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Nature Discusses Therapeutic Genome Editing, Presents Fitness Consequence Map of Rice, More

University of California, Berkeley, researcher and CRISPR pioneer Jennifer Doudna reviews the scientific, technical, and ethical aspects of using the genome editing technology for therapeutic applications in this week's Nature. In her review, she presents examples highlighting both the potential and pitfalls of these efforts, and calls for "active efforts to ensure that this breakthrough technology is used responsibly to treat, cure, and prevent genetic disease."

A fitness consequence map for rice (Oryza sativa) is reported in Nature Plants this week, providing a new resource to improve the understanding of selection in this key crop species and potentially guide the identification of functional components of genome structure for future breeding efforts. A team led by New York University scientists inferred fitness consequence scores for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, which were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae tribe. Among their findings is evidence of weak negative selection, frequently at candidate regulatory sites, in around 2 percent of the rice genome.

A new method for targeted nanopore sequencing that uses Cas9 to ligate adapters is described in Nature Biotechnology this week. Called nCATS — short for nanopore Cas9-targeted sequencing — the approach uses targeted cleavage of chromosomal DNA with Cas9 to ligate adapters for nanopore sequencing, and is shown by its developers at Johns Hopkins to be capable of simultaneously assessing haplotype-resolved single-nucleotide variants, structural variations, and CpG methylation. The investigators also apply nCATS to four cell lines, to a cell-line-derived xenograft, and to normal, and paired tumor/normal primary human breast tissue, achieving median sequencing coverage of 675x using a MinION flow cell and 34x using the smaller Flongle flow cell. Requiring only around 3 micrograms of genomic DNA and capable of targeting a large number of loci in a single reaction, "the method will facilitate the use of long-read sequencing in research and in the clinic," the scientists write.

The draft genome of the hornwort Anthoceros angustus is published by Chinese Academy of Sciences researchers in Nature Plants this week. Among the findings in the genome are a lack of evidence for whole-genome duplication, as well as low genetic redundancy for networks underlying the plant's simple body plan. The team also finds that hornworts have retained the essential components of the CO2-concentrating mechanism found in green algae in response to the atmospheric changes in terrestrial environments, and a gene inventory expanded primarily through tandem duplication and horizontal gene transfer.