Here, we report on the development of a computational pipeline for chromosome-scale sequence assembly of wheat and barley genomes. An open-source assembly pipeline with comparable accuracy, completeness, and speed similar to available commercial platforms would greatly reduce the cost per assembled genome, thus extending the scope of pan-genome projects in the Triticeae. Similar projects are under way in bread wheat ( ). A cornerstone of our strategy is the construction of high-quality sequence assemblies for multiple genotypes representative of major germplasm groups. We have recently outlined a proposal for pan-genomics in barley. Another important concern is the high computational cost for a long-read (hybrid) assembly, estimated at 470,000 CPU hours or 6.5 months in wall-clock time. But still, the contiguity of these assemblies is lower than that of the scaffolds constructed using the DeNovoMagic algorithm. In addition, long-read assemblies have been generated for Ae. Short-read assemblies of the wheat genome have been generated by open-source alternatives such as w2rap or Meraculous. Indeed, efforts to develop a low-cost, open-source alternative are still required to allow assembly of multiple genomes within a species to comparable contiguity. Despite being robust, the assembly algorithm used in these projects was closed-source, potentially limiting its application to the broader community.
#PEARSON PROTEIN SCAFFOLD CHROMOSOME FULL#
Within months, a fully annotated, highly contiguous sequence was assembled, capturing the full organizational context of the 21 wheat chromosomes, some of which have been validated using other approaches. The wild emmer wheat, and subsequently the bread and durum wheat, genome projects used a whole-genome shotgun (WGS) approach based on Illumina short-read sequencing of shotgun libraries with multiple insert sizes. However, BAC-by-BAC assembly is laborious and time-consuming and has become an obsolete method of sequence assembly. Assembling bacterial artificial chromosomes (BACs) guided by a physical map yielded megabase-sized scaffolds, which were then arranged into chromosomal super-scaffolds (so-called pseudomolecules) by long-range linkage information afforded by ultra-dense genetic maps, chromosome conformation capture sequencing (Hi-C), or Bionano optical mapping. The genome projects of barley, bread wheat, and the A and D genome progenitors had initially followed the hierarchical shotgun approach as had been employed by the human genome project, but adopted second-generation sequencing methods for sequencing as they became available. dicoccoides (wild emmer wheat, AB genome). urartu (wheat A genome progenitor), and T. durum) as well as the wheat wild relatives Aegilops tauschii (wheat D genome progenitor), T. Recently, chromosome-scale reference sequence assemblies have come available for barley ( Hordeum vulgare), hexaploid bread wheat ( Triticum aestivum), and tetraploid durum wheat ( T. Large genome sizes, high content of transposable elements (TEs), and polyploidy (in the case of wheat) have long impeded genome assembly projects in the Triticeae. The Triticeae species wheat and barley were among the founder crops of Neolithic agriculture in Western Asia and continue to dominate agriculture in temperate regions of the world to the present day.
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