![]() Pseudomolecules (hereafter referred to as chromosomes, which are numbered according to a previously published single-nucleotide polymorphism (SNP) linkage. 1) of 6,403 unique markers spans a total length of 2,034 centimorgans (cM) and consists of 18 linkage groups (Supplementary Table 7), corresponding to the haploid chromosome number of quinoa. ![]() ![]() To combine scaffolds into pseudomolecules, an existing linkage map from quinoa 13 was integrated with two new linkage maps. The total assembly size of 1.39 gigabases (Gb) is similar to the reported size estimates of the quinoa genome (1.45-1.50 Gb (refs 11,12)). The assembly contains 3,486 scaffolds, with a scaffold N50 of 3.84 Mb and 90% of the assembled genome contained in 439 scaffolds (Table 1). Sequencing, assembly and annotationWe sequenced and assembled the genome of the coastal Chilean quinoa accession PI 614886 (BioSample accession code SAMN04338310) using single-molecule real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) and optical and chromosome-contact maps from BioNano Genomics 9 and Dovetail Genomics 10. Together, these resources provide the foundation for accelerating the genetic improvement of the crop, with the objective of enhancing global food security for a growing world population. Moreover, we sequenced the genomes of additional diploid and tetraploid Chenopodium species to characterize genetic diversity within the primary germplasm pool for quinoa and to understand sub-genome evolution in quinoa. We demonstrate the utility of the genome sequence by identifying a gene that probably regulates the presence of seed triterpenoid saponin content. To accelerate the improvement of quinoa, we present here the allotetraploid quinoa genome. Breeding efforts to improve the crop for important agronomic traits are needed to expand quinoa production worldwide. This potential was recognized when the United Nations declared 2013 as the International Year of Quinoa, this being one of only three times a plant has received such a designation.Despite its agronomic potential, quinoa is still an underutilized crop 7, with relatively few active breeding programs 8. Quinoa has the potential to provide a highly nutritious food source that can be grown on marginal lands not currently suitable for other major crops. Quinoa has gained international attention because of the nutritional value of its seeds, which are gluten-free, have a low glycaemic index 5, and contain an excellent balance of essential amino acids, fibre, lipids, carbohydrates, vitamins, and minerals 6. Quinoa has adapted to the high plains of the Andean Altiplano (> 3,500 m above sea level), where it has developed tolerance to several abiotic stresses. It was presumably first domesticated more than 7,000 years ago by pre-Columbian cultures and was known as the 'mother grain' of the Incan Empire 1. Quinoa (Chenopodium quinoa Willd., 2n = 4x = 36) is a highly nutritious crop that is adapted to thrive in a wide range of agroecosystems. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected.
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