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 “These genome assemblies will greatly foster further research on
these difficult weed species, including better understanding the
ways in which they evade damage from herbicides,” says Pat
Tranel, professor and associate head of the Department of Crop
Sciences at the University of Illinois and co-author on the
Genome Biology and Evolution study.
Draft genomes had already been published for waterhemp and
Palmer amaranth, but techniques used in the Genome Biology and
Evolution study provide a much clearer and richer picture of the
species’ gene sequences, a requisite for many genomic studies.
All three genomes were assembled using advanced long-read
sequencing, which maintains the integrity and continuity of the
genome similar to the way large puzzle pieces provide a clearer
picture of the whole than small pieces. In Palmer amaranth, an
additional sequencing technology (chromatin conformation capture
sequencing) was used to further order pieces of the genome that
were assembled using the long-read information.
“The goal of any genome assembly is to reveal the complete
arrangement of genes in the genome, broken into chromosome-sized
fragments. Unfortunately, until recently, quality genome
assemblies have been very labor intensive and expensive. The
previously published draft genomes for these species reported
the genome broken into thousands of pieces, while the assemblies
we report are down to hundreds. The vast majority of the
sequence is now assembled into very large fragments,” says Jacob
Montgomery, a graduate student working with Tranel and first
author on the study.
To further improve the assembly of the genomes for waterhemp and
smooth pigweed, the team used an innovative approach known as
trio binning, developed in cattle. Not only had this technique
never before been fully utilized in plants, it had also not been
used with parents from different species.
In normal reproduction, male and female parents each contribute
one copy of every gene to their offspring. In this case,
offspring are diploid, meaning they have two copies of every
gene. In the study, the team created hybrid offspring from two
separate species: waterhemp and smooth pigweed. These offspring
are still diploid, but the trio binning technique allowed the
researchers to pull apart and isolate the two copies from each
parent species, resulting in haploid (single copy) genomes for
each.
“This approach resolved a problem in the previous waterhemp
genome assembly. When parent alleles (copies of each gene) are
very different from each other, as is often the case in
outcrossing species such as waterhemp, the genome assembly
program interprets them to be different genes,” Tranel says.
“With only one allele from each species, we were able to obtain
a much cleaner assembly of their gene sequences.”
Detlef Weigel, director of the Max Planck Institute for
Developmental Biology and co-author on the study, adds, “I am a
big fan of the new advanced sequencing techniques, but even
though they should theoretically be sufficient to sort out the
arrangement of genes, in practice they are not. This is where
genetics can help out, using information on whether genes were
inherited from mom or dad. This allowed us to assign each gene
to either a maternal or paternal chromosome.”
The researchers specifically chose waterhemp as
the male parent in the smooth pigweed × waterhemp cross because
the previously published waterhemp genome was from a female
plant. Tranel is pursuing research to understand the genetic
basis for maleness and femaleness in waterhemp and Palmer
amaranth, with potential applications toward introducing female
sterility as a future control method.
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“The genomes of the male waterhemp and Palmer
amaranth already have enabled my group to make rapid progress on
identifying the potential genes that could be responsible for the
determination of sex (male or female) in both species,” Tranel says.
Importantly, the genomes for all three species could start to chip
away at the problem of herbicide resistance in these weeds. More and
more, scientists are uncovering evidence of non-target-site or
metabolic resistance in waterhemp and Palmer amaranth, allowing the
weeds to detoxify herbicides before they can cause damage.
Unfortunately, it is usually very difficult to determine which
specific enzyme, among hundreds, is responsible for detoxifying the
herbicide.
Now, researchers will essentially be able to sort through a list to
find the culprit with the hope of either knocking out the enzyme
responsible or modifying the herbicide molecule to evade
detoxification.
“Innovation is essential for the future of agriculture. We at BASF
are working continuously on improving our products and services
including sustainable solutions for the management of
herbicide-resistant weeds. We want to better understand the amaranth
biochemical resistance mechanisms in order to offer farmers new
products and solutions for optimal control of key weeds,” says Jens
Lerchl, head of early biology research on herbicides at BASF and
study co-author. Lerchl coordinated the Palmer amaranth genome work
with KeyGene/Wageningen -The Netherlands.
“The area of genome sequencing is highly dynamic. That is why BASF
chose KeyGene as the partner for both latest sequencing technology
and bioinformatics. Together with the expertise of the University of
Illinois and Max Planck Society, we were able to compare genomes and
address specific biological topics,” Lerchl says. In addition to
collaborating on this research, BASF is also a founding member of
the International Weed Genomics Consortium (https://www.weedgenomics.org/),
led by Colorado State University aiming at the sequencing and
analysis of ten high priority key weeds.
Co-authors from KeyGene endorse the societal relevance of the
results and of the public availability of the data. “In plant
sciences, studying weed genetics is important for sustainability of
future agriculture. Our results will hopefully stimulate scientists
around the globe to start, continue, and boost research on the
genetics of important weeds that currently reduce yields, increase
costs, and cause environmental burden,” says Antoine Janssen, genome
informatics expert at KeyGene.
The article, “Draft genomes of Amaranthus tuberculatus, Amaranthus
hybridus, and Amaranthus palmeri,” is published in Genome Biology
and Evolution [DOI: 10.1093/gbe/evaa177]. The research was supported
by USDA’s National Institute of Food and Agriculture, the
International Max Planck Research School, and the Max Planck
Society.
The Department of Crop Sciences is in the College of Agricultural,
Consumer and Environmental Sciences at the University of Illinois.
[Sources: Pat Tranel,
Jacob Montgomery,
Detlef Weigel,
Jens Lerchl,
Antoine Janssen,
News writer: Lauren Quinn,] |
