NEW FINDINGS — AGRICULTURE
Plant Gene Atlas The first plant reference genome, Arabidopsis thaliana , was released in 2000. Since then, thousands of increasingly more complex plant reference genomes have been produced for model plant species and agriculturally important plants. These genomes help scientists unravel the relationship between gene function and environment. By figuring out how different genes react to dif- ferent situations, scientists can help plants grow better. However, locating results from the few published functional studies is often difficult, limiting the collaborative reach of the studies. The Joint Genome Institute compiled all of the known functional studies for plant genes, including large-scale tran- scriptomics projects, and combined that with additional genomic data to create a database of plant gene function. The Plant Gene Atlas, released in 2023, includes expression-derived annotations for more than 60,000 plant genes with previously undescribed functions. Key findings include regulation of important classes of genes across model plants’ developmental stages and gene expression changes based on varying nitrogen sources. This lays the groundwork for new potential targets for genome editing or directed breeding. Producing the Atlas led to the development of bioinformatics tools for standardizing data so that experimental results using different methods can be compared to more accurately predict homologous gene function in other plant species. By developing a baseline of evolutionarily conserved gene regions in plants and pat- terns of tissue-specific gene expression, this new database could dramatically increase the pace of plant gene function discovery. n REFERENCES: Sreedasyam, A., et al. JGI Plant Gene Atlas: an updateable tran- scriptome resource to improve functional gene descriptions across the plant kingdom, Nucleic Acids Research (2023) 51(16) 8383-8401 doi.org/10.1093/nar/gkad616 Sun, Y. et al.Twenty years of plant genome sequencing: achievements and challenges. Trends in Plant Science (2022) 27(4): 391-401 doi.org/10.1016/j.tplants.2021.10.006
Spilling the tea on tea genes Tea is a traditional drink consumed on every continent. Produced from young leaves of the Camellia sinensis plant, tea’s popularity is attributed to its flavor, aroma, and potential health benefits. Developing new cultivars of Camellia using conventional breed- ing is challenging because it is a perennial plant that does not self-fertilize. Tea-related research has increased dramatically since genome reference sequences for tea plants were released in 2018, 2019, and 2020. 2023 saw an explosion of discoveries largely due to major updates to the Tea Plant Information Archive, a database for Camellia genomics. Sequencing of 350 tea plant varieties iden- tified more than 15 million genetic variants, single nucleotide polymorphisms (SNPs), as well as small insertions and deletions. High-quality genome sequencing of many tea plants reveals pop- ulation structures and points to genes that play a role in helping Through a series of experiments, the team determined that the sex of Sphagnum is linked to its growth in peat bogs and how it contends with its acidic environment. Female Sphagnum mosses produce thicker, larger leaves, enabling greater carbon storage. In males, interactions between sex chromosomes and genetic variation on non-sex chromo- somes allowed some males to grow better under stressful pH environments. These newly discovered interactions between sex chromosomes, autosomes, and environmental factors open up new avenues of research in this valuable carbon sequestration tool. n REFERENCE: Healey, A.L., et al. Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics. Nat. Plants (2023) 9, 238–254. doi.org/10.1038/s41477-022-01333-5 The HudsonAlpha Genome Sequencing Center and the laboratory of HudsonAlpha faculty researcher Alex Harkess, PhD, contributed to this work. Peat moss sex chromosomes impact carbon sequestration Peat bogs are marshy, wetland areas covering about three percent of the earth’s land mass. They store twice as much carbon as all the trees on the planet, aptly earning them the moniker ‘carbon sink.’ Harvesting peat from bogs releases underground carbon stores into the atmosphere as carbon dioxide and methane. Five percent of our annual greenhouse gas emissions are estimated to come from the millions of acres of harvested peatland. Sphagnum mosses are an important part of the peat bog ecosystem, keeping the bogs moist and at the appropriate pH. Understanding Sphagnum’s response to our warming climate is critical for protecting peat bogs. A group of sci- entists produced high-quality reference genomes for two Sphagnum species. The genomes reveal the first Sphagnum moss sex chromosomes to be identified. These are the smallest sex chromosomes observed in nature.
The HudsonAlpha Genome Sequencing Center, led by faculty researchers Jane Grimwood, PhD and Jeremy Schmutz, contributed to this work.
plants thrive in specific regions. Scientists discovered several genes that control specific traits, including leaf structure, disease resistance, and drought tolerance genes. Extensive efforts have been made to charac- terize and preserve genetic diversity in tea plant
seed stock. Genome-wide association studies also revealed mark- ers associated with tiny molecules that play a role in the unique flavors, colors, and aromas of several tea varieties. Population genomics research is unraveling the evolutionary history of Camellia and shining light on the domestication of the tea plant. n REFERENCES: Li H, et al. Application of Multi-Perspectives in Tea Breeding and the Main Directions. Int J Mol Sci. (2023) 24(16):12643. doi: 10.3390/ijms241612643 Li, JW, et al. Molecular markers in tea plant (Camellia sinensis): Applications to evo- lution, genetic identification, and molecular breeding. Plant Physiol Biochem (2023) 198:107704. doi: 10.1016/j.plaphy.2023.107704
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