Enzymatic properties of the ferredoxin-dependent nitrite reductase from Chlamydomonas reinhardtii. Evidence for hydroxylamine as a late intermediate in ammonia production.Photosynthesis research · 2010Article
- ESTPiper--a web-based analysis pipeline for expressed sequence tags.BMC genomics · 2009Article
- Update of the Diatom EST Database: a new tool for digital transcriptomics.Nucleic acids research · 2009Article
- Eukaryotic complex I: functional diversity and experimental systems to unravel the assembly process.Molecular genetics and genomics : MGG · 2008Review
- Article
- High quality metabolomic data for Chlamydomonas reinhardtii.Plant methods · 2008Article
- Chlamydomonas reinhardtii: a convenient model system for the study of DNA repair in photoautotrophic eukaryotes.Current genetics · 2008Review
- The Chlamydomonas genome reveals the evolution of key animal and plant functions.Science (New York, N.Y.) · 2007Article
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7 authors.
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Abstract
Clustering and assembly of expressed sequence tags (ESTs) constitute the basis for most genomewide descriptions of a transcriptome. This approach is limited by the decline in sequence quality toward the end of each EST, impacting both sequence clustering and assembly. Here, we exploit the available draft genome sequence of the unicellular green alga Chlamydomonas reinhardtii to guide clustering and to correct errors in the ESTs. We have grouped all available EST and cDNA sequences into 12,063 ACEGs (assembly of contiguous ESTs based on genome) and generated 15,857 contigs of average length 934 nt. We predict that roughly 3000 of our contigs represent full-length transcripts. Compared to previous assemblies, ACEGs show extended contig length, increased accuracy and a reduction in redundancy. Because our assembly protocol also uses ESTs with no corresponding genomic sequences, it provides sequence information for genes interrupted by sequence gaps. Detailed analysis of randomly sampled ACEGs reveals several hundred putative cases of alternative splicing, many overlapping transcription units and new genes not identified by gene prediction algorithms. Our protocol, although developed for and tailored to the C. reinhardtii dataset, can be exploited by any eukaryotic genome project for which both a draft genome sequence and ESTs are available.
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