A chromosome‐scale draft sequence of the Canada fleabane genome

Abstract

Background: Due to the accessibility of underlying technologies the 'Omics', in particular genomics, are becoming commonplace in several fields of research, including the study of agricultural pests. The weed community is starting to embrace these approaches; genome sequences have been made available in the past years, with several other sequencing projects underway, as promoted by the International Weed Genome Consortium. Chromosome-scale sequences are essential to fully exploit the power of genetics and genomics.Results: We report such an assembly for Conyza canadensis, an important agricultural weed. Third-generation sequencing technology was used to create a genome assembly of 426 megabases, of which nine chromosome-scale scaffolds cover more than 98% of the entire assembled sequence. As this weed was the first to be identified with glyphosate resistance, and since we do not have a firm handle on the genetic mechanisms responsible for several herbicide resistances in the species, the genome sequence was annotated with genes known to be associated with herbicide resistance. A high number of ABC-type transporters, cytochrome P450 and glycosyltransferases (159, 352 and 181, respectively) were identified among the list of ab initio predicted genes.Conclusion: As C. canadensis has a small genome that is syntenic with other Asteraceaes, has a short life cycle and is relatively easy to cross, it has the potential to become a model weed species and, with the chromosome-scale genome sequence, contribute to a paradigm shift in the way non-target site resistance is studied.

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

“…Recombination frequency across the genome could be derived from future linkage studies to validate the order of these contigs and further develop this genomic resource. These results confirm the efficacy of this “PacBio-plus-Hi-C” genome assembly approach, even in species known to be highly heterozygous ( Laforest et al. 2020 ).…”

Mechanisms of evolved herbicide resistance

“…Draft genomes have recently been obtained for some of our most important herbicide-resistant weeds, including A. tuberculatus (156), C. canadensis (157), B. scoparia (64), R. raphanistrum (158), E. crus-galli (159), and E. indica (160). Although some of these genomes are still highly fragmented, those of A. tuberculatus, C. canadensis, and E. crus-galli have N50s greater than 1.5 Mb (N50 is the length of a computationally-assembled contiguous sequence for which 50% of the sequences in an assembly are longer and 50% are shorter; longer N50 indicates a better assembly).…”

Herbicide resistance in Amaranthus tuberculatus†

“…I anticipate that, over the next few years, genetic mapping will become a new standard approach for identifying NTS resistance genes in A. tuberculatus, as well as in other species as their genomes become available. 90 A clear trend emerges when cataloging the various resistance mechanisms that have been elucidated in A. tuberculatus over time: NTS-resistance mechanisms are becoming increasingly common in this species (Table 1)…”

“…If overexpression instead is due to a change in a transcription factor, genetic mapping likely would be the easiest approach to identify the gene encoding it. I anticipate that, over the next few years, genetic mapping will become a new standard approach for identifying NTS resistance genes in A. tuberculatus , as well as in other species as their genomes become available 90 …”