Sugarcane’s Complicated Genome Sequencing plant genomes is notoriously difficult. Plants have tough cell walls that complicate DNA extraction, and many plants produce compounds that can contaminate samples. Additionally, plant genomes are massive, often far larger than the human genome, and filled with repetitive DNA sequences that make genome assembly difficult. Many plants are also polyploid, with multiple copies of each chromosome. This makes it challenging to determine where each DNA sequence belongs within the genome. Despite the challenges, studying plant genomes is crucial for two key reasons: understanding how plant species are related and identifying the genetic changes that contribute to desirable and harmful traits. Sugarcane ( Saccharum officinarum ), the world’s most harvested crop by weight, is a vital source of sugar, biofuel, and biomaterials. However, its complex genetic makeup has long hindered the creation of a high-quality reference genome. This complexity stems from its massive genome size (12 copies of each chromosome, more than 100 chromosomes per cell) and large amounts of repetitive DNA. Recent work by scientists at the HudsonAlpha Institute for Biotechnology and the Department of Energy Joint Genome Institute finally made a high-quality sugarcane reference genome possible. Using advanced sequencing techniques, they successfully tackled the challenges of the sugarcane genome and assembled a high-quality genome for the sugarcane variety known as R570. The use of long-read sequencing was critical, allowing researchers to capture longer DNA fragments and more easily piece together overlapping sequences. Parkinson’s and Pesticides Parkinson’s disease (PD) is a progressive neurological disorder caused by the build-up of misfolded alpha-synuclein particles in brain cells. The clumps of alpha-synuclein, known as Lewy bodies, disrupt nerve cell function and lead to the muscle tremors commonly seen in patients with PD. As the U.S. population ages, the incidence of this common neurodegenerative disorder is rising. PD is a multifactorial condition influenced by a mix of genetic and environmental factors. While rare familial cases that are linked to single genetic changes occur, most PD cases result from multiple interacting risk factors. Research has long suggested a link between pesticide exposure and Parkinson’s Disease (PD) risk. However, exposure alone does not guarantee the development of PD, as some exposed individuals never develop the disease, while others do so without pesticide contact. A recent study analyzed genetic data from patients with PD who were exposed to pesticides for a long time, especially those used on cotton. This study identified genetic variants that may account for differences in disease risk. Notably, 26 of the genes with identified variation are related to lysosome function. Lysosomes are organelles that break down dam- aged proteins and recycle cellular components through a process
called autophagy. Scientists propose that lysosomal dysfunction in clearing misfolded alpha-synuclein could start the formation of Lewy bodies and, ultimately, the onset of PD. The study also revealed that combining genetic risk variants
with pesticide exposure may amplify the risk of lysosomal failure.
This interplay highlights the importance of studying environmental
triggers alongside genetic predispositions. Most of the genetic variants identified would only cause minor changes in lysosomal function and
not lead to disease on their own. However, when combined with prolonged pesticide exposure, the risk of lysosome failure and development of PD is significantly higher. This study provides new insights into complex gene-environment interactions and could open up new potential treatment pathways for Parkinson’s disease. n REFERENCE: Ngo, K.J., et al. Lysosomal genes contribute to Parkinson’s disease near agriculture with high intensity pesticide use. NPJ Parkinson's Dis. (2024) 10, 87. https://doi.org/10.1038/s41531-024-00703-4
This milestone is transformative for the sugarcane industry. Scientists have already identified two key genes that help protect sugarcane from brown rust disease, a significant threat to farmers. Access to this genome data will accelerate breeding programs and increase the presence of desirable traits in sugarcane, ensuring its long-term sustainability as a vital crop. n
REFERENCE: Healey, A.L., et al., The complex polyploid genome architecture of sugarcane. Nature 628, 804–810 (2024). https://doi.org/10.1038/s41586-024-07231-4
The HudsonAlpha Genome Sequencing Center, led by faculty researchers Jane Grimwood, PhD and Jeremy Schmutz, contributed to this work.
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