Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.)
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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2019.00323/full |
| _version_ | 1819263025153048576 |
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| author | Krishna Kishore Gali Bunyamin Tar’an Mohammed-Amin Madoui Edwin van der Vossen Jan van Oeveren Karine Labadie Helene Berges Abdelhafid Bendahmane Reddy V. B. Lachagari Judith Burstin Tom Warkentin |
| author_facet | Krishna Kishore Gali Bunyamin Tar’an Mohammed-Amin Madoui Edwin van der Vossen Jan van Oeveren Karine Labadie Helene Berges Abdelhafid Bendahmane Reddy V. B. Lachagari Judith Burstin Tom Warkentin |
| author_sort | Krishna Kishore Gali |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-23T20:07:01Z |
| format | Article |
| id | doaj.art-1a44cf610c2c46579288fa36175eb306 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-23T20:07:01Z |
| publishDate | 2019-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-1a44cf610c2c46579288fa36175eb3062022-12-21T17:32:55ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-03-011010.3389/fpls.2019.00323450169Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.)Krishna Kishore Gali0Bunyamin Tar’an1Mohammed-Amin Madoui2Edwin van der Vossen3Jan van Oeveren4Karine Labadie5Helene Berges6Abdelhafid Bendahmane7Reddy V. B. Lachagari8Judith Burstin9Tom Warkentin10Crop Development Centre, University of Saskatchewan, Saskatoon, SK, CanadaCrop Development Centre, University of Saskatchewan, Saskatoon, SK, CanadaAtomic Energy and Alternative Energies Commission (CEA), Genomics Institute (IG), Évry, FranceKeygene N.V., Wageningen, NetherlandsKeygene N.V., Wageningen, NetherlandsKeygene N.V., Wageningen, NetherlandsINRA-CNRGV, Castanet-Tolosan, FranceINRA/CNRS – URGV, Évry, FranceAgriGenome Labs Pvt. Ltd., BTIC, MN iHub, Shamirpet, IndiaJ. Burstin, INRA, UMRLEG, Dijon, FranceCrop Development Centre, University of Saskatchewan, Saskatoon, SK, CanadaWhole 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.https://www.frontiersin.org/article/10.3389/fpls.2019.00323/fullbacterial artificial chromosomefingerprinted contigsPisum sativumsequence-based physical mapwhole genome profiling |
| spellingShingle | Krishna Kishore Gali Bunyamin Tar’an Mohammed-Amin Madoui Edwin van der Vossen Jan van Oeveren Karine Labadie Helene Berges Abdelhafid Bendahmane Reddy V. B. Lachagari Judith Burstin Tom Warkentin Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.) Frontiers in Plant Science bacterial artificial chromosome fingerprinted contigs Pisum sativum sequence-based physical map whole genome profiling |
| title | Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.) |
| title_full | Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.) |
| title_fullStr | Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.) |
| title_full_unstemmed | Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.) |
| title_short | Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.) |
| title_sort | development of a sequence based reference physical map of pea pisum sativum l |
| topic | bacterial artificial chromosome fingerprinted contigs Pisum sativum sequence-based physical map whole genome profiling |
| url | https://www.frontiersin.org/article/10.3389/fpls.2019.00323/full |
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