Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

Autores
Cavagnaro, Pablo Federico; Senalik, Douglas A.; Yang, Luming; Simon, Philipp W.; Harkins, Timothy T.; Kodira, Chinnappa D.; Huang, S.; Weng, Yiqun
Año de publicación
2010
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line ‘9930’ and the North American pickling type inbred line ‘Gy14’. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber. Results: A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newlydiscovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available. Conclusions: The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.
Fil: Cavagnaro, Pablo Federico. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Senalik, Douglas A.. University of Wisconsin; Estados Unidos. United States Department of Agriculture. Agriculture Research Service; Estados Unidos
Fil: Yang, Luming. University of Wisconsin; Estados Unidos
Fil: Simon, Philipp W.. United States Department of Agriculture. Agriculture Research Service; Estados Unidos
Fil: Harkins, Timothy T.. No especifíca;
Fil: Kodira, Chinnappa D.. No especifíca;
Fil: Huang, S.. Chinese Academy of Agricultural Sciences; China
Fil: Weng, Yiqun. University of Wisconsin; Estados Unidos. United States Department of Agriculture. Agriculture Research Service; Estados Unidos
Materia
CUCUMBER
MICROSATELLITES
GENOME SEQUENCE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/243234

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network_name_str CONICET Digital (CONICET)
spelling Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)Cavagnaro, Pablo FedericoSenalik, Douglas A.Yang, LumingSimon, Philipp W.Harkins, Timothy T.Kodira, Chinnappa D.Huang, S.Weng, YiqunCUCUMBERMICROSATELLITESGENOME SEQUENCEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line ‘9930’ and the North American pickling type inbred line ‘Gy14’. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber. Results: A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newlydiscovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available. Conclusions: The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.Fil: Cavagnaro, Pablo Federico. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Senalik, Douglas A.. University of Wisconsin; Estados Unidos. United States Department of Agriculture. Agriculture Research Service; Estados UnidosFil: Yang, Luming. University of Wisconsin; Estados UnidosFil: Simon, Philipp W.. United States Department of Agriculture. Agriculture Research Service; Estados UnidosFil: Harkins, Timothy T.. No especifíca;Fil: Kodira, Chinnappa D.. No especifíca;Fil: Huang, S.. Chinese Academy of Agricultural Sciences; ChinaFil: Weng, Yiqun. University of Wisconsin; Estados Unidos. United States Department of Agriculture. Agriculture Research Service; Estados UnidosBioMed Central2010-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/243234Cavagnaro, Pablo Federico; Senalik, Douglas A.; Yang, Luming; Simon, Philipp W.; Harkins, Timothy T.; et al.; Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.); BioMed Central; BMC Genomics; 11; 1; 10-2010; 569-5861471-2164CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-569info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-11-569info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:07:26Zoai:ri.conicet.gov.ar:11336/243234instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:07:27.191CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
title Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
spellingShingle Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
Cavagnaro, Pablo Federico
CUCUMBER
MICROSATELLITES
GENOME SEQUENCE
title_short Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
title_full Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
title_fullStr Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
title_full_unstemmed Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
title_sort Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
dc.creator.none.fl_str_mv Cavagnaro, Pablo Federico
Senalik, Douglas A.
Yang, Luming
Simon, Philipp W.
Harkins, Timothy T.
Kodira, Chinnappa D.
Huang, S.
Weng, Yiqun
author Cavagnaro, Pablo Federico
author_facet Cavagnaro, Pablo Federico
Senalik, Douglas A.
Yang, Luming
Simon, Philipp W.
Harkins, Timothy T.
Kodira, Chinnappa D.
Huang, S.
Weng, Yiqun
author_role author
author2 Senalik, Douglas A.
Yang, Luming
Simon, Philipp W.
Harkins, Timothy T.
Kodira, Chinnappa D.
Huang, S.
Weng, Yiqun
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv CUCUMBER
MICROSATELLITES
GENOME SEQUENCE
topic CUCUMBER
MICROSATELLITES
GENOME SEQUENCE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line ‘9930’ and the North American pickling type inbred line ‘Gy14’. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber. Results: A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newlydiscovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available. Conclusions: The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.
Fil: Cavagnaro, Pablo Federico. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Senalik, Douglas A.. University of Wisconsin; Estados Unidos. United States Department of Agriculture. Agriculture Research Service; Estados Unidos
Fil: Yang, Luming. University of Wisconsin; Estados Unidos
Fil: Simon, Philipp W.. United States Department of Agriculture. Agriculture Research Service; Estados Unidos
Fil: Harkins, Timothy T.. No especifíca;
Fil: Kodira, Chinnappa D.. No especifíca;
Fil: Huang, S.. Chinese Academy of Agricultural Sciences; China
Fil: Weng, Yiqun. University of Wisconsin; Estados Unidos. United States Department of Agriculture. Agriculture Research Service; Estados Unidos
description Background: Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line ‘9930’ and the North American pickling type inbred line ‘Gy14’. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber. Results: A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newlydiscovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available. Conclusions: The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.
publishDate 2010
dc.date.none.fl_str_mv 2010-10
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 http://hdl.handle.net/11336/243234
Cavagnaro, Pablo Federico; Senalik, Douglas A.; Yang, Luming; Simon, Philipp W.; Harkins, Timothy T.; et al.; Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.); BioMed Central; BMC Genomics; 11; 1; 10-2010; 569-586
1471-2164
CONICET Digital
CONICET
url http://hdl.handle.net/11336/243234
identifier_str_mv Cavagnaro, Pablo Federico; Senalik, Douglas A.; Yang, Luming; Simon, Philipp W.; Harkins, Timothy T.; et al.; Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.); BioMed Central; BMC Genomics; 11; 1; 10-2010; 569-586
1471-2164
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
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info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-11-569
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc/2.5/ar/
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dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
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reponame_str CONICET Digital (CONICET)
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instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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