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Genome Research Papers on Chromatin Accessibility, Malaria Mosquitoes, Bacterial Pan-Genome Method

Researchers from Massachusetts Institute of Technology, Brigham and Women's Hospital, and the Netherlands' Hubrecht Institute present a multiplexed reporter assay aimed at profiling chromatin accessibility with the help of a synthetic oligonucleotide library and restricted enzymes for selectively slicing certain sequences. The team used this method — known as the "multiplexed integrated accessibility assay" (MIAA) — to take a look at the consequences of transcription factor motifs in embryonic stem cells and stem cell-derived endoderm cells from mice. "[W]e aim to develop an assay that takes advantage of adenine methyltransferase and restriction enzyme digestion for measuring the local DNA accessibility of genomically integrated, large-scale reporter libraries, and probe the regulatory sequence determinants driving differential chromatin accessibility between stem cells and definitive endoderm," the authors write.

Members of the Anopheles gambiae 1000 Genomes Consortium tally genomic variation in more than 1,100 mosquitoes collected in 13 African countries, focusing on Anopheles gambiae and A. coluzzii species that can transmit malaria parasites. Using new genome sequences for 377 mosquitoes caught in The Gambia, Côte d'Ivoire, Ghana, Mayotte island, and Bioko island, as well as sequences from hundreds more mosquitoes grown in the lab or caught in the wild and sequenced during an earlier stage of the project, the team identified SNPs, copy-number variants, haplotypes, sites under selection, potential sources of insecticide resistance, and more in the mosquito genomes. "This data resource provides a foundation for developing new operational systems for molecular surveillance and for accelerating research and development of new vector control tools," the researchers write, adding that the work "provides a unique resource for the study of population genomics and evolutionary biology in eukaryotic species with high levels of genetic diversity under strong anthropogenic evolutionary pressures."

University of Warwick researchers describe a pipeline for putting together pan-genomes based on large sets of bacterial genome sequences. The team's PEPPAN algorithm relies on five sets of steps for uncovering gene sequences, candidate genes, and gene ortholog clusters before outputting pan-genome information and making it possible to analyze the core and accessory sequences included in these pan-genomes. Along with comparisons to available pan-genome approaches, the authors applied PEPPAN to more than 3,000 genome sequences from dozens of Streptococcus species, tracking down some tens of thousands of genes, while getting a look at gene and allelic "trees" present in accessory genes. "[T]he test case of Streptococcus illustrates the power of PEPPAN," they write, "which can now be used for defining pan-genomes of other diverse genera."