Article
|
Open Access
Featured
-
-
Article
| Open AccessWhole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum
Sorghum is a drought-resistant food and feed cereal crop used by over half a billion of the world’s poorest people. Here the authors present high-coverage resequencing genome data of 44 sorghum lines of varying geographic and taxonomic origin, which include a number of sorghum wild relatives.
- Emma S. Mace
- , Shuaishuai Tai
- & Jun Wang
-
Article
| Open AccessExtraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
Turnover of sediment organic matter contributes to global carbon cycling, yet the microorganisms involved are largely unknown. Castelleet al.reveal that an aquifer sediment core hosts a ‘zoo’ of organisms, including representatives of a previously undescribed phylum (Zixibacteria).
- Cindy J. Castelle
- , Laura A. Hug
- & Jillian F. Banfield
-
Article
| Open AccessWall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens
Horizontal gene transfer of mobile genetic elements contributes to bacterial evolution and emergence of new pathogens. Here the authors demonstrate that the highly diverse structure of wall teichoic acid polymers governs horizontal gene transfer among Gram-positive pathogens, even across long phylogenetic distances.
- Volker Winstel
- , Chunguang Liang
- & Guoqing Xia
-
Article
| Open AccessGenome analysis reveals insights into physiology and longevity of the Brandt’s bat Myotis brandtii
Bats account for 20 per cent of all mammals, these are the only mammals with powered flight, and are among the few animals that echolocate. Here, Seim et al. sequence the genome of the long-lived (>40 years) Brandt’s bat, Myotis brandtiiand provide clues to its evolution, longevity and other traits.
- Inge Seim
- , Xiaodong Fang
- & Vadim N. Gladyshev
-
Article
| Open AccessGenome sequence of the date palm Phoenix dactylifera L
The date palm is one of the most economically important plants of the palm family. Here, the authors present a high-quality genome assembly of the date palm Phoenix dactylifera, and reveal insights into the unique sugar metabolism underlying fruit ripening.
- Ibrahim S. Al-Mssallem
- , Songnian Hu
- & Jun Yu
-
Article
| Open AccessGenome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica
Oleispira antarctica is an oil-degrading bacterium found in the cold and deep sea. Here Kube et al. report the genome sequence of O. antarcticaand provide a comprehensive functional genetic and protein structural analysis, revealing insights into how this organism has adapted to its cold environment.
- Michael Kube
- , Tatyana N. Chernikova
- & Peter N. Golyshin
-
Article |
Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota
The appearance of antibiotic resistance has been attributed to the misuse of antibiotics. By analysing the diversity of antibiotic resistance genes present in 162 human gut microbiota samples, the authors find that Chinese individuals harbour a larger pool of resistance genes than Spanish or Danish counterparts.
- Yongfei Hu
- , Xi Yang
- & Baoli Zhu
-
Article |
DNA unmethylome profiling by covalent capture of CpG sites
Chemical modifications of CpG dinucleotides form part of the epigenetic code and various methods for the detection of modified CpG sites exist. Here Kriukiene and colleagues report a complementary method that allows the profiling of unmodified CpG sites within the genome, which they call the 'unmethylome'.
- Edita Kriukienė
- , Viviane Labrie
- & Saulius Klimašauskas
-
Article
| Open AccessReconstructing genome evolution in historic samples of the Irish potato famine pathogen
Phytophthora infestanscaused the potato famine in the nineteenth century. Martinet al. sequence the nuclear genomes of five archival samples of the pathogen and compare these to extant specimens allowing the reconstruction of the evolutionary history of P. infestans.
- Michael D. Martin
- , Enrico Cappellini
- & M. Thomas P. Gilbert
-
Article
| Open AccessGenome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets
Genetic interactions can reveal insights into cellular functions. Here, Lu et al.show that negative genetic interactions in protein complexes can be predicted by systematically exploring the evolutionary history of genes, which may be useful for the identification of novel targets for anti-cancer drugs.
- Xiaowen Lu
- , Philip R. Kensche
- & Richard A. Notebaart
-
Article
| Open AccessEvaluating cell lines as tumour models by comparison of genomic profiles
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 |
Genome of the red alga Porphyridium purpureum
Red algae form one of the most ancient eukaryotic lineages, and have undergone multiple symbioses. Here, Price et al. report the first genome sequence for a mesophilic red alga, and reveal significant differences between these organisms and hyperthermopilic algae.
- Debashish Bhattacharya
- , Dana C. Price
- & Hwan Su Yoon
-
Article
| Open AccessDraft genome sequence of the Tibetan antelope
The endemic Tibetan antelope is adapted to high-altitude environments with low partial pressure of oxygen and high level of ultraviolet radiation. Here Ge et al. report a draft genome of this species and by comparison with other mammals, present possible genetic bases of highland adaptation.
- Ri-Li Ge
- , Qingle Cai
- & Jian Wang
-
Article |
The genomics of selection in dogs and the parallel evolution between dogs and humans
Dogs may have been domesticated much earlier than previously thought, perhaps by initially scavenging with humans. Here Zhang et al. present genetic evidence that genes positively selected during dog domestication show extensive parallelism with human analogues.
- Guo-dong Wang
- , Weiwei Zhai
- & Ya-ping Zhang
-
Article |
G-quadruplex structures are stable and detectable in human genomic DNA
Guanine-rich DNA can form four-stranded structures called G-quadruplexes, which are thought to influence DNA replication, transcription and repair; their stability and prevalence in the genome is in need of further elucidation. Here the authors employ an antibody-based approach to sensitively map G-quadruplexes in the genome.
- Enid Yi Ni Lam
- , Dario Beraldi
- & Shankar Balasubramanian
-
Article
| Open AccessGenomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont
Cyanobacterial symbionts of marine diatoms can localize intracellularly or externally to their host partners. Here Hilton et al. describe the genomes of two diazotroph cyanobacterial symbionts of diatoms and show that the location of the symbiont affects expression of nitrogen assimilation genes.
- Jason A. Hilton
- , Rachel A. Foster
- & Tracy A. Villareal
-
Article
| Open AccessWhole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution
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 AccessGenome of the Chinese tree shrew
The Chinese tree shrew, Tupaia belangeri chinensis, has been proposed as a potential animal model in biomedical research and drug safety testing. This study presents the full genome of the Chinese tree shrew, identifying common features between the tree shrew and primates.
- Yu Fan
- , Zhi-Yong Huang
- & Yong-Gang Yao
-
Article
| Open AccessThe genome of Prunus mume
The Prunus mume was domesticated in China over 3,000 years ago and is an important ornamental plant and fruit. Here Qixiang Zhang et al.obtain the first assembly of its genome with a combination of next-generation sequencing, whole-genome mapping and restriction-site-associated DNA.
- Qixiang Zhang
- , Wenbin Chen
- & Jun Wang
-
Article
| Open AccessGenome sequences of wild and domestic bactrian camels
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 AccessA multi-omic map of the lipid-producing yeast Rhodosporidium toruloides
The ability of oleaginous fungi to produce lipids for biofuels remains untapped, in part due to a lack of genetic information required to engineer industrial strains. Zhuet al. present the genome of R. toruloides, and identify transcriptomic and proteomic changes associated with lipid production.
- Zhiwei Zhu
- , Sufang Zhang
- & Zongbao K. Zhao
-
Article |
An atlas of DNA methylomes in porcine adipose and muscle tissues
Epigenetic and genetic factors have a role in obesity but the role of epigenetics in this disease is unclear. Here, Liet al. investigated global DNA methylation patterns in three breeds of pigs that have different fat contents, providing a resource for the further analysis of differentially methylated gene promoters in obesity.
- Mingzhou Li
- , Honglong Wu
- & Ruiqiang Li
-
Article |
Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution
APOBEC3 is a DNA editing enzyme that is important for antiviral responses. In this study, Carmi and colleagues show that APOBEC3 editing of retrotransposon sequences in mammalian genomes is widespread, with implications for the evolution of retrotransposons.
- Shai Carmi
- , George M. Church
- & Erez Y. Levanon
-
Article
| Open AccessComparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis
The conservation of embryonic development across species is of great interest in evolutionary biology. Here, using transcriptome analysis, the authors show that the pharyngula stage of development—in mid-embryogenesis—is conserved between mice, chickens, frogs and zebrafish.
- Naoki Irie
- & Shigeru Kuratani
-
Article
| Open AccessThe complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis
A comparison of related genomes provides valuable information about how they evolve. Here, the complete sequence of the smallest known nuclear genome from the microsporidiaE. intestinalis is described and compared with its larger sister E. cuniculi, revealing what parts are indispensable in even the most reduced genomes.
- Nicolas Corradi
- , Jean-François Pombert
- & Patrick J. Keeling