RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.
Identifieur interne : 001769 ( PubMed/Checkpoint ); précédent : 001768; suivant : 001770RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.
Auteurs : Keng-See Chow [Malaisie] ; Ahmad-Kamal Ghazali ; Chee-Choong Hoh ; Zainorlina Mohd-ZainuddinSource :
- BMC research notes [ 1756-0500 ] ; 2014.
Descripteurs français
- KwdFr :
- ARN des plantes (), ARN des plantes (biosynthèse), ARN des plantes (génétique), ARN des plantes (isolement et purification), ARN messager (), ARN messager (biosynthèse), ARN messager (génétique), ARN messager (isolement et purification), Analyse de profil d'expression de gènes (), Banque de gènes, Bases de données génétiques, Cadres ouverts de lecture, Feuilles de plante (métabolisme), Gènes de plante, Hevea (), Hevea (génétique), Protéines végétales (génétique), Reproductibilité des résultats, Régulation de l'expression des gènes végétaux, Séquençage nucléotidique à haut débit, Transcriptome, Écorce (métabolisme).
- MESH :
- biosynthèse : ARN des plantes, ARN messager.
- génétique : ARN des plantes, ARN messager, Hevea, Protéines végétales.
- isolement et purification : ARN des plantes, ARN messager.
- métabolisme : Feuilles de plante, Écorce.
- ARN des plantes, ARN messager, Analyse de profil d'expression de gènes, Banque de gènes, Bases de données génétiques, Cadres ouverts de lecture, Gènes de plante, Hevea, Reproductibilité des résultats, Régulation de l'expression des gènes végétaux, Séquençage nucléotidique à haut débit, Transcriptome.
English descriptors
- KwdEn :
- Databases, Genetic, Gene Expression Profiling (methods), Gene Expression Regulation, Plant, Gene Library, Genes, Plant, Hevea (chemistry), Hevea (genetics), High-Throughput Nucleotide Sequencing, Open Reading Frames, Plant Bark (metabolism), Plant Leaves (metabolism), Plant Proteins (genetics), RNA, Messenger (biosynthesis), RNA, Messenger (chemistry), RNA, Messenger (genetics), RNA, Messenger (isolation & purification), RNA, Plant (biosynthesis), RNA, Plant (chemistry), RNA, Plant (genetics), RNA, Plant (isolation & purification), Reproducibility of Results, Transcriptome.
- MESH :
- chemical , biosynthesis : RNA, Messenger, RNA, Plant.
- chemical , chemistry : RNA, Messenger, RNA, Plant.
- chemical , genetics : Plant Proteins, RNA, Messenger, RNA, Plant.
- chemistry : Hevea.
- genetics : Hevea.
- chemical , isolation & purification : RNA, Messenger, RNA, Plant.
- metabolism : Plant Bark, Plant Leaves.
- methods : Gene Expression Profiling.
- Databases, Genetic, Gene Expression Regulation, Plant, Gene Library, Genes, Plant, High-Throughput Nucleotide Sequencing, Open Reading Frames, Reproducibility of Results, Transcriptome.
Abstract
One of the concerns of assembling de novo transcriptomes is determining the amount of read sequences required to ensure a comprehensive coverage of genes expressed in a particular sample. In this report, we describe the use of Illumina paired-end RNA-Seq (PE RNA-Seq) reads from Hevea brasiliensis (rubber tree) bark to devise a transcript mapping approach for the estimation of the read amount needed for deep transcriptome coverage.
DOI: 10.1186/1756-0500-7-69
PubMed: 24484543
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:24484543Le document en format XML
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<term>Banque de gènes</term>
<term>Bases de données génétiques</term>
<term>Cadres ouverts de lecture</term>
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<term>Gene Library</term>
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<front><div type="abstract" xml:lang="en">One of the concerns of assembling de novo transcriptomes is determining the amount of read sequences required to ensure a comprehensive coverage of genes expressed in a particular sample. In this report, we describe the use of Illumina paired-end RNA-Seq (PE RNA-Seq) reads from Hevea brasiliensis (rubber tree) bark to devise a transcript mapping approach for the estimation of the read amount needed for deep transcriptome coverage.</div>
</front>
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<ArticleTitle>RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.</ArticleTitle>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">One of the concerns of assembling de novo transcriptomes is determining the amount of read sequences required to ensure a comprehensive coverage of genes expressed in a particular sample. In this report, we describe the use of Illumina paired-end RNA-Seq (PE RNA-Seq) reads from Hevea brasiliensis (rubber tree) bark to devise a transcript mapping approach for the estimation of the read amount needed for deep transcriptome coverage.</AbstractText>
<AbstractText Label="FINDINGS" NlmCategory="RESULTS">We optimized the assembly of a Hevea bark transcriptome based on 16 Gb Illumina PE RNA-Seq reads using the Oases assembler across a range of k-mer sizes. We then assessed assembly quality based on transcript N50 length and transcript mapping statistics in relation to (a) known Hevea cDNAs with complete open reading frames, (b) a set of core eukaryotic genes and (c) Hevea genome scaffolds. This was followed by a systematic transcript mapping process where sub-assemblies from a series of incremental amounts of bark transcripts were aligned to transcripts from the entire bark transcriptome assembly. The exercise served to relate read amounts to the degree of transcript mapping level, the latter being an indicator of the coverage of gene transcripts expressed in the sample. As read amounts or datasize increased toward 16 Gb, the number of transcripts mapped to the entire bark assembly approached saturation. A colour matrix was subsequently generated to illustrate sequencing depth requirement in relation to the degree of coverage of total sample transcripts.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">We devised a procedure, the "transcript mapping saturation test", to estimate the amount of RNA-Seq reads needed for deep coverage of transcriptomes. For Hevea de novo assembly, we propose generating between 5-8 Gb reads, whereby around 90% transcript coverage could be achieved with optimized k-mers and transcript N50 length. The principle behind this methodology may also be applied to other non-model plants, or with reads from other second generation sequencing platforms.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chow</LastName>
<ForeName>Keng-See</ForeName>
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<AffiliationInfo><Affiliation>Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor, Malaysia. kschow@lgm.gov.my.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Ghazali</LastName>
<ForeName>Ahmad-Kamal</ForeName>
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<Author ValidYN="Y"><LastName>Hoh</LastName>
<ForeName>Chee-Choong</ForeName>
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</Author>
<Author ValidYN="Y"><LastName>Mohd-Zainuddin</LastName>
<ForeName>Zainorlina</ForeName>
<Initials>Z</Initials>
</Author>
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<MeshHeading><DescriptorName UI="D028482" MajorTopicYN="N">Hevea</DescriptorName>
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<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
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<MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName>
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<MeshHeading><DescriptorName UI="D024301" MajorTopicYN="N">Plant Bark</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
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<MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName>
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<affiliations><list><country><li>Malaisie</li>
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