Genomics articles within Nature Communications

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  • Perspective
    | Open Access

    Indigenous peoples are still underrepresented in genetic research. Here, the authors propose an ethical framework consisting of six major principles that encourages researchers and Indigenous communities to build strong and equal partnerships to increase trust, engagement and diversity in genomic studies.

    • Katrina G. Claw
    • , Matthew Z. Anderson
    •  & Joseph M. Yracheta

  • Article
    | Open Access

    Single-cell RNA-barcoding and sequencing is an efficient, genome-wide method to characterize cellular identities. Here the authors systematically evaluate the protocol and develop molecular crowding SCRB-seq with improved sensitivity and cost-efficiency.

    • Johannes W. Bagnoli
    • , Christoph Ziegenhain
    •  & Wolfgang Enard

  • Article
    | Open Access

    While ChIP-exo is low noise and highly informative regarding genome-wide binding proteins, libraries are difficult to construct. Here the authors present a simplified ChIP-exo method for high-resolution detection of interactions.

    • Matthew J. Rossi
    • , William K. M. Lai
    •  & B. Franklin Pugh

  • Article
    | Open Access

    Large-scale patterns of genomic repeat element evolution have been studied mainly in birds and mammals. Here, the authors analyze the genomes of over 60 squamate reptiles and show high variation in repeat elements compared to mammals and birds, and particularly high microsatellite seeding in snakes.

    • Giulia I. M. Pasquesi
    • , Richard H. Adams
    •  & Todd A. Castoe

  • Article
    | Open Access

    Ducks, one of the most common domestic fowls, originated from mallards. Here, the authors perform whole-genome sequencing of mallards, indigenous-breed ducks, and Pekin ducks, as well as 1026 ducks from a population generated by wild × domestic crosses to identify selection signals and map variants associated with body size and plumage color.

    • Zhengkui Zhou
    • , Ming Li
    •  & Yu Jiang

  • Article
    | Open Access

    As melanoma progresses, it evolves. Here, in advanced melanoma the authors study genomic evolution, highlighting trunk mutations dominated by the ultraviolet damage signature, common late truncal whole-genome duplication events, as well as selective copy number gain of mutant BRAF.

    • E. Birkeland
    • , S. Zhang
    •  & P. E. Lønning

  • Article
    | Open Access

    The 16p11.2 deletion leads to a range of neurodevelopmental phenotypes, but to date, sequencing studies have not been able to pinpoint individual genes that are causative for the disease on their own. Here, using Drosophila homologs of 14 16p11.2 genes, the authors take a combinatorial approach to show that gene interactions contribute to a neurological phenotype.

    • Janani Iyer
    • , Mayanglambam Dhruba Singh
    •  & Santhosh Girirajan

  • Article
    | Open Access

    Parasitic lifestyles leave unique genomic footprints. Here, the authors describe the genome sequence of a parasitic plant, Cuscuta campestris, and find that gene losses and host gene acquisitions reflect the independence from photosynthesis and the ability to retain and express chunks of foreign genomic DNA.

    • Alexander Vogel
    • , Rainer Schwacke
    •  & Kirsten Krause

  • Article
    | Open Access

    Urinary tract infections are one of the most common infections in humans. Here, the authors use urinary cell-free DNA (cfDNA) to comprehensively monitor host and pathogen dynamics in bacterial and viral urinary tract infections, and show that it is a versatile analyte for monitoring urinary tract infections.

    • Philip Burnham
    • , Darshana Dadhania
    •  & Iwijn De Vlaminck

  • Article
    | Open Access

    It is unclear if experimental evolution is a good model for natural processes. Here, Clerissi et al. find parallels between the evolution of symbiosis in rhizobia after horizontal transfer of a plasmid over 10 million years ago and experimentally evolved symbionts.

    • Camille Clerissi
    • , Marie Touchon
    •  & Eduardo P. C. Rocha

  • Article
    | Open Access

    Giant viruses are visible by light microscopy and have unusually long genomes. Here, the authors report three new members of the Pandoraviridae family and investigate their evolution and diversity.

    • Matthieu Legendre
    • , Elisabeth Fabre
    •  & Jean-Michel Claverie

  • Article
    | Open Access

    A proportion of neurodevelopmental disorder and congenital anomaly cases remain without a genetic diagnosis. Here, the authors study aberrations of DNA methylation in such cases and find that epivariations might provide an explanation for some of these undiagnosed patients.

    • Mafalda Barbosa
    • , Ricky S. Joshi
    •  & Andrew J. Sharp

  • Article
    | Open Access

    The use of synthetic chromosomes and the recombinase-based SCRaMbLE system could enable rapid strain evolution through massive chromosome rearrangements. Here the authors present ReSCuES, which uses auxotrophic markers to rapidly identify yeast with rearrangements for strain engineering.

    • Zhouqing Luo
    • , Lihui Wang
    •  & Junbiao Dai

  • Article
    | Open Access

    SCRaMbLE has been used to rearrange synthetic chromosomes that have been introduced into host yeast. Here the authors produce semi-synthetic heterozygous diploid strains for rapid selection of phenotypes and map the rearrangements underlying selected phenotypes such as thermoresistance and caffeine resistance.

    • Michael J. Shen
    • , Yi Wu
    •  & Jef D. Boeke

  • Article
    | Open Access

    The SCRaMbLE system integrated into Sc2.0’s synthetic yeast chromosome project allows rapid strain evolution. Here the authors use a genetic logic gate to control induction of recombination in a haploid and diploid yeast carrying synthetic chromosomes.

    • Bin Jia
    • , Yi Wu
    •  & Ying-Jin Yuan

  • Article
    | Open Access

    Ancient diapsids diverged into the lineages leading to turtles and birds over 250 million years ago. Here, the authors use genomic and molecular cytogenetic analyses of modern species to infer the genome structure of the diapsid common ancestor (DCA) and the changes occurring along the lineage to birds through theropod dinosaurs.

    • Rebecca E. O’Connor
    • , Michael N. Romanov
    •  & Darren K. Griffin

  • Article
    | Open Access

    Animals, the Metazoa, co-opted numerous unicellular genes in their transition to multicellularity. Here, the authors use phylogenomic analyses to infer the genome composition of the ancestor of extant animals and show there was also a burst of novel gene groups associated with this transition.

    • Jordi Paps
    •  & Peter W. H. Holland

  • Article
    | Open Access

    Mating-type switching enables self-compatible reproduction in fungi, but switching ability is variable even within species. Here, the authors find de novo evolution of switching genotypes in experimentally evolved fission yeast populations and show a trade-off between mating success and growth.

    • Bart P. S. Nieuwenhuis
    • , Sergio Tusso
    •  & Simone Immler

  • Article
    | Open Access

    The American cockroach (Periplaneta americana) is an hemimetabolous insect with rapid growth, high fecundity, and remarkable tissue-regeneration capability. Here Li et al sequence its 3.38-Gb genome and perform the functional studies, yielding insights into its environmental adaptation and developmental plasticity.

    • Sheng Li
    • , Shiming Zhu
    •  & Shuai Zhan

  • Article
    | Open Access

    Phenotypic plasticity—the ability to express multiple phenotypes from the same genome—is a widespread adaptation to environmental variability. Here, Oostra et al analyze transcriptomes of an African butterfly with distinct seasonal phenotypes, and observe lack of variation for plasticity, limiting potential for evolutionary responses to climate change.

    • Vicencio Oostra
    • , Marjo Saastamoinen
    •  & Christopher W. Wheat

  • Article
    | Open Access

    The population of Madagascar arose from admixture of Austronesian and Bantu genetic backgrounds. Analyzing local ancestry in genomes of 700 Malagasy, Pierron et al. identify signals of recent positive selection for African ancestry in a region on chromosome 1 with implications for physiology and disease risk.

    • Denis Pierron
    • , Margit Heiske
    •  & Thierry Letellier

  • Article
    | Open Access

    RNA levels in post-mortem tissue can differ greatly from those before death. Studying the effect of post-mortem interval on the transcriptome in 36 human tissues, Ferreira et al. find that the response to death is largely tissue-specific and develop a model to predict time since death based on RNA data.

    • Pedro G. Ferreira
    • , Manuel Muñoz-Aguirre
    •  & Roderic Guigó

  • Article
    | Open Access

    The population history of Europe is complex and its very north has not yet been comprehensively studied at a genetic level. Here, Mittnik et al. report genome-wide data from 38 ancient individuals from the Eastern Baltic, Russia and Scandinavia to analyse gene flow throughout the Mesolithic and Bronze Age.

    • Alissa Mittnik
    • , Chuan-Chao Wang
    •  & Johannes Krause

  • Article
    | Open Access

    Marine microbial eukaryotes and zooplankton display enormous diversity and largely unexplored physiologies. Here, the authors use metatranscriptomics to analyze four organismal size fractions from open-ocean stations, providing the largest reference collection of eukaryotic transcripts from any single biome.

    • Quentin Carradec
    • , Eric Pelletier
    •  & Patrick Wincker

  • Article
    | Open Access

    The genetic basis of metabolic diseases is incompletely understood. Here, by high-throughput phenotyping of 2,016 knockout mouse strains, Rozman and colleagues identify candidate metabolic genes, many of which are associated with unexplored regulatory gene networks and metabolic traits in human GWAS.

    • Jan Rozman
    • , Birgit Rathkolb
    •  & Martin Hrabe de Angelis

  • Article
    | Open Access

    Spatial localization of genetic information is important for tissue heterogeneity but difficult to capture with current analytical techniques. Here the authors present “Pixelated RT-LAMP”, an approach that uses parallel on-chip reactions to provide the distribution of target sequences directly from tissue.

    • A. Ganguli
    • , A. Ornob
    •  & R. Bashir

  • Article
    | Open Access

    Selaginella lepidophylla is a clubmoss with extreme desiccation tolerance. Here, the authors assemble its highly heterozygotic haplotypes and examine gene expression changes during desiccation, which shed light on the mechanisms for maintaining a small genome size and adaptation to extreme drying.

    • Robert VanBuren
    • , Ching Man Wai
    •  & Todd P. Michael

  • Article
    | Open Access

    The role of differential gene content in the evolution and function of eukaryotic genomes remains poorly explored. Here the authors assemble and annotate the Brachypodium distachyon pan-genome consisting of 54 diverse lines and reveal the differential present genes as a major driver of phenotypic variation.

    • Sean P. Gordon
    • , Bruno Contreras-Moreira
    •  & John P. Vogel

  • Article
    | Open Access

    The evolution of new sex chromosomes potentially generates reproductive isolation. Here, Bracewell et al. combine crossing experiments with population and functional genomics to characterize neo-sex chromosome evolution and incipient speciation in the mountain pine beetle, Dendroctonus ponderosae.

    • Ryan R. Bracewell
    • , Barbara J. Bentz
    •  & Jeffrey M. Good

  • Article
    | Open Access

    The canonical scenario of sex chromosome evolution is through the differentiation of ancestral pairs of autosomes. Here, Fraïsse and colleagues use a comparative genomic analysis that shows the deep conservation of the Z chromosome in Lepidoptera and supports a non-canonical origin of the W chromosome.

    • Christelle Fraïsse
    • , Marion A. L. Picard
    •  & Beatriz Vicoso

  • Article
    | Open Access

    The globally-distributed Ranidae (true frogs) are the largest frog family. Here, Hammond et al. present a draft genome of the North American bullfrog, Rana (Lithobates) catesbeiana, as a foundation for future understanding of true frog genetics as amphibian species face difficult environmental challenges.

    • S. Austin Hammond
    • , René L. Warren
    •  & Inanc Birol

  • Article
    | Open Access

    Expression quantitative trait loci (eQTL) are widely studied, yet the mechanisms by which they exert their effects are largely unknown. Here, performing CAGE-seq on 154 lymphoblastoid cell lines, the authors map regulatory variants associated with promoter usage (puQTLs) and enhancer activity (eaQTLs).

    • Marco Garieri
    • , Olivier Delaneau
    •  & Alexandre Fort

  • Article
    | Open Access

    The detection of structural variants can be difficult with short-read sequencing technology, especially when variants are highly complex. Here, the authors use a MinION nanopore sequencer to analyse two patient genomes and develop NanoSV to map known and novel structural variants in long read data.

    • Mircea Cretu Stancu
    • , Markus J. van Roosmalen
    •  & Wigard P. Kloosterman

  • Article
    | Open Access

    Haplotype information is important in investigating many biological phenomena. Here, Porubsky et al. combine Strand-seq with long-read or linked-read sequencing to obtain complete and genome-wide haplotypes of a single individual genome at manageable costs.

    • David Porubsky
    • , Shilpa Garg
    •  & Tobias Marschall

  • Article
    | Open Access

    Several models have been proposed to explain the emergence of sex chromosomes. Here, through comparative genomics and mutant analysis, Harkess et al. show that linked but separate genes on the Y chromosome are responsible for sex determination in Asparagus, supporting a two-gene model for sex chromosome evolution.

    • Alex Harkess
    • , Jinsong Zhou
    •  & Guangyu Chen

  • Article
    | Open Access

    A map of the activities of all genomic regulatory elements across cell types and conditions would be a tremendous resource. The computational method introduced here predicts genome-wide accessible sites from gene expression data and allows the authors to build a database of regulatory element activities using publicly available transcriptome data.

    • Weiqiang Zhou
    • , Ben Sherwood
    •  & Hongkai Ji

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