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BMC Biol. 2017 Aug 31;15(1):74. doi: 10.1186/s12915-017-0412-4.

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

Author information

1
Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), KAUST Environmental Epigenetic Program (KEEP), Thuwal, 23955-6900, Saudi Arabia.
2
Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
3
National Center for Genome Resources, Santa Fe, NM, 87505, USA.
4
Department of Plant & Wildlife Sciences, Brigham Young University, 5144 LSB, Provo, UT, 84602, USA.
5
Department of Plant & Wildlife Sciences, Brigham Young University, 5144 LSB, Provo, UT, 84602, USA. Jeff_Maughan@byu.edu.

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.

KEYWORDS:

Amaranth; Amaranthaceae; Chromatin contact maps; Chromosome evolution; Genome evolution; Hi-C; Proximity-guided assembly; Pseudochromosomes

PMID:
28854926
PMCID:
PMC5577786
DOI:
10.1186/s12915-017-0412-4
[Indexed for MEDLINE]
Free PMC Article

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