1. Development of a sequence-based reference physical map of pea (Pisum sativum L.)
- Author
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Abdelhafid Bendahmane, Reddy V. B. Lachagari, Jan van Oeveren, Mohammed-Amin Madoui, Bunyamin Tar’an, Edwin A. G. van der Vossen, Thomas D. Warkentin, Karine Labadie, Krishna K. Gali, Judith Burstin, Hélène Bergès, Crop Development Centre, University of Saskatchewan, Genomics Institute, Clemson University, Keygene N.V., Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), AgriGenome Labs Pvt Ltd, Partenaires INRAE, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Saskatchewan Pulse Growers (SPG), University of Saskatchewan [Saskatoon] (U of S), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), and Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)
- Subjects
0106 biological sciences ,0301 basic medicine ,Positional cloning ,Plant Science ,Computational biology ,lcsh:Plant culture ,01 natural sciences ,Genome ,DNA sequencing ,Restriction fragment ,analyse de génome ,03 medical and health sciences ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,lcsh:SB1-1110 ,sequence-based physical map ,Pisum sativum ,Original Research ,030304 developmental biology ,Whole genome sequencing ,0303 health sciences ,Bacterial artificial chromosome ,Vegetal Biology ,biology ,Contig ,food and beverages ,bacterial artificial chromosome ,fingerprinted contigs ,whole genome profiling ,030104 developmental biology ,biology.protein ,cartographie ,Restriction digest ,Biologie végétale ,010606 plant biology & botany - Abstract
Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (~4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.
- Published
- 2019
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