RESUMEN
Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.
Asunto(s)
Variación Genética , Genoma de Planta/genética , Genómica , Internacionalidad , Fitomejoramiento/métodos , Triticum/genética , Aclimatación/genética , Animales , Centrómero/genética , Centrómero/metabolismo , Mapeo Cromosómico , Clonación Molecular , Variaciones en el Número de Copia de ADN/genética , Elementos Transponibles de ADN/genética , Grano Comestible/genética , Grano Comestible/crecimiento & desarrollo , Genes de Plantas/genética , Introgresión Genética , Haplotipos , Insectos/patogenicidad , Proteínas NLR/genética , Enfermedades de las Plantas/genética , Proteínas de Plantas/genética , Polimorfismo de Nucleótido Simple/genética , Poliploidía , Triticum/clasificación , Triticum/crecimiento & desarrolloRESUMEN
Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated Pacific Biosciences (PacBio) long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding. Despite their technical differences, optical mapping and chromosome conformation capture performed similarly and doubled N50 values. After improving both integration methods, assembly contiguity reached chromosome-arm-levels. We rigorously assessed the quality of contigs and scaffolds using Illumina mate-pair libraries and genetic map information. This showed that PacBio assemblies have high sequence accuracy but can contain several misassemblies, which join unlinked regions of the genome. Most, but not all, of these misjoints were removed during the integration of the optical mapping and chromosome conformation capture data. Even though none of the centromeres were fully assembled, the scaffolds revealed large parts of some centromeric regions, even including some of the heterochromatic regions, which are not present in gold standard reference sequences.
Asunto(s)
Cromosomas de las Plantas/química , Mapeo Contig/métodos , Genoma de Planta , Genómica/métodos , Programas Informáticos , Arabidopsis/genética , Cromosomas de las Plantas/genética , Mapeo Contig/normas , Genómica/normasRESUMEN
Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.
Asunto(s)
Mapeo Contig/métodos , Genoma de Planta , Anotación de Secuencia Molecular/métodos , Proteínas de Plantas/genética , Translocación Genética , Triticum/genética , Algoritmos , Mapeo Contig/normas , Anotación de Secuencia Molecular/normas , Polimorfismo Genético , PoliploidíaRESUMEN
Long mate pair (LMP) or "jump" libraries are invaluable for producing contiguous genome assemblies and assessing structural variation. However the consistent production of high quality (low duplication rate, accurately sized) LMP libraries has proven problematic in many genome projects. Input DNA length and quantity are key issues that can affect success. Here we demonstrate how 12 libraries covering a wide range of jump sizes can be constructed from <10 µg of DNA, thus ensuring production of the best LMP libraries from a given DNA sample. Finally, we demonstrate the accuracy of the insert sizes by mapping reads from each library back to an existing assembly.