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Maritime pine (Pinus pinaster) de novo transcriptome assembly

hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorLABEL, Philippe
hal.structure.identifierUnité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) [UBIA]
dc.contributor.authorNOIROT, Céline
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLE PROVOST, Grégoire
hal.structure.identifierInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology [INIA]
dc.contributor.authorCERVERA, María-Teresa
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierUnité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) [UBIA]
dc.contributor.authorKLOPP, Christophe
dc.date.issued2011
dc.date.conference2011-04-14
dc.description.abstractEnRationale Fast increase of world population leads to a correlative increase on wood demand (heating, pulp and paper, building). Consequently, the cultivated forest has a leading role to play to fill this growing demand. Developing an abundant wood ressource calls for improvement of sylvicultural practices as well as deployment of genetically improved trees varieties in the frame of a sustainable forestry. Maintaining french forest competitivity will depend on the integration of new technologies in breeding programs, especially for intensively cultivated forest species such as maritime pine (Pinus pinaster). Second generation sequencing platforms provide tremendous and relatively cheap amounts of data to biologists. However, the main characteristic of this data is to be extremely puzzled with about 20 millions of short sequences averaging 100bp length per sample. Aligning such data along a reference genome is a routine task nowadays. But in the case of maritime pine, de novo assembling of a transcriptome (i.e. without reference genome) from the 300 millions of sequences available, mixing 1% of Sanger and 454 long sequences and 99% of such short reads, is quite challenging and calls for delicate algorithmic approaches (Wall et al. 2009). Nevertheless, applying short sequences to transcriptomics is already possible (Wheat 2010) using for instance informations provided by orthologous genes (Birzele et al. 2010) and promises to be an acceptable experimental solution for many non-model agronomical species. Many different algorithms for transcriptome assembly are available (Miller et al. 2010, Surget-Groba & Montoya-Burgos 2010). Kumar & Blaxter (2010) compared CAP3, MIRA3, Newbler, SeqMan and CLC for the de novo assembly of Litomosoides sigmodontis nematode transcriptome. In the latter paper, an interesting idea was to fuse different assemblies to maximise cooperation of different algorithms in the final assembly. Aims In this poster, we will describe a preliminary assembly of 454 sequences by TGICL (Pertea et al. 2003) and we propose to study the usability of several tools of transcriptome assembly, such as MIRA3 (Chevreux et al. 2004), Velvet (Zerbino & Birney 2008), ABySS (Birol et al. 2009) and SOAPdeNovo (Li et al. 2010), integrating massive short reads, and define an acceptable method to apply to maritime pine transcriptomics.
dc.language.isoen
dc.subjectBIOINFORMATICS
dc.subject.enMARITIME PINE
dc.subject.enFOREST TREE BREEDING
dc.subject.enASSEMBLY
dc.subject.enSHORT READS
dc.subject.enPIN MARITIME
dc.subject.enCOURTE SEQUENCE
dc.title.enMaritime pine (Pinus pinaster) de novo transcriptome assembly
dc.typeCommunication dans un congrès
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halMathématiques [math]
dc.subject.halInformatique [cs]
bordeaux.conference.title3. workshop on "Statistical challenges on the 1000€ genome sequences in plants";StatSeq'2011
bordeaux.countryFR
bordeaux.conference.cityToulouse
bordeaux.peerReviewednon
hal.identifierhal-02750183
hal.version1
hal.invitedoui
hal.conference.end2011-04-15
hal.popularnon
hal.audienceNationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02750183v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.date=2011&rft.au=LABEL,%20Philippe&NOIROT,%20C%C3%A9line&LE%20PROVOST,%20Gr%C3%A9goire&CERVERA,%20Mar%C3%ADa-Teresa&PLOMION,%20Christophe&rft.genre=unknown


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