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<identifier>oai:HAL:hal-01032439v1</identifier>
<datestamp>2018-01-11</datestamp>
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<publisher>HAL CCSD</publisher>
<title lang=en>High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species</title>
<creator>Brousseau, Louise</creator>
<creator>Tinaut, Alexandra</creator>
<creator>Duret, Caroline</creator>
<creator>Lang, Tiange</creator>
<creator>Garnier-Gere, Pauline</creator>
<creator>Scotti, Ivan</creator>
<contributor>Ecologie des forêts de Guyane (ECOFOG) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) - Institut National de la Recherche Agronomique (INRA) - Université des Antilles et de la Guyane (UAG) - AgroParisTech - Centre National de la Recherche Scientifique (CNRS)</contributor>
<contributor>Ecologie et Ecophysiologie Forestières (EEF) ; Institut National de la Recherche Agronomique (INRA) - Université de Lorraine (UL)</contributor>
<contributor>Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden ; Chinese Academy of Sciences [Changchun Branch] (CAS)</contributor>
<contributor>Biodiversité, Gènes et Communautés ; Institut National de Recherche Agronomique</contributor>
<source>ISSN: 1471-2164</source>
<source>BMC Genomics</source>
<publisher>BioMed Central</publisher>
<identifier>hal-01032439</identifier>
<identifier>https://hal.archives-ouvertes.fr/hal-01032439</identifier>
<identifier>https://hal.archives-ouvertes.fr/hal-01032439/document</identifier>
<identifier>https://hal.archives-ouvertes.fr/hal-01032439/file/art_10-1186_1471-2164-15-238.pdf</identifier>
<source>https://hal.archives-ouvertes.fr/hal-01032439</source>
<source>BMC Genomics, BioMed Central, 2014, 15, 13 p. 〈10.1186/1471-2164-15-238〉</source>
<identifier>DOI : 10.1186/1471-2164-15-238</identifier>
<relation>info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-15-238</relation>
<language>en</language>
<subject lang=en>tropical rainforest tree species</subject>
<subject lang=en>polymorphism discovery</subject>
<subject lang=en>454-pyrosequencing</subject>
<subject>[SDV.SA] Life Sciences [q-bio]/Agricultural sciences</subject>
<type>info:eu-repo/semantics/article</type>
<type>Journal articles</type>
<description lang=en>[b]Background[/b][br/] [br/] The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources.[br/] [br/] [b]Results[/b][br/] [br/] In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.[br/] [br/] [b]Conclusion[/b][br/] [br/] The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.</description>
<date>2014</date>
</dc>
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