Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

Putnam, Nicholas H.; O’Connell, Brendan; Stites, Jonathan C.; Rice, Brandon J.; Blanchette, Marco; Calef, Robert; Troll, Christopher J.; Fields, Andrew J.; Hartley, Philip; Sugnet, Charles W.; Haussler, David; Rokhsar, Daniel S.; Green, Edward

doi:10.1101/gr.193474.115

Cited by 757 publications

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“…Chicago library preparation and sequencing. Using the same DNA prepared for PacBio sequencing, a Chicago library was prepared as described previously 10 . The library was sequenced on an Illumina HiSeq 2500.…”

Section: Methodsmentioning

confidence: 99%

“…Scaffolding the PacBio and BioNano assemblies with HiRise. Chicago sequence data (in FASTQ format) was used to scaffold the PacBio-BioNano hybrid assembly using HiRise, a software pipeline designed specifically for using Chicago data to assemble genomes 10 . Chicago library sequences were aligned to the draft input assembly using a modified SNAP read mapper (http://snap.cs.berkeley.edu).…”

Section: Methodsmentioning

confidence: 99%

“…We 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 . 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).…”

Section: Sequencing Assembly and Annotationmentioning

confidence: 99%

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The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

601

706

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Quinoa (Chenopodium quinoa Willd., 2n = 4x = 36) is a highly nutritious crop that is adapted to thrive in a wide range of agroecosystems. 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 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 [2][3][4] . 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 the potential to provide a highly nutritious food source that can be grown on marginal lands not currently suitable for other major crops. 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 . Breeding efforts to improve the crop for important agronomic traits are needed to expand quinoa production worldwide. To accelerate the improvement of quinoa, we present here the allotetraploid quinoa genome. We demonstrate the utility of the genome sequence by identifying a gene that probably regulates the presence of seed triterpenoid saponin content. 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. 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. 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 . 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). 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)). To combine scaffolds into pseudomolecules, an existing linkage map from quinoa 13 was integrated with two new linkage maps. The resulting map (Extended Data Fig. 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. Pseudomolecules (hereafter referred to as chromosomes, which are numbered according to a previously published single-nucleotide polymorphism (SNP) linkage ...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Sequencing Assembly and Annotationmentioning

confidence: 99%

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The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

601

706

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“…Given the recent examples of long-range scaffolding with the help of chromosome contact maps 9,10 , a de novo assembly of chromosome 2D was obtained by combining short-read Illumina sequences and proximity ligation of in vitro reconstituted chromatin, also known as Chicago 5 (Online Methods). In contrast to the in vivo Hi-C method, Chicago has been demonstrated to be more suitable to generate high-quality assemblies from short Illumina reads in vertebrates 5 .…”

mentioning

confidence: 99%

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

et al. 2017

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Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago longrange linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.DOI: https://doi.org/10.1038/nbt.3877Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-144182 Journal Article Accepted Version Originally published at: Thind, Anupriya Kaur; Wicker, Thomas; Šimková, Hana; Fossati, Dario; Moullet, Odile; Brabant, Cécile; Vrána, Jan; Doležel, Jaroslav; Krattinger, Simon G (2017). Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nature Biotechnology, 35(8) Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene using molecular marker information and EMS mutants and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis RPM1 protein.While the world population continues to grow, the arable land per capita is decreasing 6 . To ensure food security, agriculture will require high-yielding crops that can withstand diseases, pests and adverse climatic conditions. A better understanding of genes that control these important traits may enable breeding of crop cultivars capable of feeding the 9-10 billion people expected by 2050. triticina isolates [13][14][15][16] . The Lr22a-mediated resistance is not present in young seedlings (<20 days) but is only visible in wheat plants from ~25 days of age.First, in order to evaluate the effectiveness of Lr22a against Swiss P. triticina isolates we inoculated the Lr22a-containing backcross line RL6044 ('Thatcher Lr22a') and the spring wheat cultivar 'Thatcher' with ten P. triticina isolates that were collected in Switzerland. The first leaves of RL6044 developed leaf rust pustules of similar size as the susceptible control 'Thatcher', while we observed complete to moderate resistance on the third leaves of 30-dayold RL6044 plants in comparison to 'Thatcher' (Fig. 1, Supplementary Fig. 1).Lr22a was previously mapped to the short arm of wheat chromosome 2D using microsatellite analysis of the Lr22a-containing wheat line 98B34-T4B 13 . In order to...

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“…The bacterialartificial-chromosome-based sequence of the 5 Gb barley genome has recently been ordered into chromosome-scale super-scaffolds using in vivo chromatin proximity ligation 39 . In vitro reconstituted chromatin provided useful links across genomic distances of up to 500 kb and enabled very large scaffolds to be generated for the human and alligator genomes 40 . The 1.4 Gb genome of quinoa (Chenopodium quinoa), a nutritious grain, has also been assembled 41 into very long scaffolds (90% of the genome represented by 439 scaffolds) by combining long reads, in vitro chromatin links and optical maps from BioNano Genomics.…”

Section: Methods For Linking Sequences In Genome Assemblymentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

341

240

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Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genome structure and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access to the large and complex genomes of crops and their wild relatives. Sequencing of wild crop relatives is identifying a wide spectrum of genetic variation, permitting the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems. In the twentieth century, famines caused by political crises, mismanagement of food production or genocide killed an estimated 70 million people and were second only to war as the greatest manmade cause of death 1 . The father of the Green Revolution, Norman Borlaug, summarized the importance of crops: "Without food, people perish, social and political organizations disintegrate, and civilizations collapse. " For thousands of years, people have dedicated considerable resources to securing food supplies; for example, grain supplies to ancient Rome were secured through an extensive network of long-distance transport, and the distribution of grain was coordinated and subsidized by the cura annonae ('care for the grain supply'), an important figure who contributed to the maintenance of political unity and power.During the past 10,000 years, a period known as the Holocene, Earth's environment has been unusually stable. This probably facilitated the domestication of crops from wild species, resulting in steadily improved yields and adaptation to new agricultural areas. The production of food is now carried out on a vast scale, with 38% of Earth's surface dedicated to agriculture 2 . This increased production is having a pervasive influence on ecosystems worldwide: nitrogen production for agriculture accounts for 1.2% of global energy consumption 3 ; photosynthesis can no longer maintain stable levels of atmospheric carbon dioxide; and food production consumes around 70% of freshwater supplies. The modelling of crop responses to increases in temperature predicts that there will be a considerable reduction in the yield of rice, an important crop around the world 4 . Climate change could also alter the dynamics of crop pathogenic agents by altering the range of vectors and by compromising the immune response of crops 5 .Crop production must therefore adapt to more variable environments and the substantial impact it has on the environment needs to be reduced. Productivity must also increase at a much greater rate than in the past to meet the needs of Earth's growing population 6 . Genetic improvements in crop performance continue to be crucial for increasing crop productivity, but current rates of improvement are unable to meet the demands of sustainability and food security 7 . Plant genomics has a central role in the improvement of crops, includi...

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Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

Cited by 757 publications

References 38 publications

The genome of Chenopodium quinoa

The genome of Chenopodium quinoa

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

Genomic innovation for crop improvement

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