TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms.
Identifieur interne : 000C25 ( Main/Exploration ); précédent : 000C24; suivant : 000C26TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms.
Auteurs : Pedro Seoane [Espagne] ; Marina Espigares [Espagne] ; Rosario Carmona [Espagne] ; Álvaro Polonio [Espagne] ; Julia Quintana [États-Unis] ; Enrico Cretazzo [Espagne] ; Josefina Bota [Espagne] ; Alejandro Pérez-García [Espagne] ; Juan De Dios Alché [Espagne] ; Luis G Mez [Espagne] ; M Gonzalo Claros [Espagne]Source :
- BMC bioinformatics [ 1471-2105 ] ; 2018.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Analyse de séquence d'ARN (MeSH), Analyse en composantes principales (MeSH), Appariement de bases (génétique), Champignons (génétique), Flux de travaux (MeSH), Logiciel (MeSH), Plantes (génétique), Reproductibilité des résultats (MeSH), Transcriptome (génétique).
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
BACKGROUND
The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant reproducibility, repetitivity and the selection of the best possible transcriptome. Workflows and pipelines are becoming an absolute requirement for such a purpose, but the issue of assembling evaluation for de novo transcriptomes in organisms lacking a sequenced genome remains unsolved. An automated, reproducible and flexible framework called TransFlow to accomplish this task is described.
RESULTS
TransFlow with its five independent modules was designed to build different workflows depending on the nature of the original reads. This architecture enables different combinations of Illumina and Roche/454 sequencing data, and can be extended to other sequencing platforms. Its capabilities are illustrated with the selection of reliable plant reference transcriptomes and the assembling six transcriptomes (three case studies for grapevine leaves, olive tree pollen, and chestnut stem, and other three for haustorium, epiphytic structures and their combination for the phytopathogenic fungus Podosphaera xanthii). Arabidopsis and poplar transcriptomes revealed to be the best references. A common result regarding de novo assemblies is that Illumina paired-end reads of 100 nt in length assembled with OASES can provide reliable transcriptomes, while the contribution of longer reads is noticeable only when they complement a set of short, single-reads.
CONCLUSIONS
TransFlow can handle up to 181 different assembling strategies. Evaluation based on principal component analyses allows its self-adaptation to different sets of reads to provide a suitable transcriptome for each combination of reads and assemblers. As a result, each case study has its own behaviour, prioritises evaluation parameters, and gives an objective and automated way for detecting the best transcriptome within a pool of them. Sequencing data type and quantity (preferably several hundred millions of 2×100 nt or longer), assemblers (OASES for Illumina, MIRA4 and EULER-SR reconciled with CAP3 for Roche/454) and strategy (preferably scaffolding with OASES, and probably merging with Roche/454 when available) arise as the most impacting factors.
DOI: 10.1186/s12859-018-2384-y
PubMed: 30453874
PubMed Central: PMC6245506
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estación Experimental del Zaidín. 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Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estación Experimental del Zaidín. 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Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation></author><author><name sortKey="Polonio, Alvaro" sort="Polonio, Alvaro" uniqKey="Polonio A" first="Álvaro" last="Polonio">Álvaro Polonio</name><affiliation wicri:level="4"><nlm:affiliation>Departamento de Microbiología, and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departamento de Microbiología, and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Malaga</settlement></placeName><orgName type="university">Université de Malaga</orgName></affiliation></author><author><name sortKey="Quintana, Julia" sort="Quintana, Julia" uniqKey="Quintana J" first="Julia" last="Quintana">Julia Quintana</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609-2280, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609-2280</wicri:regionArea><wicri:noRegion>01609-2280</wicri:noRegion></affiliation></author><author><name sortKey="Cretazzo, Enrico" sort="Cretazzo, Enrico" uniqKey="Cretazzo E" first="Enrico" last="Cretazzo">Enrico Cretazzo</name><affiliation wicri:level="2"><nlm:affiliation>Instituto Andaluz de Investigación y Formación Agraria (IFAPA), Centro de Churriana, Cortijo de la Cruz s/n, Churriana, 29140, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto Andaluz de Investigación y Formación Agraria (IFAPA), Centro de Churriana, Cortijo de la Cruz s/n, Churriana, 29140</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation></author><author><name sortKey="Bota, Josefina" sort="Bota, Josefina" uniqKey="Bota J" first="Josefina" last="Bota">Josefina Bota</name><affiliation wicri:level="2"><nlm:affiliation>Grup de Recerca en Biologia de les Plantes en Condicions Mediterrànies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa, km 7.5, Palma de Mallorca, 07122, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Grup de Recerca en Biologia de les Plantes en Condicions Mediterrànies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa, km 7.5, Palma de Mallorca, 07122</wicri:regionArea><placeName><region nuts="2" type="communauté">Îles Baléares</region></placeName></affiliation></author><author><name sortKey="Perez Garcia, Alejandro" sort="Perez Garcia, Alejandro" uniqKey="Perez Garcia A" first="Alejandro" last="Pérez-García">Alejandro Pérez-García</name><affiliation wicri:level="4"><nlm:affiliation>Departamento de Microbiología, and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departamento de Microbiología, and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Malaga</settlement></placeName><orgName type="university">Université de Malaga</orgName></affiliation></author><author><name sortKey="Dios Alche, Juan De" sort="Dios Alche, Juan De" uniqKey="Dios Alche J" first="Juan De" last="Dios Alché">Juan De Dios Alché</name><affiliation wicri:level="2"><nlm:affiliation>Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation></author><author><name sortKey="G Mez, Luis" sort="G Mez, Luis" uniqKey="G Mez L" first="Luis" last="G Mez">Luis G Mez</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Sistemas y Recursos Naturales, ETSI Forestal, de Montes y del Medio Natural, Universidad Politécnica de Madrid, Ciudad Universitaria, Madrid, 28040, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departamento de Sistemas y Recursos Naturales, ETSI Forestal, de Montes y del Medio Natural, Universidad Politécnica de Madrid, Ciudad Universitaria, Madrid, 28040</wicri:regionArea><placeName><region nuts="2" type="communauté">Communauté de Madrid</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>CBGP, INIA-Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>CBGP, INIA-Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223</wicri:regionArea><placeName><region nuts="2" type="communauté">Communauté de Madrid</region></placeName></affiliation></author><author><name sortKey="Claros, M Gonzalo" sort="Claros, M Gonzalo" uniqKey="Claros M" first="M Gonzalo" last="Claros">M Gonzalo Claros</name><affiliation wicri:level="4"><nlm:affiliation>Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus de Teatinos s/n, Malaga, 29071, Spain. claros@uma.es.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus de Teatinos s/n, Malaga, 29071</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Malaga</settlement></placeName><orgName type="university">Université de Malaga</orgName></affiliation></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Pairing (genetics)</term><term>Fungi (genetics)</term><term>Gene Expression Profiling (MeSH)</term><term>Plants (genetics)</term><term>Principal Component Analysis (MeSH)</term><term>Reproducibility of Results (MeSH)</term><term>Sequence Analysis, RNA (MeSH)</term><term>Software (MeSH)</term><term>Transcriptome (genetics)</term><term>Workflow (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de séquence d'ARN (MeSH)</term><term>Analyse en composantes principales (MeSH)</term><term>Appariement de bases (génétique)</term><term>Champignons (génétique)</term><term>Flux de travaux (MeSH)</term><term>Logiciel (MeSH)</term><term>Plantes (génétique)</term><term>Reproductibilité des résultats (MeSH)</term><term>Transcriptome (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Base Pairing</term><term>Fungi</term><term>Plants</term><term>Transcriptome</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Appariement de bases</term><term>Champignons</term><term>Plantes</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Principal Component Analysis</term><term>Reproducibility of Results</term><term>Sequence Analysis, RNA</term><term>Software</term><term>Workflow</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ARN</term><term>Analyse en composantes principales</term><term>Flux de travaux</term><term>Logiciel</term><term>Reproductibilité des résultats</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant reproducibility, repetitivity and the selection of the best possible transcriptome. Workflows and pipelines are becoming an absolute requirement for such a purpose, but the issue of assembling evaluation for de novo transcriptomes in organisms lacking a sequenced genome remains unsolved. An automated, reproducible and flexible framework called TransFlow to accomplish this task is described.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>TransFlow with its five independent modules was designed to build different workflows depending on the nature of the original reads. This architecture enables different combinations of Illumina and Roche/454 sequencing data, and can be extended to other sequencing platforms. Its capabilities are illustrated with the selection of reliable plant reference transcriptomes and the assembling six transcriptomes (three case studies for grapevine leaves, olive tree pollen, and chestnut stem, and other three for haustorium, epiphytic structures and their combination for the phytopathogenic fungus Podosphaera xanthii). Arabidopsis and poplar transcriptomes revealed to be the best references. A common result regarding de novo assemblies is that Illumina paired-end reads of 100 nt in length assembled with OASES can provide reliable transcriptomes, while the contribution of longer reads is noticeable only when they complement a set of short, single-reads.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>TransFlow can handle up to 181 different assembling strategies. Evaluation based on principal component analyses allows its self-adaptation to different sets of reads to provide a suitable transcriptome for each combination of reads and assemblers. As a result, each case study has its own behaviour, prioritises evaluation parameters, and gives an objective and automated way for detecting the best transcriptome within a pool of them. Sequencing data type and quantity (preferably several hundred millions of 2×100 nt or longer), assemblers (OASES for Illumina, MIRA4 and EULER-SR reconciled with CAP3 for Roche/454) and strategy (preferably scaffolding with OASES, and probably merging with Roche/454 when available) arise as the most impacting factors.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">30453874</PMID><DateCompleted><Year>2018</Year><Month>12</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>24</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>19</Volume><Issue>Suppl 14</Issue><PubDate><Year>2018</Year><Month>Nov</Month><Day>20</Day></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms.</ArticleTitle><Pagination><MedlinePgn>416</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12859-018-2384-y</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant reproducibility, repetitivity and the selection of the best possible transcriptome. Workflows and pipelines are becoming an absolute requirement for such a purpose, but the issue of assembling evaluation for de novo transcriptomes in organisms lacking a sequenced genome remains unsolved. An automated, reproducible and flexible framework called TransFlow to accomplish this task is described.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">TransFlow with its five independent modules was designed to build different workflows depending on the nature of the original reads. This architecture enables different combinations of Illumina and Roche/454 sequencing data, and can be extended to other sequencing platforms. Its capabilities are illustrated with the selection of reliable plant reference transcriptomes and the assembling six transcriptomes (three case studies for grapevine leaves, olive tree pollen, and chestnut stem, and other three for haustorium, epiphytic structures and their combination for the phytopathogenic fungus Podosphaera xanthii). Arabidopsis and poplar transcriptomes revealed to be the best references. A common result regarding de novo assemblies is that Illumina paired-end reads of 100 nt in length assembled with OASES can provide reliable transcriptomes, while the contribution of longer reads is noticeable only when they complement a set of short, single-reads.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">TransFlow can handle up to 181 different assembling strategies. Evaluation based on principal component analyses allows its self-adaptation to different sets of reads to provide a suitable transcriptome for each combination of reads and assemblers. As a result, each case study has its own behaviour, prioritises evaluation parameters, and gives an objective and automated way for detecting the best transcriptome within a pool of them. Sequencing data type and quantity (preferably several hundred millions of 2×100 nt or longer), assemblers (OASES for Illumina, MIRA4 and EULER-SR reconciled with CAP3 for Roche/454) and strategy (preferably scaffolding with OASES, and probably merging with Roche/454 when available) arise as the most impacting factors.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Seoane</LastName><ForeName>Pedro</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus de Teatinos s/n, Malaga, 29071, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Espigares</LastName><ForeName>Marina</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus de Teatinos s/n, Malaga, 29071, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Carmona</LastName><ForeName>Rosario</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Polonio</LastName><ForeName>Álvaro</ForeName><Initials>Á</Initials><AffiliationInfo><Affiliation>Departamento de Microbiología, and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Quintana</LastName><ForeName>Julia</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609-2280, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cretazzo</LastName><ForeName>Enrico</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Instituto Andaluz de Investigación y Formación Agraria (IFAPA), Centro de Churriana, Cortijo de la Cruz s/n, Churriana, 29140, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bota</LastName><ForeName>Josefina</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Grup de Recerca en Biologia de les Plantes en Condicions Mediterrànies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa, km 7.5, Palma de Mallorca, 07122, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pérez-García</LastName><ForeName>Alejandro</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Departamento de Microbiología, and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dios Alché</LastName><ForeName>Juan de</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gómez</LastName><ForeName>Luis</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Departamento de Sistemas y Recursos Naturales, ETSI Forestal, de Montes y del Medio Natural, Universidad Politécnica de Madrid, Ciudad Universitaria, Madrid, 28040, Spain.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>CBGP, INIA-Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Claros</LastName><ForeName>M Gonzalo</ForeName><Initials>MG</Initials><AffiliationInfo><Affiliation>Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus de Teatinos s/n, Malaga, 29071, Spain. claros@uma.es.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>11</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Bioinformatics</MedlineTA><NlmUniqueID>100965194</NlmUniqueID><ISSNLinking>1471-2105</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020029" MajorTopicYN="N">Base Pairing</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005658" MajorTopicYN="N">Fungi</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D025341" MajorTopicYN="N">Principal Component Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="Y">Sequence Analysis, RNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D057188" MajorTopicYN="N">Workflow</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Assembling</Keyword><Keyword MajorTopicYN="N">Non-model organism</Keyword><Keyword MajorTopicYN="N">PCA</Keyword><Keyword 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last="Pérez-García">Alejandro Pérez-García</name><name sortKey="Polonio, Alvaro" sort="Polonio, Alvaro" uniqKey="Polonio A" first="Álvaro" last="Polonio">Álvaro Polonio</name></country><country name="États-Unis"><noRegion><name sortKey="Quintana, Julia" sort="Quintana, Julia" uniqKey="Quintana J" first="Julia" last="Quintana">Julia Quintana</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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