DNA sequencing articles within Nature Communications

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  • Article
    | Open Access

    Haplotype information inferred by phasing is useful in genetic and genomic analysis. Here, the authors develop SHAPEIT4, a phasing method that exhibits sub-linear running time, provides accurate haplotypes and enables integration of external phasing information.

    • Olivier Delaneau
    • , Jean-François Zagury
    •  & Emmanouil T. Dermitzakis

  • Article
    | Open Access

    Structural variants may be omitted in sequence analysis despite their importance in genome variation and phenotypic impact. Here the authors present GraphTyper2, which uses pangenome graphs to genotype structural variants using short-reads and can be applied in large-scale sequencing studies.

    • Hannes P. Eggertsson
    • , Snaedis Kristmundsdottir
    •  & Pall Melsted

  • Article
    | Open Access

    Meiotic crossovers (COs) generate genetic variation and ensure proper chromosome segregation. Here, the authors develop a method for identifying COs at kilobase resolution in pooled recombinants using linked-read sequencing data, and apply it to investigate genome-wide CO landscapes of Arabidopsis thaliana.

    • Hequan Sun
    • , Beth A. Rowan
    •  & Korbinian Schneeberger

  • Article
    | Open Access

    Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.

    • Zhenchang Liang
    • , Shengchang Duan
    •  & Yang Dong

  • Article
    | Open Access

    Adenine base editors are an important contribution to the genome editing toolbox. Here the authors present EndoV-seq, an endonuclease-based assay for evaluating genomewide off-target effects of base editing.

    • Puping Liang
    • , Xiaowei Xie
    •  & Zhou Songyang

  • Article
    | Open Access

    Single-cell DNA methylome profiling allows the study of epigenomic heterogeneity in tissues but has been impeded by library quality. Here the authors demonstrate snmC-seq2 which improves mapping, throughput and library complexity.

    • Chongyuan Luo
    • , Angeline Rivkin
    •  & Joseph R. Ecker

  • Article
    | Open Access

    Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.

    • Todd P. Michael
    • , Florian Jupe
    •  & Joseph R. Ecker

  • 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

    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

    Biomphalaria glabrata is a fresh water snail that acts as a host for trematode Schistosoma mansoni that causes intestinal infection in human. This work describes the genome and transcriptome analyses from 12 different tissues of B glabrata, and identify genes for snail behavior and evolution.

    • Coen M. Adema
    • , LaDeana W. Hillier
    •  & Richard K. Wilson

  • Article
    | Open Access

    The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) aims to better understand population genetics of the African diaspora. Here, it uses deeply sequenced whole-genomes to describe the impact of admixture and potential disease burden of deleterious variants.

    • Rasika Ann Mathias
    • , Margaret A. Taub
    •  & Kathleen C. Barnes

  • Article
    | Open Access

    The ability to accurately sequence long DNA molecules is important across biology. Here, Lan et al. report a droplet-based method that barcodes single DNA molecules, allowing the full-length molecules to be sequenced with multi-fold coverage using short-read next-generation sequencing.

    • Freeman Lan
    • , John R. Haliburton
    •  & Adam R. Abate

  • Article
    | Open Access

    DNA N6-methyladenine is prevalent in prokaryotes, and is recently also detected in eukaryotes such as roundworm and fly. Here, Luo et al. report a DpnI-assisted base resolution method that detects 6mA genome-wide with nanograms of input DNA and lower sequencing depth than the previous restriction enzyme-based approach.

    • Guan-Zheng Luo
    • , Fang Wang
    •  & Chuan He

  • Article
    | Open Access

    Read mapping and alignment tools are critical for many applications based on MinION sequencers. Here, the authors present GraphMap, a mapping algorithm designed to analyze nanopore sequencing reads, that progressively refines candidate alignments to handle potentially high error rates to align long reads.

    • Ivan Sović
    • , Mile Šikić
    •  & Niranjan Nagarajan

  • Article
    | Open Access

    Cancer genetics has benefited from the advent of next generation sequencing, yet a comparison of sequencing and analysis techniques is lacking. Here, the authors sequence a normal-tumour pair and perform data analysis at multiple institutes and highlight some of the pitfalls associated with the different methods.

    • Tyler S. Alioto
    • , Ivo Buchhalter
    •  & Ivo G. Gut

  • Article
    | Open Access

    Osteosarcomas are a heterogenous group of tumours and little is known about how these tumours evolve. Here, Kovac et al. use exome sequencing and discover that although no driver gene explains the majority of these tumours, they are characterized by specific mutation signatures and genomic instability typical of BRCA1/2-deficient tumours.

    • Michal Kovac
    • , Claudia Blattmann
    •  & Daniel Baumhoer

  • Article
    | Open Access

    The Tohoku Medical Megabank Organization establishes a biobank with detailed patient health care and genome information. Here the authors analyse whole-genome sequences of 1,070 Japanese individuals, allowing them to catalogue 21 million single-nucleotide variants including 12 million novel ones.

    • Masao Nagasaki
    • , Jun Yasuda
    •  & Masayuki Yamamoto

  • Article
    | Open Access

    Bacterial DNA methylation is involved in many processes, from host defense to antibiotic resistance, however current methods for examining methylated genomes lack single-cell resolution. Here Beaulaurier et al. present Single Molecule Modification Analysis of Long Reads, a new tool for de novodetection of epigenetic heterogeneity.

    • John Beaulaurier
    • , Xue-Song Zhang
    •  & Gang Fang

  • Article
    | Open Access

    Anaplastic oligodendrogliomas are rare and incurable primary brain tumours with few treatment options. Here Labrecheet al. perform whole-exome sequencing and identify recurring mutations in transcription factor TCF12, which are associated with aggressive tumours.

    • Karim Labreche
    • , Iva Simeonova
    •  & Michel Wager

  • Article
    | Open Access

    DNA phasing information — the determination of which specific sequences belong to the same DNA molecule—is not easily obtained from sequencing applications that rely on short reads. Here the authors develop a phasing method based on massively parallel barcoding of single DNA molecules.

    • Erik Borgström
    • , David Redin
    •  & Afshin Ahmadian

  • Article |

    Artifacts caused by whole-genome amplification bias are a recurrent challenge in single-cell sequencing analysis. Here, the authors develop statistical models and demonstrate an efficient strategy for controlling amplification errors by a joint analysis of single cell genomes.

    • Cheng-Zhong Zhang
    • , Viktor A. Adalsteinsson
    •  & J. Christopher Love

  • Article
    | Open Access

    Pulmonary hypertension and congestive right heart failure afflict some cattle living at high altitude in an autosomal dominant pattern, yet no responsible genes have been identified. Here Newman et al.use whole-exome sequencing to identify variants in the hypoxia inducible factor gene, EPAS1.

    • John H. Newman
    • , Timothy N. Holt
    •  & Rizwan Hamid

  • Article |

    Characterizing mammalian gene expression regulation by enhancer elements is complicated by the size and complexity of the genome. Here Vanhille et al.demonstrate CapStarr-Seq, a novel high-throughput method for assessing potential enhancers and deciphering the mechanisms regulating transcription

    • Laurent Vanhille
    • , Aurélien Griffon
    •  & Salvatore Spicuglia

  • Article
    | Open Access

    Diagnosis of pancreatic ductal adenocarcinoma (PDA) has poor long-term survival rates with limited therapy options. Here Witkiewicz et al.use microdissection and whole-exome sequencing to identify novel recurrent PDA mutations, highlighting the genetic diversity of this aggressive cancer.

    • Agnieszka K. Witkiewicz
    • , Elizabeth A. McMillan
    •  & Erik S. Knudsen

  • Article |

    Triple-negative breast cancers (TNBCs) are a heterogeneous group of cancers with varying prognoses. Here, the authors carry out whole-genome methylation capture sequencing from TNBC samples and matched normal samples, and identify differentially methylated regions that define a potentially novel TNBC signature.

    • Clare Stirzaker
    • , Elena Zotenko
    •  & Susan J. Clark

  • Article
    | Open Access

    Next-generation sequencing technologies vary in performance, which is often measured by metrics such as sequencing speed, accuracy and read length. Here, the authors present a new sequencing by synthesis method that monitors polymerase binding to DNA, and suggest that this method has the potential to generate longer and faster reads.

    • Michael John Robert Previte
    • , Chunhong Zhou
    •  & Molly Min He

  • Article
    | Open Access

    Type 2 diabetes (T2D) is a highly heterogeneous disease with a strong genetic component. Here the authors examine genome-wide methylation patterns in T2D-discordant, T2D-concordant and healthy concordant monozygotic twin pairs, and identify DNA methylation signals that may represent new biomarkers or drug targets for T2D.

    • Wei Yuan
    • , Yudong Xia
    •  & Tim D. Spector

  • Article
    | Open Access

    King Richard III was a controversial English King whose remains are presumably deposited in Grey Friars in Leicester. Here the authors sequence the mitochondrial genome and Y-chromosome DNA of the skeletal remains and living relatives of Richard III and confirm that the remains belong to King Richard III.

    • Turi E. King
    • , Gloria Gonzalez Fortes
    •  & Kevin Schürer

  • Article
    | Open Access

    Plasmodium falciparum, known to cause malaria in humans, evolved from parasites of African Great Apes. Here, the authors compare the genome of the human parasite, P. falciparum, with those of two related chimpanzee parasites, P. reichenowi and P. gaboni, and provide insight into the genetic basis of P. falciparumadaptation to human hosts.

    • Thomas D. Otto
    • , Julian C. Rayner
    •  & Matthew Berriman

  • Article |

    Although psoriasis is a chronic disorder affecting approximately 2% of the population, little is known about the underlying genetic architecture. Here, the authors carry out exome sequencing in a large Han Chinese cohort of psoriasis patients and healthy controls, and identify three new genes that may increase risk of developing the disease.

    • Yujun Sheng
    • , Xin Jin
    •  & Xuejun Zhang

  • Article |

    Semiconductor-based, non-optical DNA sequencing technologies such as Ion Torrent sequencing offer speed and cost advantages compared with alternative techniques. Cheng et al. demonstrate a protocol allowing the use of Ion Torrent technology to sequence DNA from chromatin immunoprecipitation experiments.

    • Christine S. Cheng
    • , Kunal Rai
    •  & Ido Amit

  • Article
    | Open Access

    The wild rice species can be used as germplasm resources for this crop’s genetic improvement. Here Chen and colleagues report the de novo sequencing of the O. brachyanthagenome, and identify the origin of genome size variation, the role of gene movement and its implications on heterochromatin evolution in the rice genome.

    • Jinfeng Chen
    • , Quanfei Huang
    •  & Mingsheng Chen

  • 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

  • Article
    | Open Access

    Ganoderma lucidumis a macrofungus in traditional Chinese medicine known to produce different bioactive compounds. In this study, the genome ofG. lucidumis sequenced, making this organism a potential model system for future studies of secondary metabolic pathways and their regulation in medicinal fungi.

    • Shilin Chen
    • , Jiang Xu
    •  & Chao Sun

  • Article |

    Modern female horses are genetically diverse but male horses are relatively homogenous. Lippoldet al. sequence the Y chromosome of nine ancient horses and detect diversity in the ancestral paternal lineage, demonstrating ancient Y-chromosomal DNA sequencing can provide insights into evolution.

    • Sebastian Lippold
    • , Michael Knapp
    •  & Michael Hofreiter

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