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Nature Papers on Bread Wheat Genome Assembly, Population Genomic Analysis of E. Coli, M6A Transcriptome Mapping

A chromosome-scale genome assembly of South African bread wheat (Triticum aestivum) is reported in Nature Genetics this week. A team led by scientists from the King Abdullah University of Science and Technology generated the assembly of the T. aestivum cultivar Kariega — which is an order of magnitude more contiguous than previous wheat assemblies — using a combination of high-fidelity long reads, optical mapping, and chromosome conformation capture. The assembly, they write, was completed in a short period of time and at a fraction of the cost of previous chromosome-scale wheat assemblies and did not require "the time-consuming, laborious complexity reduction required with previous genomics-based gene cloning methods in wheat." It also revealed a gene that contributes to resistance to a key bread wheat pathogen and is allelic to a gene that provides resistance to a different pathogen.

A population genomic analysis of Escherichia coli in livestock-keeping households in Kenya is presented in Nature Microbiology this week, highlighting the need for a surveillance framework to identify the emergence of zoonotic pathogens. In the study — part of the Epidemiology, Ecology, and Socio-Economics of Disease Emergence in Nairobi, or UrbanZoo, project — a team led by investigators from the University of Edinburgh performed whole-genome sequencing of 1,338 E. coli isolates obtained from humans, livestock, and peri-domestic wildlife in 99 households in Nairobi. They find that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type and uncover evidence for inter-household and inter-host sharing and between humans and animals. "These findings indicate that household bacterial distribution is predominantly, although not exclusively, driven by dispersal limitation, whereas within the household, the host niche is the strongest driver for bacterial sharing (and their genetic pools) distribution," the scientists write. They also find that the similarities in the resistome of the isolates did not match the patterns of shared genomes, presumably reflecting common antibiotic usage practices, particularly in poultry. The study, the researchers conclude, underscores the need to undertake surveillance for emerging pathogens at the appropriate scale — in this case, households — and to "account for patterns of interconnectivity where epidemiological links might be created by livestock, wildlife, or humans themselves."

A new method for the whole-transcriptome mapping of N6-methyladenosine (m6A) at single-nucleotide resolution is published in this week's Nature Biotechnology. While the biological importance of m6A modifications are well-established, the inability to map individual m6A-modified sites in whole transcriptomes limits research. To address this, University of Chicago researchers developed m6A-selective allyl chemical labeling and sequencing, or m6A-SAC-seq, which maps m6A sites in the entire transcriptome at single-base resolution, requiring only around 30 nanograms of input RNA. They use the approach to map m6A modification stoichiometries in RNA from cell lines and during in vitro monocytopoiesis from human hematopoietic stem and progenitor cells, identifying numerous cell-state-specific m6A sites whose methylation status was highly dynamic during cell differentiation. "We think m6A-SAC-seq will serve as a gold standard that overcomes the current technological bottleneck for quantitative m6A sequencing and enables new biological discoveries," the scientists write.

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