A draft genome of Prunus avium 'Karina' as a tool for genomic studies

J. Cáceres-Molina, K. Rothkegel, E. Sánchez, T. Carrasco-Valenzuela, C. Meneses, H. Prieto, A. M. Almeida

Resultado de la investigación: Article

Resumen

Here we present the construction of a partial draft genome of the sweet cherry Prunus avium 'Karina' (2n=2x=16) taking advantage of the NGS technologies available and by implementing a de novo assembly strategy. The estimated assembly size was 352.5 Mb, comprising 904,813 contigs with a N50 of 9,188 bp. The contig merging process resulted in 898,488 scaffolds with a N50 of 13,235 bp and a maximum scaffold length of 419,819 bp. We performed a search for known genes with agronomical importance such as the dormancy-associated MADS-box transcription factors (DAM) and two members of the eIF4G gene subfamily. The search results showed that six putative DAM genes are present in an apparent tandem array with a mean identity of 89.14% with the genomic sequences of Prunus persica. Similar results were achieved for the eIFG genes, obtaining 89.76% of identity with the genomic sequences of Prunus persica and 60.36% of identity with the genomic sequences of Arabidopsis thaliana. With this we are hoping to obtain valuable data to perform genomic studies and to contribute to the better understanding of the genetic background of this cultivar and to obtain a tool to perform genomic studies in sweet cherry.

Idioma originalEnglish
Páginas (desde-hasta)85-91
Número de páginas7
PublicaciónActa Horticulturae
Volumen1235
DOI
EstadoPublished - 1 ene 2019

Huella dactilar

Prunus avium
genomics
genome
Prunus persica
genes
genetic background
dormancy
Arabidopsis thaliana
transcription factors
cultivars

ASJC Scopus subject areas

  • Horticulture

Citar esto

Cáceres-Molina, J., Rothkegel, K., Sánchez, E., Carrasco-Valenzuela, T., Meneses, C., Prieto, H., & Almeida, A. M. (2019). A draft genome of Prunus avium 'Karina' as a tool for genomic studies. Acta Horticulturae, 1235, 85-91. https://doi.org/10.17660/ActaHortic.2019.1235.11
Cáceres-Molina, J. ; Rothkegel, K. ; Sánchez, E. ; Carrasco-Valenzuela, T. ; Meneses, C. ; Prieto, H. ; Almeida, A. M. / A draft genome of Prunus avium 'Karina' as a tool for genomic studies. En: Acta Horticulturae. 2019 ; Vol. 1235. pp. 85-91.
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abstract = "Here we present the construction of a partial draft genome of the sweet cherry Prunus avium 'Karina' (2n=2x=16) taking advantage of the NGS technologies available and by implementing a de novo assembly strategy. The estimated assembly size was 352.5 Mb, comprising 904,813 contigs with a N50 of 9,188 bp. The contig merging process resulted in 898,488 scaffolds with a N50 of 13,235 bp and a maximum scaffold length of 419,819 bp. We performed a search for known genes with agronomical importance such as the dormancy-associated MADS-box transcription factors (DAM) and two members of the eIF4G gene subfamily. The search results showed that six putative DAM genes are present in an apparent tandem array with a mean identity of 89.14{\%} with the genomic sequences of Prunus persica. Similar results were achieved for the eIFG genes, obtaining 89.76{\%} of identity with the genomic sequences of Prunus persica and 60.36{\%} of identity with the genomic sequences of Arabidopsis thaliana. With this we are hoping to obtain valuable data to perform genomic studies and to contribute to the better understanding of the genetic background of this cultivar and to obtain a tool to perform genomic studies in sweet cherry.",
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Cáceres-Molina, J, Rothkegel, K, Sánchez, E, Carrasco-Valenzuela, T, Meneses, C, Prieto, H & Almeida, AM 2019, 'A draft genome of Prunus avium 'Karina' as a tool for genomic studies', Acta Horticulturae, vol. 1235, pp. 85-91. https://doi.org/10.17660/ActaHortic.2019.1235.11

A draft genome of Prunus avium 'Karina' as a tool for genomic studies. / Cáceres-Molina, J.; Rothkegel, K.; Sánchez, E.; Carrasco-Valenzuela, T.; Meneses, C.; Prieto, H.; Almeida, A. M.

En: Acta Horticulturae, Vol. 1235, 01.01.2019, p. 85-91.

Resultado de la investigación: Article

TY - JOUR

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AU - Cáceres-Molina, J.

AU - Rothkegel, K.

AU - Sánchez, E.

AU - Carrasco-Valenzuela, T.

AU - Meneses, C.

AU - Prieto, H.

AU - Almeida, A. M.

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Here we present the construction of a partial draft genome of the sweet cherry Prunus avium 'Karina' (2n=2x=16) taking advantage of the NGS technologies available and by implementing a de novo assembly strategy. The estimated assembly size was 352.5 Mb, comprising 904,813 contigs with a N50 of 9,188 bp. The contig merging process resulted in 898,488 scaffolds with a N50 of 13,235 bp and a maximum scaffold length of 419,819 bp. We performed a search for known genes with agronomical importance such as the dormancy-associated MADS-box transcription factors (DAM) and two members of the eIF4G gene subfamily. The search results showed that six putative DAM genes are present in an apparent tandem array with a mean identity of 89.14% with the genomic sequences of Prunus persica. Similar results were achieved for the eIFG genes, obtaining 89.76% of identity with the genomic sequences of Prunus persica and 60.36% of identity with the genomic sequences of Arabidopsis thaliana. With this we are hoping to obtain valuable data to perform genomic studies and to contribute to the better understanding of the genetic background of this cultivar and to obtain a tool to perform genomic studies in sweet cherry.

AB - Here we present the construction of a partial draft genome of the sweet cherry Prunus avium 'Karina' (2n=2x=16) taking advantage of the NGS technologies available and by implementing a de novo assembly strategy. The estimated assembly size was 352.5 Mb, comprising 904,813 contigs with a N50 of 9,188 bp. The contig merging process resulted in 898,488 scaffolds with a N50 of 13,235 bp and a maximum scaffold length of 419,819 bp. We performed a search for known genes with agronomical importance such as the dormancy-associated MADS-box transcription factors (DAM) and two members of the eIF4G gene subfamily. The search results showed that six putative DAM genes are present in an apparent tandem array with a mean identity of 89.14% with the genomic sequences of Prunus persica. Similar results were achieved for the eIFG genes, obtaining 89.76% of identity with the genomic sequences of Prunus persica and 60.36% of identity with the genomic sequences of Arabidopsis thaliana. With this we are hoping to obtain valuable data to perform genomic studies and to contribute to the better understanding of the genetic background of this cultivar and to obtain a tool to perform genomic studies in sweet cherry.

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EP - 91

JO - Acta Horticulturae

JF - Acta Horticulturae

SN - 0567-7572

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Cáceres-Molina J, Rothkegel K, Sánchez E, Carrasco-Valenzuela T, Meneses C, Prieto H y otros. A draft genome of Prunus avium 'Karina' as a tool for genomic studies. Acta Horticulturae. 2019 ene 1;1235:85-91. https://doi.org/10.17660/ActaHortic.2019.1235.11