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

Abstract

Amaranth (Amaranthus hypochondriacus 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 (2n = 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 50 of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which Copia-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 (A. hypochondriacus, A. caudatus, and A. cruentus) and their putative progenitor (A. hybridus) were resequenced. A single nucleotide polymorphism (SNP) phylogeny supported the classification of A. hybridus as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for A. hypochondriacus 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 50 of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet (Beta vulgaris L.) and estimated, using K s analysis, the age of the most recent polyploidization event in amaranth.

Target-Site Resistances to ALS and PPO Inhibitors Are Linked in Waterhemp (Amaranthus tuberculatus)

“…The published grain amaranth genome (Clouse et al 2016) contained complete sequence coverage of both ALS and PPX2 genes. These two genes were found to be present on the same scaffold, scaffold 30, which is about 1.3 Mb in length (Figure 1).…”

“…Although an assembled genome for waterhemp is not available, a draft assembly is available for the closely related species, grain amaranth (Clouse et al 2016). Both ALS and PPX2 gene sequences from grain amaranth (obtained previously by Maughan et al [2008]) were used in BLAST searches of the grain amaranth contigs available at CoGe (id 40120, https://genomevolution.org/coge).…”

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

“…For example, hybrid scaffolding was used to enhance the genome assemblies of amaranth (Amaranthus hypochondriacus; Clouse et al, 2016), barley (Hordeum vulgare; Mascher et al, 2017), and quinoa (Chenopodium quinoa; Jarvis et al, 2017). In amaranth, the hybrid assembly reduced the number of scaffolds from 343 to 241 and nearly doubled the final scaffold N50 by making several key connections between existing large scaffolds.…”

“…Indeed, the sequencing and assembly methods required to achieve a high level of contiguity are well within reach of many laboratories, including those working with trees (Neale et al, 2014), minor crops (Clouse et al, 2016;Jarvis et al, 2017), or ecological systems (Martínez-García et al, 2016;Olsen et al, 2016;Tang et al, 2016;Vining et al, 2017). If a research group invests in mate-pair or long-read sequencing at high depth, it is natural to proceed to genome assembly, even though the assembly may never be used for map-based cloning or genetic analysis in the traditional sense.…”

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“…Additionally, the amount of seeds can be controlled, which allows the production of large offspring populations for genetic mapping. Furthermore, amaranth has a relatively small genome ( 500 Mbp) with a reference sequence, and a large number of genotyped genebank accessions are available (Clouse et al, 2015;Stetter et al, 2015). Taken together, these resources and the possibility of interspecific crosses make the grain amaranth species a very suitable model organism for studying fundamental processes such as adaptation, speciation, heterosis, C 4 photosynthetic metabolism, or domestication.…”