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Nature Papers Present Tomato Pangenome, Genomic Evolution of Potatoes, More

The graph pangenome of the tomato is reported in Nature this week, providing a new tool for advancing breeding efforts for this important crop plant. To construct the pangenome, a team led by scientists from the Chinese Academy of Agricultural Sciences catalogued more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. They demonstrate its utility by using it for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. "Our study advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding," the researchers write.

A study examining the genomic evolution and diversity of wild and cultivated potatoes is presented in Nature this week, helping advance efforts to construct a pangenome for the food crop. A group led by investigators from the Chinese Academy of Agricultural Sciences assembled and analyzed 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions, as well as two species in a neighboring section. Through the work, the researchers uncover insights into the alteration of potato genomes during the evolution of tuberization, which will enable genome design for new diploid hybrids, they write.

The discovery of adaptive immunity in humans to the CRISPR enzyme CAS13d is reported in this week's Nature Medicine, highlighting the potential dangers of using the RNA-editing enzyme for therapeutic applications. As efforts to use CRISPR genome editing to treat disease accelerate, efforts are underway to identify CRISPR nucleases with improved characteristics over the well-known Cas9 enzyme. One of these, Cas13d from the bacteria Ruminococcus flavefaciens (RfxCas13d), is of particular interest owing to its small size and high specificity. However, the existence of pre-existing immunity against RfxCas13d is unclear. To investigate, a team led by researchers from the National University of Singapore evaluated antibody and T cell responses to RfxCas13d in healthy donors using ELISA and T cell culture assays. They find RfxCas13d-reactive antibodies and CD4 and CD8 T cell responses in most donors. "Our findings argue for caution in the use of RfxCas13d as a therapeutic, particularly if the enzyme is to be expressed in the long term," they write.

The Scan

Open Pediatric Brain Tumor Atlas Team Introduces Genomic Data Collection, Analytical Tools

A study in Cell Genomics outlines open-source methods being used to analyze and translate whole-genome, exome, and RNA sequence data from the Pediatric Brain Tumor Atlas.

Neurological Outcomes Linked to Innate Immune Features After Cardiac Arrest

Researchers reporting in Med dig into immune features found a few hours after cardiac arrest that correspond with neurological outcomes.

Mouse Study Finds Circadian Rhythm-Related Gene Expression Changes Linked to Sleep Apnea

A paper in PLOS Biology reveals tissue-specific circadian rhythm and gene expression patterns in an intermittent hypoxia-based mouse model of obstructive sleep apnea.

Polygenic Risk Score to Predict Preeclampsia, Gestational Hypertension in Pregnant Women

Researchers in Nature Medicine provide new mechanistic insights into the development of hypertensive disorders of pregnancy, which may help develop therapeutics.