Comparative genomics articles within Nature Communications

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  • 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 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

    Horizontal gene transfer (HGT) is an important mechanism for genome evolution and adaptation in bacteria. Here, Oliveira and colleagues find HGT hotspots comprising  ~ 1% of the chromosomal regions in 80 bacterial species.

    • Pedro H. Oliveira
    • , Marie Touchon
    •  & Eduardo P. C. Rocha

  • Article
    | Open Access

    High-quality reference genomes facilitate analysis of genome structure and variation. Here Duet al. create a near-complete assembly of the indicarice genome by combining single molecule sequencing with mapping data and fosmid sequences and identify genetic variants by comparison with other rice genomes.

    • Huilong Du
    • , Ying Yu
    •  & Chengzhi Liang

  • Article
    | Open Access

    Batrachochytrium dendrobatidis and B. salamandrivoransare both important pathogens of amphibians, but they differ in their host ranges, infection strategies, and host immune responses. Here, Farrer and colleagues compare their genomes and transcriptomes to identify the genetic basis of these differences.

    • Rhys A. Farrer
    • , An Martel
    •  & Christina A. Cuomo

  • Article
    | Open Access

    The fungal Ascomycota provide a model phylum to investigate the evolution of complex multicellularity. Here, the authors combine genome sequencing with comparative and functional genomics to identify diverse endomembrane related machineries associated with the gain and loss of fungal complexity.

    • Tu Anh Nguyen
    • , Ousmane H. Cissé
    •  & Gregory Jedd

  • Article
    | Open Access

    Shotgun DNA sequencing experiments for microbial genomic analysis are often impractical due to minimum sample input requirements. Here the authors develop a microfluidic sample preparation platform that reduces sample input requirements 100-fold and enables high throughput sequencing from low numbers of cells.

    • Soohong Kim
    • , Joachim De Jonghe
    •  & Paul C. Blainey

  • Article
    | Open Access

    Brassica oleracea is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing B. oleraceareference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits

    • Agnieszka A. Golicz
    • , Philipp E. Bayer
    •  & David Edwards

  • Article
    | Open Access

    Mutualisms in which ants protect plants in exchange for food and shelter have arisen independently multiple times. Here, Rubin and Moreau sequence the genomes of three mutualistic ant species and four of their non-mutualistic relatives and show that the transition to mutualism is associated with elevated evolutionary rates across the genome

    • Benjamin E. R. Rubin
    •  & Corrie S. Moreau

  • Article
    | Open Access

    Nitrogen fixation in oceans is facilitated by associations between marine phytoplankton and cyanobacteria such as UCYN-A. Here, Cornejo-Castillo et al. show that UCYN-A diversified in the late Cretaceous under strong purifying selection to become lineage-specific symbiont partners with different prymnesiophytes.

    • Francisco M. Cornejo-Castillo
    • , Ana M. Cabello
    •  & Silvia G. Acinas

  • Article
    | Open Access

    Toxoplasma gondii is a parasite that causes zoonotic infections in humans. Here, the authors identify tandem amplification and diversification of secretory pathogenesis determinants in the T. gondiigenome and show that clade-specific inheritance of conserved haploblocks enriched for these determinants shapes population structure.

    • Hernan Lorenzi
    • , Asis Khan
    •  & L. David Sibley

  • Article |

    Comparative genomics can provide valuable insights on adaptations to hostile environments. Here, the authors sequence the genomes and transcriptomes of the Bactrian camel, dromedary and alpaca, to reveal the demographic history of the group as well as metabolic adaptations to the desert environment.

    • Huiguang Wu
    • , Xuanmin Guang
    •  & Jun Wang

  • Article
    | Open Access

    The African chironomid midge, Polypedilum vanderplanki, is able to withstand extreme desiccation. Here the authors sequence the genomes of a desiccation-tolerant and desiccation-sensitive species of chironomid midge and pinpoint genes that may have a role in conferring resistance to desiccation.

    • Oleg Gusev
    • , Yoshitaka Suetsugu
    •  & Takahiro Kikawada

  • Article
    | Open Access

    Rice false smut, caused by the pathogenic ascomycete fungus Ustilaginoidea virens (Cooke) Takah, has a significant economic impact on crop production. Here, Zhang et al. report the draft genome sequence of U. virensand provide insight into the evolution of genes involved in pathogenicity and adaptation to a biotrophic and floret-infecting lifestyle.

    • Yong Zhang
    • , Kang Zhang
    •  & Wenxian Sun

  • Article
    | Open Access

    Common tobacco (Nicotiana tabacum) is a widely cultivated and economically important non-food crop. Here, the authors report the draft genome sequences for three of the most common tobacco varieties and provide insights into the evolution of tobacco through a comparative analysis with closely related species.

    • Nicolas Sierro
    • , James N.D. Battey
    •  & Nikolai V. Ivanov

  • Article
    | Open Access

    Tigers are an endangered species and therefore understanding their genetic architecture could aid conservation efforts. Here, the authors report the first genome sequence of the Amur tiger and, through close species comparative genomic analysis, provide insight into the genome organization, evolutionary divergence and diversity of big cats.

    • Yun Sung Cho
    • , Li Hu
    •  & Jong Bhak

  • Article
    | Open Access

    Cell lines are widely used in cancer research to study tumour biology. Here Domcke et al.compare genomic data from ovarian cancer cell lines with those from clinical ovarian tumour samples and identify cell lines that most closely resemble the genomic features of high-grade serous ovarian cancer.

    • Silvia Domcke
    • , Rileen Sinha
    •  & Nikolaus Schultz

  • Article
    | Open Access

    Camels are essential means of transport in deserts, but we know little about the biology of these extraordinary mammals. This study reports the genome sequences of the wild and domestic bactrian camel, offering a glimpse into the camels’ genetic adaptation to harsh environments.

    • Jirimutu
    • , Zhen Wang
    •  & He Meng

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