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dc.contributor.authorLightfoot, Damien
dc.contributor.authorJarvis, David Erwin
dc.contributor.authorRamaraj, T.
dc.contributor.authorLee, R.
dc.contributor.authorJellen, E. N.
dc.contributor.authorMaughan, P. J.
dc.date.accessioned2017-10-01T05:07:27Z
dc.date.available2017-10-01T05:07:27Z
dc.date.issued2017-08-29
dc.identifier.citationLightfoot DJ, Jarvis DE, Ramaraj T, Lee R, Jellen EN, et al. (2017) Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution. BMC Biology 15. Available: http://dx.doi.org/10.1186/s12915-017-0412-4.
dc.identifier.issn1741-7007
dc.identifier.pmid28854926
dc.identifier.doi10.1186/s12915-017-0412-4
dc.identifier.urihttp://hdl.handle.net/10754/625523
dc.description.abstractBackground: Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of the developing world. Here, we present a reference-quality assembly of the amaranth genome which will assist the agronomic development of the species.
dc.description.abstractResults: Utilizing single-molecule, real-time sequencing (Pacific Biosciences) and chromatin interaction mapping (Hi-C) to close assembly gaps and scaffold contigs, respectively, we improved our previously reported Illumina-based assembly to produce a chromosome-scale assembly with a scaffold N50 of 24.4 Mb. The 16 largest scaffolds contain 98% of the assembly and likely represent the haploid chromosomes (n = 16). To demonstrate the accuracy and utility of this approach, we produced physical and genetic maps and identified candidate genes for the betalain pigmentation pathway. The chromosome-scale assembly facilitated a genome-wide syntenic comparison of amaranth with other Amaranthaceae species, revealing chromosome loss and fusion events in amaranth that explain the reduction from the ancestral haploid chromosome number (n = 18) for a tetraploid member of the Amaranthaceae.
dc.description.abstractConclusions: The assembly method reported here minimizes cost by relying primarily on short-read technology and is one of the first reported uses of in vivo Hi-C for assembly of a plant genome. Our analyses implicate chromosome loss and fusion as major evolutionary events in the 2n = 32 amaranths and clearly establish the homoeologous relationship among most of the subgenome chromosomes, which will facilitate future investigations of intragenomic changes that occurred post polyploidization.
dc.description.sponsorshipThe Erza Taft Benson Agriculture and Food Institute, The Holmes Family Foundation, and the King Abdullah University of Science and Technology (KAUST) supported research reported in this publication.
dc.publisherSpringer Nature
dc.relation.urlhttps://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0412-4
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectAmaranth
dc.subjectAmaranthaceae
dc.subjectChromatin contact maps
dc.subjectPseudochromosomes
dc.subjectProximity-guided assembly
dc.subjectHi-C
dc.subjectGenome evolution
dc.subjectChromosome evolution
dc.titleSingle-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentDesert Agriculture Initiative
dc.contributor.departmentKAUST Environmental Epigenetics Research Program (KEEP)
dc.identifier.journalBMC Biology
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionNational Center for Genome Resources, Santa Fe, NM, 87505, , United States
dc.contributor.institutionBrigham Young University, Department of Plant and Wildlife Sciences, 5144 LSB, Provo, UT, 84602, , United States
kaust.personLightfoot, Damien
kaust.personJarvis, David Erwin
refterms.dateFOA2018-06-13T18:49:17Z


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This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Except where otherwise noted, this item's license is described as This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.