Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri

Abstract

Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. Here, we present the most contiguous draft assemblies of these three species to date. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact mapping information to assemble and order sequences of A. palmeri to near-chromosome-level resolution, with scaffold N50 of 20.1 Mb. To resolve the issues of heterozygosity and co-assembly of alleles in diploid species, we adapted the trio binning approach to produce haplotype assemblies of A. tuberculatus and A. hybridus. This approach resulted in an improved assembly of A. tuberculatus, and the first genome assembly for A. hybridus, with contig N50s of 2.58 and 2.26 Mb, respectively. Species-specific transcriptomes and information from related species were used to predict transcripts within each assembly. Syntenic comparisons of these species and Amaranthus hypochondriacus identified sites of genomic rearrangement, including duplication and translocation, while genetic map construction within A. tuberculatus highlighted the need for further ordering of the A. hybridus and A. tuberculatus contigs. These multiple reference genomes will accelerate genomic studies in these species to further our understanding of weedy evolution within Amaranthus.

Male‐specific Y‐chromosomal regions in waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri)

“…For A. tuberculatus , an additional set of 66 male‐specific 15 bp sequences, herein referred to as k‐mers, was obtained by comparing whole genome sequence from 23 male and 19 female plants (Kreiner et al ., 2019). The male‐specific RAD‐tags and k‐mers were aligned to their respective reference genomes (Montgomery et al ., 2020) to identify genomic regions enriched for these markers (Tables 1, 2).…”

Male Linked Genomic Region Determines Sex in DioeciousAmaranthus palmeri

“…The availability of a recent draft sequence of a male A. palmeri individual ( Montgomery et al 2020 ) allowed us place our male-specific region and extract a potential Y chromosome. We first aligned the assembled male-specific contigs to the draft sequence.…”

“…We aligned assembled male-specific scaffolds to the A. palmeri draft genome v 1.1 ( Montgomery et al 2020 ) using minimap2 ( Li 2018 ) with -ax asm5 and extracted all covered sites using samtools 1.9 depth ( Li et al 2009 ). In addition, we mapped all extracted male and female-specific reads directly to the A. palmeri draft genome using BWA-MEM ( Li 2013 ) and samtools to extract read depths for the male and female pool.…”

Herbicide resistance in Amaranthus tuberculatus†

“…For example, in the last 10 years, we have gone from generating a very rudimentary transcriptome 88 for A. tuberculatus to obtaining a very high quality transcriptome, 77 along with highquality reference genomes of both a female and male individual. 64,89 Recently, a herbicide-sensitive A. tuberculatus population has been isolated before becoming extinct and made publicly available (accession Ames 35 826 in the US National Plant Germplasm System). If adopted, this reference population will foster uniformity among A. tuberculatus researchers.…”

“…Furthermore, the emergence of ‐omics resources and capabilities provide promising opportunities not only to elucidate these mechanisms, but also to understand their regulation and evolution. For example, in the last 10 years, we have gone from generating a very rudimentary transcriptome 88 for A. tuberculatus to obtaining a very high quality transcriptome, 77 along with high‐quality reference genomes of both a female and male individual 64,89 . Recently, a herbicide‐sensitive A. tuberculatus population has been isolated before becoming extinct and made publicly available (accession Ames 35 826 in the US National Plant Germplasm System).…”