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Genome Biology Papers Present Epigenetics Benchmarking Resource, Genomic Architecture Maps of Peanuts, More

Researchers representing the FDA's Epigenomics Quality Control (EpiQC) Group have developed a new benchmarking resource. As they report in Genome Biology, the EpiQC Group generated DNA methylation data for all seven Genome in a Bottle Consortium reference cell lines using three whole-genome bisulfite sequencing approaches, oxidative bisulfite sequencing, an enzymatic deamination method, targeted methylation sequencing, single-molecule long-read nanopore sequencing, and methylation arrays. The researchers note that the choices of library preparation approach and algorithmic tools can affect the performance of the approaches. "This reference dataset can act as a benchmarking resource and a reference point for future studies as epigenetics research becomes more widespread within the field of genomics," the researchers write.

A Henan Agricultural University team has generated three-dimensional genome architecture maps of wild-type and mutant allotetraploid peanut lines by combining whole transcriptome, ATAC-seq, and Hi-C sequencing data. They found that most peanut chromosome arms harbor active regions of high gene density and transcriptional activity, and that a small portion of these inactive regions become active in the mutant lines. These newly active regions include genes involved in flavonoid biosynthesis and circadian rhythm functions, as the researchers report in their paper. They further uncovered a new topologically associated domain in the mutant line that appears to affect gibberellin synthesis and could account for the line's short height.

Finally, Chinese Academy of Tropical Agricultural Sciences-led team resequenced 388 cassava genomes, representing both cultivars and wild accessions. Through a genome-wide association study, they then tied 52 loci to a suite of agronomic traits like plant height, blight resistance, and root weight. They further identified 81 selective sweeps in the cassava genome and found that artificial selection for decreased heterozygosity contributed to the domestication of cassava's large, starchy storage root. "Our findings will contribute to elucidating the genetic basis of the variation in heterozygosity associated with key agronomic traits and cassava domestication as well as allow for the strategic exploitation for cassava improvement," the researchers write.