New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

Marcelo Helguera; Máximo Rivarola; Bernardo Clavijo; Mihaela M. Martis; Leonardo S. Vanzetti; Sergio González; Ingrid Garbus; Phillippe Leroy; Hana Šimková; Miroslav Valárik; Mario Caccamo; Jaroslav Doležel; Klaus F.X. Mayer; Catherine Feuillet; Gabriela Tranquilli; Norma Paniego; Viviana Echenique

doi:10.1016/j.plantsci.2014.12.004

New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

Marcelo Helguera, Máximo Rivarola, Bernardo Clavijo, Mihaela M. Martis, Leonardo S. Vanzetti, Sergio González, Ingrid Garbus, Phillippe Leroy, Hana Šimková, Miroslav Valárik, Mario Caccamo, Jaroslav Doležel, Klaus F.X. Mayer, Catherine Feuillet, Gabriela Tranquilli, Norma Paniego, Viviana Echenique

Research output: Contribution to journal › Article › peer-review

18 Scopus citations

Abstract

Survey sequencing of the bread wheat (. Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223. Mb) and scaffolds (65. Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34. Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ~5700 genes (~2200 on 4DS and ~3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.

Original language	English
Pages (from-to)	200-212
Number of pages	13
Journal	Plant Science
Volume	233
DOIs	https://doi.org/10.1016/j.plantsci.2014.12.004
State	Published - 1 Apr 2015
Externally published	Yes

Keywords

Chromosome 4D survey sequence
Gene annotation
Gene content
Synteny
Triticum aestivum
Virtual gene order

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10.1016/j.plantsci.2014.12.004

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Helguera, M., Rivarola, M., Clavijo, B., Martis, M. M., Vanzetti, L. S., González, S., Garbus, I., Leroy, P., Šimková, H., Valárik, M., Caccamo, M., Doležel, J., Mayer, K. F. X., Feuillet, C., Tranquilli, G., Paniego, N., & Echenique, V. (2015). New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing. Plant Science, 233, 200-212. https://doi.org/10.1016/j.plantsci.2014.12.004

@article{023b794d037c44e19dd93ee55479bf6f,

title = "New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing",

abstract = "Survey sequencing of the bread wheat (. Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223. Mb) and scaffolds (65. Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34. Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ~5700 genes (~2200 on 4DS and ~3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.",

keywords = "Chromosome 4D survey sequence, Gene annotation, Gene content, Synteny, Triticum aestivum, Virtual gene order",

author = "Marcelo Helguera and M{\'a}ximo Rivarola and Bernardo Clavijo and Martis, {Mihaela M.} and Vanzetti, {Leonardo S.} and Sergio Gonz{\'a}lez and Ingrid Garbus and Phillippe Leroy and Hana {\v S}imkov{\'a} and Miroslav Val{\'a}rik and Mario Caccamo and Jaroslav Dole{\v z}el and Mayer, {Klaus F.X.} and Catherine Feuillet and Gabriela Tranquilli and Norma Paniego and Viviana Echenique",

note = "Publisher Copyright: {\textcopyright} 2014 The Authors.",

year = "2015",

month = apr,

day = "1",

doi = "10.1016/j.plantsci.2014.12.004",

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Helguera, M, Rivarola, M, Clavijo, B, Martis, MM, Vanzetti, LS, González, S, Garbus, I, Leroy, P, Šimková, H, Valárik, M, Caccamo, M, Doležel, J, Mayer, KFX, Feuillet, C, Tranquilli, G, Paniego, N & Echenique, V 2015, 'New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing', Plant Science, vol. 233, pp. 200-212. https://doi.org/10.1016/j.plantsci.2014.12.004

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T1 - New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

AU - Helguera, Marcelo

AU - Rivarola, Máximo

AU - Clavijo, Bernardo

AU - Martis, Mihaela M.

AU - Vanzetti, Leonardo S.

AU - González, Sergio

AU - Garbus, Ingrid

AU - Leroy, Phillippe

AU - Šimková, Hana

AU - Valárik, Miroslav

AU - Caccamo, Mario

AU - Doležel, Jaroslav

AU - Mayer, Klaus F.X.

AU - Feuillet, Catherine

AU - Tranquilli, Gabriela

AU - Paniego, Norma

AU - Echenique, Viviana

PY - 2015/4/1

Y1 - 2015/4/1

N2 - Survey sequencing of the bread wheat (. Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223. Mb) and scaffolds (65. Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34. Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ~5700 genes (~2200 on 4DS and ~3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.

AB - Survey sequencing of the bread wheat (. Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223. Mb) and scaffolds (65. Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34. Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ~5700 genes (~2200 on 4DS and ~3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.

KW - Chromosome 4D survey sequence

KW - Gene annotation

KW - Gene content

KW - Synteny

KW - Triticum aestivum

KW - Virtual gene order

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DO - 10.1016/j.plantsci.2014.12.004

M3 - Article

C2 - 25711827

AN - SCOPUS:84923012691

SN - 0168-9452

VL - 233

SP - 200

EP - 212

JO - Plant Science

JF - Plant Science

ER -

New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

Abstract

Keywords

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