Gene content and distribution in the nuclear genome of Fragaria vesca
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 the...
| Main Authors: | , , , , , , , |
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| Format: | info:ar-repo/semantics/artículo |
| Language: | Inglés |
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Crop Science Society of America
2019
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| Subjects: | |
| Online Access: | 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 |
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| author | Pontaroli, Ana Clara Rogers, Rebekah L. Qian, Zhang Shields, Melanie E. Davis, Thomas M. Folta, Kevin M. SanMiguel, Phillip Bennetzen, Jeffrey L. |
| author_browse | Bennetzen, Jeffrey L. Davis, Thomas M. Folta, Kevin M. Pontaroli, Ana Clara Qian, Zhang Rogers, Rebekah L. SanMiguel, Phillip Shields, Melanie E. |
| 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_sort | Pontaroli, Ana Clara |
| collection | INTA Digital |
| 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%. |
| format | info:ar-repo/semantics/artículo |
| id | INTA5465 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Crop Science Society of America |
| publisherStr | Crop Science Society of America |
| record_format | dspace |
| spelling | INTA54652019-07-11T11:48:19Z Gene content and distribution in the nuclear genome of Fragaria vesca Pontaroli, Ana Clara Rogers, Rebekah L. Qian, Zhang Shields, Melanie E. Davis, Thomas M. Folta, Kevin M. SanMiguel, Phillip Bennetzen, Jeffrey L. Fragaria vesca Fresa Genomas ADN Secuencia Nucleotídica Genomes DNA Nucleotide Sequence Frutilla de los bosques Woodland Strawberry 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 2019-07-10T15:29:58Z 2019-07-10T15:29:58Z 2009-03 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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) application/pdf Crop Science Society of America Plant Genome 2 (1) : 93-101 (2009) |
| spellingShingle | Fragaria vesca Fresa Genomas ADN Secuencia Nucleotídica Genomes DNA Nucleotide Sequence Frutilla de los bosques Woodland Strawberry Pontaroli, Ana Clara Rogers, Rebekah L. Qian, Zhang Shields, Melanie E. Davis, Thomas M. Folta, Kevin M. SanMiguel, Phillip Bennetzen, Jeffrey L. Gene content and distribution in the nuclear genome of Fragaria vesca |
| title | 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_short | Gene content and distribution in the nuclear genome of Fragaria vesca |
| title_sort | gene content and distribution in the nuclear genome of fragaria vesca |
| topic | Fragaria vesca Fresa Genomas ADN Secuencia Nucleotídica Genomes DNA Nucleotide Sequence Frutilla de los bosques Woodland Strawberry |
| 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 |
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