The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

Amaranth ( L.) is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and ) and their putative progenitor () were resequenced. A single nucleotide polymorphism (SNP) phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics' Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L.) and estimated, using analysis, the age of the most recent polyploidization event in amaranth.

Abstract licence: CC BY-NC-ND

1. 7.

   Chromosome-scale shotgun assembly using an in vitro method for long-range linkage · 2016

2. 16.

   Assessing structural variation in a personal genome—towards a human reference diploid genome · 2015

3. 38.

   Quantitative measures for the management and comparison of annotated genomes · 2009

4. 51.

   MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects · 2011

5. 62.
   Corrected

   SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler · 2012

6. 71.

   Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology · 2014

84 more references, whose wording the paper’s licence keeps private.

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.