The draft genome sequence of European pear (Pyrus communis L. 'Bartlett').
We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffol...
Guardado en:
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Public Library of Science (PLoS)
2014
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/fefa8cc570ce41e9bbeb664e0564f202 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:fefa8cc570ce41e9bbeb664e0564f202 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:fefa8cc570ce41e9bbeb664e0564f2022021-11-18T08:25:08ZThe draft genome sequence of European pear (Pyrus communis L. 'Bartlett').1932-620310.1371/journal.pone.0092644https://doaj.org/article/fefa8cc570ce41e9bbeb664e0564f2022014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24699266/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus × domestica). The 'Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.David ChagnéRoss N CrowhurstMassimo PindoAmali ThrimawithanaCecilia DengHilary IrelandMark FiersHelge DzierzonAlessandro CestaroPaolo FontanaLuca BiancoAshley LuRoy StoreyMareike KnäbelMunazza SaeedSara MontanariYoon Kyeong KimDaniela NicoliniSimone LargerErika StefaniAndrew C AllanJudith BowenIsaac HarveyJason JohnstonMickael MalnoyMichela TroggioLaure PerchepiedGreg SawyerClaudia WiedowKyungho WonRoberto ViolaRoger P HellensLester BrewerVincent G M BusRobert J SchafferSusan E GardinerRiccardo VelascoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 4, p e92644 (2014) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q David Chagné Ross N Crowhurst Massimo Pindo Amali Thrimawithana Cecilia Deng Hilary Ireland Mark Fiers Helge Dzierzon Alessandro Cestaro Paolo Fontana Luca Bianco Ashley Lu Roy Storey Mareike Knäbel Munazza Saeed Sara Montanari Yoon Kyeong Kim Daniela Nicolini Simone Larger Erika Stefani Andrew C Allan Judith Bowen Isaac Harvey Jason Johnston Mickael Malnoy Michela Troggio Laure Perchepied Greg Sawyer Claudia Wiedow Kyungho Won Roberto Viola Roger P Hellens Lester Brewer Vincent G M Bus Robert J Schaffer Susan E Gardiner Riccardo Velasco The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). |
| description |
We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus × domestica). The 'Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development. |
| format |
article |
| author |
David Chagné Ross N Crowhurst Massimo Pindo Amali Thrimawithana Cecilia Deng Hilary Ireland Mark Fiers Helge Dzierzon Alessandro Cestaro Paolo Fontana Luca Bianco Ashley Lu Roy Storey Mareike Knäbel Munazza Saeed Sara Montanari Yoon Kyeong Kim Daniela Nicolini Simone Larger Erika Stefani Andrew C Allan Judith Bowen Isaac Harvey Jason Johnston Mickael Malnoy Michela Troggio Laure Perchepied Greg Sawyer Claudia Wiedow Kyungho Won Roberto Viola Roger P Hellens Lester Brewer Vincent G M Bus Robert J Schaffer Susan E Gardiner Riccardo Velasco |
| author_facet |
David Chagné Ross N Crowhurst Massimo Pindo Amali Thrimawithana Cecilia Deng Hilary Ireland Mark Fiers Helge Dzierzon Alessandro Cestaro Paolo Fontana Luca Bianco Ashley Lu Roy Storey Mareike Knäbel Munazza Saeed Sara Montanari Yoon Kyeong Kim Daniela Nicolini Simone Larger Erika Stefani Andrew C Allan Judith Bowen Isaac Harvey Jason Johnston Mickael Malnoy Michela Troggio Laure Perchepied Greg Sawyer Claudia Wiedow Kyungho Won Roberto Viola Roger P Hellens Lester Brewer Vincent G M Bus Robert J Schaffer Susan E Gardiner Riccardo Velasco |
| author_sort |
David Chagné |
| title |
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). |
| title_short |
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). |
| title_full |
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). |
| title_fullStr |
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). |
| title_full_unstemmed |
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). |
| title_sort |
draft genome sequence of european pear (pyrus communis l. 'bartlett'). |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2014 |
| url |
https://doaj.org/article/fefa8cc570ce41e9bbeb664e0564f202 |
| work_keys_str_mv |
AT davidchagne thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT rossncrowhurst thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT massimopindo thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT amalithrimawithana thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT ceciliadeng thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT hilaryireland thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT markfiers thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT helgedzierzon thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT alessandrocestaro thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT paolofontana thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT lucabianco thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT ashleylu thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT roystorey thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT mareikeknabel thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT munazzasaeed thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT saramontanari thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT yoonkyeongkim thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT danielanicolini thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT simonelarger thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT erikastefani thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT andrewcallan thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT judithbowen thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT isaacharvey thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT jasonjohnston thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT mickaelmalnoy thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT michelatroggio thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT laureperchepied thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT gregsawyer thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT claudiawiedow thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT kyunghowon thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT robertoviola thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT rogerphellens thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT lesterbrewer thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT vincentgmbus thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT robertjschaffer thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT susanegardiner thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT riccardovelasco thedraftgenomesequenceofeuropeanpearpyruscommunislbartlett AT davidchagne draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT rossncrowhurst draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT massimopindo draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT amalithrimawithana draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT ceciliadeng draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT hilaryireland draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT markfiers draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT helgedzierzon draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT alessandrocestaro draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT paolofontana draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT lucabianco draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT ashleylu draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT roystorey draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT mareikeknabel draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT munazzasaeed draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT saramontanari draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT yoonkyeongkim draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT danielanicolini draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT simonelarger draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT erikastefani draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT andrewcallan draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT judithbowen draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT isaacharvey draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT jasonjohnston draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT mickaelmalnoy draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT michelatroggio draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT laureperchepied draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT gregsawyer draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT claudiawiedow draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT kyunghowon draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT robertoviola draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT rogerphellens draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT lesterbrewer draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT vincentgmbus draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT robertjschaffer draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT susanegardiner draftgenomesequenceofeuropeanpearpyruscommunislbartlett AT riccardovelasco draftgenomesequenceofeuropeanpearpyruscommunislbartlett |
| _version_ |
1718421840731308032 |