Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution

Handle URI:
http://hdl.handle.net/10754/625523
Title:
Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution
Authors:
Lightfoot, D. J.; Jarvis, David Erwin ( 0000-0002-0072-9112 ) ; Ramaraj, T.; Lee, R.; Jellen, E. N.; Maughan, P. J.
Abstract:
Background: 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.; Results: 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.; Conclusions: 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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; KAUST Environmental Epigenetics Research Program (KEEP)
Citation:
Lightfoot 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.
Publisher:
Springer Nature
Journal:
BMC Biology
Issue Date:
29-Aug-2017
DOI:
10.1186/s12915-017-0412-4
Type:
Article
ISSN:
1741-7007
Sponsors:
The 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.
Additional Links:
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0412-4
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorLightfoot, D. J.en
dc.contributor.authorJarvis, David Erwinen
dc.contributor.authorRamaraj, T.en
dc.contributor.authorLee, R.en
dc.contributor.authorJellen, E. N.en
dc.contributor.authorMaughan, P. J.en
dc.date.accessioned2017-10-01T05:07:27Z-
dc.date.available2017-10-01T05:07:27Z-
dc.date.issued2017-08-29en
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.en
dc.identifier.issn1741-7007en
dc.identifier.doi10.1186/s12915-017-0412-4en
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.en
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.en
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.en
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.en
dc.publisherSpringer Natureen
dc.relation.urlhttps://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0412-4en
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.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectAmaranthen
dc.subjectAmaranthaceaeen
dc.subjectChromatin contact mapsen
dc.subjectPseudochromosomesen
dc.subjectProximity-guided assemblyen
dc.subjectHi-Cen
dc.subjectGenome evolutionen
dc.subjectChromosome evolutionen
dc.titleSingle-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolutionen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentKAUST Environmental Epigenetics Research Program (KEEP)en
dc.identifier.journalBMC Biologyen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionNational Center for Genome Resources, Santa Fe, NM, 87505, , United Statesen
dc.contributor.institutionBrigham Young University, Department of Plant and Wildlife Sciences, 5144 LSB, Provo, UT, 84602, , United Statesen
kaust.authorLightfoot, D. J.en
kaust.authorJarvis, David Erwinen
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