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A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
- Source :
- Proc. Natl. Acad. Sci. U.S.A. 110, 7940-7945 (2013)
- Publication Year :
- 2013
- Publisher :
- National Academy of Sciences, 2013.
-
Abstract
- The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii , the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.
- Subjects :
- Genetic Markers
Chromosomes, Artificial, Bacterial
Genome evolution
Centromere
Genes, Plant
Poaceae
Polymorphism, Single Nucleotide
Genome
Chromosomes, Plant
Single nucleotide polymorphism
Synteny
Gene density
Oryza
BAC contig coassembly
Evolution, Molecular
Contig Mapping
Aegilops tauschii
Triticum
Recombination, Genetic
Whole genome sequencing
Genetics
Multidisciplinary
biology
Shotgun sequencing
food and beverages
Sequence Analysis, DNA
Genome project
Biological Sciences
biology.organism_classification
Brachypodium distachyon
Genome, Plant
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Proc. Natl. Acad. Sci. U.S.A. 110, 7940-7945 (2013)
- Accession number :
- edsair.doi.dedup.....b0318862c8c3cc9c9dedae9ed311c892