2020
DOI: 10.1093/gbe/evaa177
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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 ada… Show more

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Cited by 56 publications
(71 citation statements)
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“…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).…”
Section: Resultsmentioning
confidence: 99%
“…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).…”
Section: Resultsmentioning
confidence: 99%
“…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.…”
Section: Resultsmentioning
confidence: 99%
“…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.…”
Section: Methodsmentioning
confidence: 99%
“…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.…”
Section: Future Outlookmentioning
confidence: 99%
“…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).…”
Section: Future Outlookmentioning
confidence: 99%