![]() ![]() 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. ![]() 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. This allowed us to assign each gene to either a maternal or paternal chromosome." This is where genetics can help out, using information on whether genes were inherited from mom or dad. "With only one allele from each species, we were able to obtain a much cleaner assembly of their gene sequences."ĭetlef 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. 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. "This approach resolved a problem in the previous waterhemp genome assembly. 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. In the study, the team created hybrid offspring from two separate species: waterhemp and smooth pigweed. In this case, offspring are diploid, meaning they have two copies of every gene. In normal reproduction, male and female parents each contribute one copy of every gene to their offspring. Not only had this technique never before been fully utilized in plants, it had also not been used with parents from different species. 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. 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. 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. Unfortunately, until recently, quality genome assemblies have been very labor intensive and expensive. "The goal of any genome assembly is to reveal the complete arrangement of genes in the genome, broken into chromosome-sized fragments. 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. "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.ĭraft 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.Īll 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. ![]()
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