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
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/5465
Ver los metadatos del registro completo
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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 |
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INTA Digital (INTA) |
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INTA Digital (INTA) |
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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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12.559606 |