Flow sorting and sequencing meadow fescue chromosome 4F

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Flow sorting and sequencing meadow fescue chromosome 4F. / Kopecký, David; Martis, Mihaela; Číhalíková, Jarmila; Hřibová, Eva; Vrána, Jan; Bartoš, Jan; Kopecká, Jitka; Cattonaro, Federica; Stočes, Štěpán; Novák, Petr; Neumann, Pavel; Macas, Jiří; Šimková, Hana; Studer, Bruno; Asp, Torben; Baird, James H; Navrátil, Petr; Karafiátová, Miroslava; Kubaláková, Marie; Šafář, Jan; Mayer, Klaus; Doležel, Jaroslav.

In: Plant Physiology, Vol. 163, No. 3, 11.2013, p. 1323-1237.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Kopecký, D, Martis, M, Číhalíková, J, Hřibová, E, Vrána, J, Bartoš, J, Kopecká, J, Cattonaro, F, Stočes, Š, Novák, P, Neumann, P, Macas, J, Šimková, H, Studer, B, Asp, T, Baird, JH, Navrátil, P, Karafiátová, M, Kubaláková, M, Šafář, J, Mayer, K & Doležel, J 2013, 'Flow sorting and sequencing meadow fescue chromosome 4F', Plant Physiology, vol. 163, no. 3, pp. 1323-1237. https://doi.org/10.1104/pp.113.224105

APA

Kopecký, D., Martis, M., Číhalíková, J., Hřibová, E., Vrána, J., Bartoš, J., Kopecká, J., Cattonaro, F., Stočes, Š., Novák, P., Neumann, P., Macas, J., Šimková, H., Studer, B., Asp, T., Baird, J. H., Navrátil, P., Karafiátová, M., Kubaláková, M., ... Doležel, J. (2013). Flow sorting and sequencing meadow fescue chromosome 4F. Plant Physiology, 163(3), 1323-1237. https://doi.org/10.1104/pp.113.224105

CBE

Kopecký D, Martis M, Číhalíková J, Hřibová E, Vrána J, Bartoš J, Kopecká J, Cattonaro F, Stočes Š, Novák P, Neumann P, Macas J, Šimková H, Studer B, Asp T, Baird JH, Navrátil P, Karafiátová M, Kubaláková M, Šafář J, Mayer K, Doležel J. 2013. Flow sorting and sequencing meadow fescue chromosome 4F. Plant Physiology. 163(3):1323-1237. https://doi.org/10.1104/pp.113.224105

MLA

Kopecký, David et al. "Flow sorting and sequencing meadow fescue chromosome 4F". Plant Physiology. 2013, 163(3). 1323-1237. https://doi.org/10.1104/pp.113.224105

Vancouver

Kopecký D, Martis M, Číhalíková J, Hřibová E, Vrána J, Bartoš J et al. Flow sorting and sequencing meadow fescue chromosome 4F. Plant Physiology. 2013 Nov;163(3):1323-1237. https://doi.org/10.1104/pp.113.224105

Author

Kopecký, David ; Martis, Mihaela ; Číhalíková, Jarmila ; Hřibová, Eva ; Vrána, Jan ; Bartoš, Jan ; Kopecká, Jitka ; Cattonaro, Federica ; Stočes, Štěpán ; Novák, Petr ; Neumann, Pavel ; Macas, Jiří ; Šimková, Hana ; Studer, Bruno ; Asp, Torben ; Baird, James H ; Navrátil, Petr ; Karafiátová, Miroslava ; Kubaláková, Marie ; Šafář, Jan ; Mayer, Klaus ; Doležel, Jaroslav. / Flow sorting and sequencing meadow fescue chromosome 4F. In: Plant Physiology. 2013 ; Vol. 163, No. 3. pp. 1323-1237.

Bibtex

@article{f91a5c2bde184ea0935ca474c8134d6a,
title = "Flow sorting and sequencing meadow fescue chromosome 4F",
abstract = "The analysis of large genomes is hampered by a high proportion of repetitive DNA, which makes the assembly of short sequence reads difficult. This is also the case in meadow fescue (Festuca pratensis), which is known for good abiotic stress resistance and has been used in intergeneric hybridization with ryegrasses (Lolium spp.) to produce Festulolium cultivars. In this work, we describe a new approach to analyze the large genome of meadow fescue, which involves the reduction of sample complexity without compromising information content. This is achieved by dissecting the genome to smaller parts: individual chromosomes and groups of chromosomes. As the first step, we flow sorted chromosome 4F and sequenced it by Illumina with approximately 50× coverage. This provided, to our knowledge, the first insight into the composition of the fescue genome, enabled the construction of the virtual gene order of the chromosome, and facilitated detailed comparative analysis with the sequenced genomes of rice (Oryza sativa), Brachypodium distachyon, sorghum (Sorghum bicolor), and barley (Hordeum vulgare). Using GenomeZipper, we were able to confirm the collinearity of chromosome 4F with barley chromosome 4H and the long arm of chromosome 5H. Several new tandem repeats were identified and physically mapped using fluorescence in situ hybridization. They were found as robust cytogenetic markers for karyotyping of meadow fescue and ryegrass species and their hybrids. The ability to purify chromosome 4F opens the way for more efficient analysis of genomic loci on this chromosome underlying important traits, including freezing tolerance. Our results confirm that next-generation sequencing of flow-sorted chromosomes enables an overview of chromosome structure and evolution at a resolution never achieved before.",
author = "David Kopeck{\'y} and Mihaela Martis and Jarmila {\v C}{\'i}hal{\'i}kov{\'a} and Eva H{\v r}ibov{\'a} and Jan Vr{\'a}na and Jan Barto{\v s} and Jitka Kopeck{\'a} and Federica Cattonaro and {\v S}t{\v e}p{\'a}n Sto{\v c}es and Petr Nov{\'a}k and Pavel Neumann and Ji{\v r}{\'i} Macas and Hana {\v S}imkov{\'a} and Bruno Studer and Torben Asp and Baird, {James H} and Petr Navr{\'a}til and Miroslava Karafi{\'a}tov{\'a} and Marie Kubal{\'a}kov{\'a} and Jan {\v S}af{\'a}{\v r} and Klaus Mayer and Jaroslav Dole{\v z}el",
year = "2013",
month = nov,
doi = "10.1104/pp.113.224105",
language = "English",
volume = "163",
pages = "1323--1237",
journal = "Plant Physiology",
issn = "0032-0889",
publisher = "American Society of Plant Biologists",
number = "3",

}

RIS

TY - JOUR

T1 - Flow sorting and sequencing meadow fescue chromosome 4F

AU - Kopecký, David

AU - Martis, Mihaela

AU - Číhalíková, Jarmila

AU - Hřibová, Eva

AU - Vrána, Jan

AU - Bartoš, Jan

AU - Kopecká, Jitka

AU - Cattonaro, Federica

AU - Stočes, Štěpán

AU - Novák, Petr

AU - Neumann, Pavel

AU - Macas, Jiří

AU - Šimková, Hana

AU - Studer, Bruno

AU - Asp, Torben

AU - Baird, James H

AU - Navrátil, Petr

AU - Karafiátová, Miroslava

AU - Kubaláková, Marie

AU - Šafář, Jan

AU - Mayer, Klaus

AU - Doležel, Jaroslav

PY - 2013/11

Y1 - 2013/11

N2 - The analysis of large genomes is hampered by a high proportion of repetitive DNA, which makes the assembly of short sequence reads difficult. This is also the case in meadow fescue (Festuca pratensis), which is known for good abiotic stress resistance and has been used in intergeneric hybridization with ryegrasses (Lolium spp.) to produce Festulolium cultivars. In this work, we describe a new approach to analyze the large genome of meadow fescue, which involves the reduction of sample complexity without compromising information content. This is achieved by dissecting the genome to smaller parts: individual chromosomes and groups of chromosomes. As the first step, we flow sorted chromosome 4F and sequenced it by Illumina with approximately 50× coverage. This provided, to our knowledge, the first insight into the composition of the fescue genome, enabled the construction of the virtual gene order of the chromosome, and facilitated detailed comparative analysis with the sequenced genomes of rice (Oryza sativa), Brachypodium distachyon, sorghum (Sorghum bicolor), and barley (Hordeum vulgare). Using GenomeZipper, we were able to confirm the collinearity of chromosome 4F with barley chromosome 4H and the long arm of chromosome 5H. Several new tandem repeats were identified and physically mapped using fluorescence in situ hybridization. They were found as robust cytogenetic markers for karyotyping of meadow fescue and ryegrass species and their hybrids. The ability to purify chromosome 4F opens the way for more efficient analysis of genomic loci on this chromosome underlying important traits, including freezing tolerance. Our results confirm that next-generation sequencing of flow-sorted chromosomes enables an overview of chromosome structure and evolution at a resolution never achieved before.

AB - The analysis of large genomes is hampered by a high proportion of repetitive DNA, which makes the assembly of short sequence reads difficult. This is also the case in meadow fescue (Festuca pratensis), which is known for good abiotic stress resistance and has been used in intergeneric hybridization with ryegrasses (Lolium spp.) to produce Festulolium cultivars. In this work, we describe a new approach to analyze the large genome of meadow fescue, which involves the reduction of sample complexity without compromising information content. This is achieved by dissecting the genome to smaller parts: individual chromosomes and groups of chromosomes. As the first step, we flow sorted chromosome 4F and sequenced it by Illumina with approximately 50× coverage. This provided, to our knowledge, the first insight into the composition of the fescue genome, enabled the construction of the virtual gene order of the chromosome, and facilitated detailed comparative analysis with the sequenced genomes of rice (Oryza sativa), Brachypodium distachyon, sorghum (Sorghum bicolor), and barley (Hordeum vulgare). Using GenomeZipper, we were able to confirm the collinearity of chromosome 4F with barley chromosome 4H and the long arm of chromosome 5H. Several new tandem repeats were identified and physically mapped using fluorescence in situ hybridization. They were found as robust cytogenetic markers for karyotyping of meadow fescue and ryegrass species and their hybrids. The ability to purify chromosome 4F opens the way for more efficient analysis of genomic loci on this chromosome underlying important traits, including freezing tolerance. Our results confirm that next-generation sequencing of flow-sorted chromosomes enables an overview of chromosome structure and evolution at a resolution never achieved before.

U2 - 10.1104/pp.113.224105

DO - 10.1104/pp.113.224105

M3 - Journal article

C2 - 24096412

VL - 163

SP - 1323

EP - 1237

JO - Plant Physiology

JF - Plant Physiology

SN - 0032-0889

IS - 3

ER -