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A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.

Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS - Genome Biol. (2015)

Bottom Line: Polyploid species have long been thought to be recalcitrant to whole-genome assembly.The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly.Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

View Article: PubMed Central - PubMed

Affiliation: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jarrodc@gmail.com.

ABSTRACT
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

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Related in: MedlinePlus

Validation of the POPSEQ genetic map. (A) POPSEQ positions [24] of barley high-confidence genes [45] were compared with the genetic positions of their putative orthologs in our wheat POPSEQ map. Assignment of orthologous groups agreed in 87% of the cases. Genetic positions within the orthologous group showed high collinearity (Spearman’s ρ = 0.936). Known translocation events relative to barley involving wheat chromosomes 4A, 5A and 7B [46] could be traced with high precision. (B) Collinearity with a previous genetic map of the Synthetic × Opata population constructed through genotyping by sequencing [28]. A total of 11,000 out of 20,000 genotyping-by-sequencing tags carrying SNPs could be uniquely mapped to our assembly. Chromosome assignments agreed for 99.5% of the genotyping-by-sequencing tags aligned to anchored sequence scaffolds. Genetic positions within linkage groups were highly correlated (Spearman’s ρ = 0.995). (C) Chromosome shotgun contigs were anchored to the same genetic framework as the meraculous scaffolds of W7984. Genetic positions of contigs and scaffolds matched by sequence alignment differed by less than 5 cM in 99.1% of the cases. Chromosomes are separated by blue lines, subgenomes by red lines.
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Fig4: Validation of the POPSEQ genetic map. (A) POPSEQ positions [24] of barley high-confidence genes [45] were compared with the genetic positions of their putative orthologs in our wheat POPSEQ map. Assignment of orthologous groups agreed in 87% of the cases. Genetic positions within the orthologous group showed high collinearity (Spearman’s ρ = 0.936). Known translocation events relative to barley involving wheat chromosomes 4A, 5A and 7B [46] could be traced with high precision. (B) Collinearity with a previous genetic map of the Synthetic × Opata population constructed through genotyping by sequencing [28]. A total of 11,000 out of 20,000 genotyping-by-sequencing tags carrying SNPs could be uniquely mapped to our assembly. Chromosome assignments agreed for 99.5% of the genotyping-by-sequencing tags aligned to anchored sequence scaffolds. Genetic positions within linkage groups were highly correlated (Spearman’s ρ = 0.995). (C) Chromosome shotgun contigs were anchored to the same genetic framework as the meraculous scaffolds of W7984. Genetic positions of contigs and scaffolds matched by sequence alignment differed by less than 5 cM in 99.1% of the cases. Chromosomes are separated by blue lines, subgenomes by red lines.

Mentions: The markers were clustered into linkage groups using log-odds (LOD) score thresholds by two methods, including a new, computationally efficient clustering algorithm that exploits the inherent linearity of genetic maps [41]. From the 21 resulting clusters, we subsampled robust markers with little or no missing data to build a framework genetic map using standard software [42]. Preliminary linkage maps identified 10 SynOpDH individuals with partial or complete loss of a chromosome arm, which were excluded from the final map construction. Scaffolds with co-segregating SNPs were then anchored to map locations based on a LOD score >8. Using a second iterative approach, a high confidence framework map with minimal missing data was produced using 112,687 markers and totaling 2,826 cM in 1,335 recombination bins (Table S7 in Additional file 1). As expected for a DH population, some regions of the genome showed segregation distortion [43,44] (Figure S4 in Additional file 1) with a bias for either Opata (on 6AS and 6DS) or for W7984 (4DL). Shotgun sequence-based maps made with the two independent approaches show near perfect agreement. For example, of scaffolds placed on the map by both methods, only 0.002% are discordant with respect to chromosome identity, and map coordinates between the two methods are correlated (with a Pearson r-value of 0.95) and with an independently generated genetic map [28] (Figure 4B).Figure 4


A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.

Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS - Genome Biol. (2015)

Validation of the POPSEQ genetic map. (A) POPSEQ positions [24] of barley high-confidence genes [45] were compared with the genetic positions of their putative orthologs in our wheat POPSEQ map. Assignment of orthologous groups agreed in 87% of the cases. Genetic positions within the orthologous group showed high collinearity (Spearman’s ρ = 0.936). Known translocation events relative to barley involving wheat chromosomes 4A, 5A and 7B [46] could be traced with high precision. (B) Collinearity with a previous genetic map of the Synthetic × Opata population constructed through genotyping by sequencing [28]. A total of 11,000 out of 20,000 genotyping-by-sequencing tags carrying SNPs could be uniquely mapped to our assembly. Chromosome assignments agreed for 99.5% of the genotyping-by-sequencing tags aligned to anchored sequence scaffolds. Genetic positions within linkage groups were highly correlated (Spearman’s ρ = 0.995). (C) Chromosome shotgun contigs were anchored to the same genetic framework as the meraculous scaffolds of W7984. Genetic positions of contigs and scaffolds matched by sequence alignment differed by less than 5 cM in 99.1% of the cases. Chromosomes are separated by blue lines, subgenomes by red lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4373400&req=5

Fig4: Validation of the POPSEQ genetic map. (A) POPSEQ positions [24] of barley high-confidence genes [45] were compared with the genetic positions of their putative orthologs in our wheat POPSEQ map. Assignment of orthologous groups agreed in 87% of the cases. Genetic positions within the orthologous group showed high collinearity (Spearman’s ρ = 0.936). Known translocation events relative to barley involving wheat chromosomes 4A, 5A and 7B [46] could be traced with high precision. (B) Collinearity with a previous genetic map of the Synthetic × Opata population constructed through genotyping by sequencing [28]. A total of 11,000 out of 20,000 genotyping-by-sequencing tags carrying SNPs could be uniquely mapped to our assembly. Chromosome assignments agreed for 99.5% of the genotyping-by-sequencing tags aligned to anchored sequence scaffolds. Genetic positions within linkage groups were highly correlated (Spearman’s ρ = 0.995). (C) Chromosome shotgun contigs were anchored to the same genetic framework as the meraculous scaffolds of W7984. Genetic positions of contigs and scaffolds matched by sequence alignment differed by less than 5 cM in 99.1% of the cases. Chromosomes are separated by blue lines, subgenomes by red lines.
Mentions: The markers were clustered into linkage groups using log-odds (LOD) score thresholds by two methods, including a new, computationally efficient clustering algorithm that exploits the inherent linearity of genetic maps [41]. From the 21 resulting clusters, we subsampled robust markers with little or no missing data to build a framework genetic map using standard software [42]. Preliminary linkage maps identified 10 SynOpDH individuals with partial or complete loss of a chromosome arm, which were excluded from the final map construction. Scaffolds with co-segregating SNPs were then anchored to map locations based on a LOD score >8. Using a second iterative approach, a high confidence framework map with minimal missing data was produced using 112,687 markers and totaling 2,826 cM in 1,335 recombination bins (Table S7 in Additional file 1). As expected for a DH population, some regions of the genome showed segregation distortion [43,44] (Figure S4 in Additional file 1) with a bias for either Opata (on 6AS and 6DS) or for W7984 (4DL). Shotgun sequence-based maps made with the two independent approaches show near perfect agreement. For example, of scaffolds placed on the map by both methods, only 0.002% are discordant with respect to chromosome identity, and map coordinates between the two methods are correlated (with a Pearson r-value of 0.95) and with an independently generated genetic map [28] (Figure 4B).Figure 4

Bottom Line: Polyploid species have long been thought to be recalcitrant to whole-genome assembly.The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly.Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

View Article: PubMed Central - PubMed

Affiliation: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jarrodc@gmail.com.

ABSTRACT
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

Show MeSH
Related in: MedlinePlus