Gene content and distribution in the nuclear genome of Fragaria vesca

Autores
Pontaroli, Ana Clara; Rogers, Rebekah L.; Qian, Zhang; Shields, Melanie E.; Davis, Thomas M.; Folta, Kevin M.; SanMiguel, Phillip; Bennetzen, Jeffrey L.
Año de publicación
2009
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Thirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ∼4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ∼1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ∼200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.
EEA Balcarce
Fil: Pontaroli, Ana Clara. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. University of Georgia. Department of Genetics; Estados Unidos
Fil: Rogers, Rebekah L. Harvard University. Department of Organismic and Evolutionary Biology; Estados Unidos. University of Georgia. Department of Genetics; Estados Unidos
Fil: Qian, Zhang. University of New Hampshire. Department of Biological Sciences; Estados Unidos
Fil: Shields, Melanie E. University of New Hampshire. Department of Biological Sciences; Estados Unidos
Fil: Davis, Thomas M. University of New Hampshire. Department of Biological Sciences; Estados Unidos
Fil: Folta, Kevin M. University of Florida. Horticultural Sciences Department; Estados Unidos
Fil: SanMiguel, Phillip. Purdue University. Department of Horticulture and Landscape Architecture; Estados Unidos
Fil: Bennetzen, Jeffrey L. University of Georgia. Department of Genetics; Estados Unidos
Fuente
Plant Genome 2 (1) : 93-101 (2009)
Materia
Fragaria vesca
Fresa
Genomas
ADN
Secuencia Nucleotídica
Genomes
DNA
Nucleotide Sequence
Frutilla de los bosques
Woodland Strawberry
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/5465

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oai_identifier_str oai:localhost:20.500.12123/5465
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network_name_str INTA Digital (INTA)
spelling Gene content and distribution in the nuclear genome of Fragaria vescaPontaroli, Ana ClaraRogers, Rebekah L.Qian, ZhangShields, Melanie E.Davis, Thomas M.Folta, Kevin M.SanMiguel, PhillipBennetzen, Jeffrey L.Fragaria vescaFresaGenomasADNSecuencia NucleotídicaGenomesDNANucleotide SequenceFrutilla de los bosquesWoodland StrawberryThirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ∼4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ∼1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ∼200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.EEA BalcarceFil: Pontaroli, Ana Clara. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. University of Georgia. Department of Genetics; Estados UnidosFil: Rogers, Rebekah L. Harvard University. Department of Organismic and Evolutionary Biology; Estados Unidos. University of Georgia. Department of Genetics; Estados UnidosFil: Qian, Zhang. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Shields, Melanie E. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Davis, Thomas M. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Folta, Kevin M. University of Florida. Horticultural Sciences Department; Estados UnidosFil: SanMiguel, Phillip. Purdue University. Department of Horticulture and Landscape Architecture; Estados UnidosFil: Bennetzen, Jeffrey L. University of Georgia. Department of Genetics; Estados UnidosCrop Science Society of America2019-07-10T15:29:58Z2019-07-10T15:29:58Z2009-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://dl.sciencesocieties.org/publications/tpg/articles/2/1/93http://hdl.handle.net/20.500.12123/54651940-3372https://doi.org/10.3835/plantgenome2008.09.0007Plant Genome 2 (1) : 93-101 (2009)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-29T13:44:43Zoai:localhost:20.500.12123/5465instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:44:43.344INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Gene content and distribution in the nuclear genome of Fragaria vesca
title Gene content and distribution in the nuclear genome of Fragaria vesca
spellingShingle Gene content and distribution in the nuclear genome of Fragaria vesca
Pontaroli, Ana Clara
Fragaria vesca
Fresa
Genomas
ADN
Secuencia Nucleotídica
Genomes
DNA
Nucleotide Sequence
Frutilla de los bosques
Woodland Strawberry
title_short Gene content and distribution in the nuclear genome of Fragaria vesca
title_full Gene content and distribution in the nuclear genome of Fragaria vesca
title_fullStr Gene content and distribution in the nuclear genome of Fragaria vesca
title_full_unstemmed Gene content and distribution in the nuclear genome of Fragaria vesca
title_sort Gene content and distribution in the nuclear genome of Fragaria vesca
dc.creator.none.fl_str_mv Pontaroli, Ana Clara
Rogers, Rebekah L.
Qian, Zhang
Shields, Melanie E.
Davis, Thomas M.
Folta, Kevin M.
SanMiguel, Phillip
Bennetzen, Jeffrey L.
author Pontaroli, Ana Clara
author_facet Pontaroli, Ana Clara
Rogers, Rebekah L.
Qian, Zhang
Shields, Melanie E.
Davis, Thomas M.
Folta, Kevin M.
SanMiguel, Phillip
Bennetzen, Jeffrey L.
author_role author
author2 Rogers, Rebekah L.
Qian, Zhang
Shields, Melanie E.
Davis, Thomas M.
Folta, Kevin M.
SanMiguel, Phillip
Bennetzen, Jeffrey L.
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Fragaria vesca
Fresa
Genomas
ADN
Secuencia Nucleotídica
Genomes
DNA
Nucleotide Sequence
Frutilla de los bosques
Woodland Strawberry
topic Fragaria vesca
Fresa
Genomas
ADN
Secuencia Nucleotídica
Genomes
DNA
Nucleotide Sequence
Frutilla de los bosques
Woodland Strawberry
dc.description.none.fl_txt_mv Thirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ∼4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ∼1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ∼200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.
EEA Balcarce
Fil: Pontaroli, Ana Clara. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. University of Georgia. Department of Genetics; Estados Unidos
Fil: Rogers, Rebekah L. Harvard University. Department of Organismic and Evolutionary Biology; Estados Unidos. University of Georgia. Department of Genetics; Estados Unidos
Fil: Qian, Zhang. University of New Hampshire. Department of Biological Sciences; Estados Unidos
Fil: Shields, Melanie E. University of New Hampshire. Department of Biological Sciences; Estados Unidos
Fil: Davis, Thomas M. University of New Hampshire. Department of Biological Sciences; Estados Unidos
Fil: Folta, Kevin M. University of Florida. Horticultural Sciences Department; Estados Unidos
Fil: SanMiguel, Phillip. Purdue University. Department of Horticulture and Landscape Architecture; Estados Unidos
Fil: Bennetzen, Jeffrey L. University of Georgia. Department of Genetics; Estados Unidos
description Thirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ∼4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ∼1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ∼200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.
publishDate 2009
dc.date.none.fl_str_mv 2009-03
2019-07-10T15:29:58Z
2019-07-10T15:29:58Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://dl.sciencesocieties.org/publications/tpg/articles/2/1/93
http://hdl.handle.net/20.500.12123/5465
1940-3372
https://doi.org/10.3835/plantgenome2008.09.0007
url https://dl.sciencesocieties.org/publications/tpg/articles/2/1/93
http://hdl.handle.net/20.500.12123/5465
https://doi.org/10.3835/plantgenome2008.09.0007
identifier_str_mv 1940-3372
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Crop Science Society of America
publisher.none.fl_str_mv Crop Science Society of America
dc.source.none.fl_str_mv Plant Genome 2 (1) : 93-101 (2009)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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