RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis
Identifieur interne : 001B12 ( Main/Exploration ); précédent : 001B11; suivant : 001B13RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis
Auteurs : Keng-See Chow [Malaisie] ; Ahmad-Kamal Ghazali [Malaisie] ; Chee-Choong Hoh [Malaisie] ; Zainorlina Mohd-Zainuddin [Malaisie]Source :
- 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
We optimized the assembly of a
We devised a procedure, the “transcript mapping saturation test”, to estimate the amount of RNA-Seq reads needed for deep coverage of transcriptomes. For
Url:
DOI: 10.1186/1756-0500-7-69
PubMed: 24484543
PubMed Central: 3926681
Affiliations:
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Le document en format XML
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Selangor</wicri:regionArea><wicri:noRegion>Selangor</wicri:noRegion></affiliation></author><author><name sortKey="Ghazali, Ahmad Kamal" sort="Ghazali, Ahmad Kamal" uniqKey="Ghazali A" first="Ahmad-Kamal" last="Ghazali">Ahmad-Kamal Ghazali</name><affiliation wicri:level="1"><nlm:aff id="I2">Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong 43200, Seri Kembangan Balakong, Selangor, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong 43200, Seri Kembangan Balakong, Selangor</wicri:regionArea><wicri:noRegion>Selangor</wicri:noRegion></affiliation></author><author><name sortKey="Hoh, Chee Choong" sort="Hoh, Chee Choong" uniqKey="Hoh C" first="Chee-Choong" last="Hoh">Chee-Choong Hoh</name><affiliation wicri:level="1"><nlm:aff id="I2">Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong 43200, Seri Kembangan Balakong, Selangor, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong 43200, Seri Kembangan Balakong, Selangor</wicri:regionArea><wicri:noRegion>Selangor</wicri:noRegion></affiliation></author><author><name sortKey="Mohd Zainuddin, Zainorlina" sort="Mohd Zainuddin, Zainorlina" uniqKey="Mohd Zainuddin Z" first="Zainorlina" last="Mohd-Zainuddin">Zainorlina Mohd-Zainuddin</name><affiliation wicri:level="1"><nlm:aff id="I1">Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor</wicri:regionArea><wicri:noRegion>Selangor</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Research Notes</title><idno type="eISSN">1756-0500</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Genetic</term><term>Gene Expression Profiling (methods)</term><term>Gene Expression Regulation, Plant</term><term>Gene Library</term><term>Genes, Plant</term><term>Hevea (chemistry)</term><term>Hevea (genetics)</term><term>High-Throughput Nucleotide Sequencing</term><term>Open Reading Frames</term><term>Plant Bark (metabolism)</term><term>Plant Leaves (metabolism)</term><term>Plant Proteins (genetics)</term><term>RNA, Messenger (biosynthesis)</term><term>RNA, Messenger (chemistry)</term><term>RNA, Messenger (genetics)</term><term>RNA, Messenger (isolation & purification)</term><term>RNA, Plant (biosynthesis)</term><term>RNA, Plant (chemistry)</term><term>RNA, Plant (genetics)</term><term>RNA, Plant (isolation & purification)</term><term>Reproducibility of Results</term><term>Transcriptome</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes ()</term><term>ARN des plantes (biosynthèse)</term><term>ARN des plantes (génétique)</term><term>ARN des plantes (isolement et purification)</term><term>ARN messager ()</term><term>ARN messager (biosynthèse)</term><term>ARN messager (génétique)</term><term>ARN messager (isolement et purification)</term><term>Analyse de profil d'expression de gènes ()</term><term>Banque de gènes</term><term>Bases de données génétiques</term><term>Cadres ouverts de lecture</term><term>Feuilles de plante (métabolisme)</term><term>Gènes de plante</term><term>Hevea ()</term><term>Hevea (génétique)</term><term>Protéines végétales (génétique)</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes végétaux</term><term>Séquençage nucléotidique à haut débit</term><term>Transcriptome</term><term>Écorce (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>ARN des plantes</term><term>ARN messager</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Hevea</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Hevea</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term><term>ARN messager</term><term>Hevea</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ARN des plantes</term><term>ARN messager</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plant Bark</term><term>Plant Leaves</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Feuilles de plante</term><term>Écorce</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Gene Expression Regulation, Plant</term><term>Gene Library</term><term>Genes, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Open Reading Frames</term><term>Reproducibility of Results</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN des plantes</term><term>ARN messager</term><term>Analyse de profil d'expression de gènes</term><term>Banque de gènes</term><term>Bases de données génétiques</term><term>Cadres ouverts de lecture</term><term>Gènes de plante</term><term>Hevea</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes végétaux</term><term>Séquençage nucléotidique à haut débit</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>One of the concerns of assembling <italic>de novo</italic> 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 <italic>Hevea brasiliensis</italic> (rubber tree) bark to devise a transcript mapping approach for the estimation of the read amount needed for deep transcriptome coverage.</p></sec><sec><title>Findings</title><p>We optimized the assembly of a <italic>Hevea</italic> 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 <italic>Hevea</italic> cDNAs with complete open reading frames, (b) a set of core eukaryotic genes and (c) <italic>Hevea</italic> 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.</p></sec><sec><title>Conclusions</title><p>We devised a procedure, the “transcript mapping saturation test”, to estimate the amount of RNA-Seq reads needed for deep coverage of transcriptomes. For <italic>Hevea de novo</italic> 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.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wang, Z" uniqKey="Wang Z">Z Wang</name></author><author><name sortKey="Gerstein, M" uniqKey="Gerstein M">M Gerstein</name></author><author><name sortKey="Snyder, M" uniqKey="Snyder M">M Snyder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ozsolak, F" uniqKey="Ozsolak F">F Ozsolak</name></author><author><name sortKey="Milos, Pm" uniqKey="Milos P">PM Milos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Verk, Mc" uniqKey="Van Verk M">MC Van Verk</name></author><author><name sortKey="Hickman, R" uniqKey="Hickman R">R Hickman</name></author><author><name sortKey="Pieterse, Cmj" uniqKey="Pieterse C">CMJ Pieterse</name></author><author><name sortKey="Van Wees, Scm" uniqKey="Van Wees S">SCM Van Wees</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schulz, Mh" uniqKey="Schulz M">MH Schulz</name></author><author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name></author><author><name sortKey="Vingron, M" uniqKey="Vingron M">M Vingron</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, R" uniqKey="Li R">R Li</name></author><author><name sortKey="Zhu, H" uniqKey="Zhu H">H Zhu</name></author><author><name sortKey="Ruan, J" uniqKey="Ruan J">J Ruan</name></author><author><name sortKey="Qian, W" uniqKey="Qian W">W Qian</name></author><author><name sortKey="Fang, X" uniqKey="Fang X">X 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Korf</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kush, A" uniqKey="Kush A">A Kush</name></author><author><name sortKey="Goyvaerts, E" uniqKey="Goyvaerts E">E Goyvaerts</name></author><author><name sortKey="Chye, Ml" uniqKey="Chye M">ML Chye</name></author><author><name sortKey="Chua, Nh" uniqKey="Chua N">NH Chua</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mackenzie, Dj" uniqKey="Mackenzie D">DJ MacKenzie</name></author><author><name sortKey="Mclean, Ma" uniqKey="Mclean M">MA McLean</name></author><author><name sortKey="Mukerji, S" uniqKey="Mukerji S">S Mukerji</name></author><author><name sortKey="Green, M" uniqKey="Green M">M Green</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Slater, Gs" uniqKey="Slater G">GS Slater</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Malaisie</li></country></list><tree><country name="Malaisie"><noRegion><name sortKey="Chow, Keng See" sort="Chow, Keng See" uniqKey="Chow K" first="Keng-See" last="Chow">Keng-See Chow</name></noRegion><name sortKey="Ghazali, Ahmad Kamal" sort="Ghazali, Ahmad Kamal" uniqKey="Ghazali A" first="Ahmad-Kamal" last="Ghazali">Ahmad-Kamal Ghazali</name><name sortKey="Hoh, Chee Choong" sort="Hoh, Chee Choong" uniqKey="Hoh C" first="Chee-Choong" last="Hoh">Chee-Choong Hoh</name><name sortKey="Mohd Zainuddin, Zainorlina" sort="Mohd Zainuddin, Zainorlina" uniqKey="Mohd Zainuddin Z" first="Zainorlina" last="Mohd-Zainuddin">Zainorlina Mohd-Zainuddin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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