Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak
<p>Abstract</p> <p>Background</p> <p>The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the <it>Quercus </it>family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks,...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-11-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/650 |
| _version_ | 1818583988728496128 |
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| author | Léger Patrick Cabane Cyril Abadie Pierre Derory Jérémy Brendel Oliver Murat Florent Abrouk Michael Salse Jérôme Salin Franck Frigerio Jean-Marc Noirot Céline Klopp Christophe Léger Valérie Le Provost Grégoire Ueno Saneyoshi Barré Aurélien de Daruvar Antoine Couloux Arnaud Wincker Patrick Reviron Marie-Pierre Kremer Antoine Plomion Christophe |
| author_facet | Léger Patrick Cabane Cyril Abadie Pierre Derory Jérémy Brendel Oliver Murat Florent Abrouk Michael Salse Jérôme Salin Franck Frigerio Jean-Marc Noirot Céline Klopp Christophe Léger Valérie Le Provost Grégoire Ueno Saneyoshi Barré Aurélien de Daruvar Antoine Couloux Arnaud Wincker Patrick Reviron Marie-Pierre Kremer Antoine Plomion Christophe |
| author_sort | Léger Patrick |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the <it>Quercus </it>family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity.</p> <p>Results</p> <p>We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser <url>http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html</url>.</p> <p>Conclusions</p> <p>This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.</p> |
| first_indexed | 2024-12-16T08:14:02Z |
| format | Article |
| id | doaj.art-ed5aa4ef74064f58bf8035357338d84a |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-16T08:14:02Z |
| publishDate | 2010-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-ed5aa4ef74064f58bf8035357338d84a2022-12-21T22:38:19ZengBMCBMC Genomics1471-21642010-11-0111165010.1186/1471-2164-11-650Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oakLéger PatrickCabane CyrilAbadie PierreDerory JérémyBrendel OliverMurat FlorentAbrouk MichaelSalse JérômeSalin FranckFrigerio Jean-MarcNoirot CélineKlopp ChristopheLéger ValérieLe Provost GrégoireUeno SaneyoshiBarré Auréliende Daruvar AntoineCouloux ArnaudWincker PatrickReviron Marie-PierreKremer AntoinePlomion Christophe<p>Abstract</p> <p>Background</p> <p>The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the <it>Quercus </it>family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity.</p> <p>Results</p> <p>We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser <url>http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html</url>.</p> <p>Conclusions</p> <p>This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.</p>http://www.biomedcentral.com/1471-2164/11/650 |
| spellingShingle | Léger Patrick Cabane Cyril Abadie Pierre Derory Jérémy Brendel Oliver Murat Florent Abrouk Michael Salse Jérôme Salin Franck Frigerio Jean-Marc Noirot Céline Klopp Christophe Léger Valérie Le Provost Grégoire Ueno Saneyoshi Barré Aurélien de Daruvar Antoine Couloux Arnaud Wincker Patrick Reviron Marie-Pierre Kremer Antoine Plomion Christophe Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak BMC Genomics |
| title | Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak |
| title_full | Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak |
| title_fullStr | Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak |
| title_full_unstemmed | Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak |
| title_short | Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak |
| title_sort | bioinformatic analysis of ests collected by sanger and pyrosequencing methods for a keystone forest tree species oak |
| url | http://www.biomedcentral.com/1471-2164/11/650 |
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