Article
Parasitology
JunHua Tian, Xin Hou, MiHong Ge, HongBin Xu, Bin Yu, Jing Liu, RenFu Shao, Edward C. Holmes, ChaoLiang Lei, Mang Shi
Summary: This study used metagenomic sequencing to analyze the genetic diversity of ticks in China. It discovered new mitochondrial genome sequences and cryptic species, as well as identified various pathogenic bacteria and revealed the long-term evolutionary relationship between ticks and their associated bacteria.
PARASITES & VECTORS
(2022)
Letter
Environmental Sciences
Lu Miao, Tang Guang Peng, Bai Xiao Song, Qin Xin Cheng, Wang Wen, Guo Wen Ping, Li Kun
Summary: The study investigated the epidemiology and genetic diversity of bacteria and protozoa carried by ticks in Chengmai county of Hainan province, China. Results revealed a wide diversity of bacteria and protozoa in ticks collected from dogs, cattle, and goats, emphasizing the importance of understanding tick-borne pathogen infections in animals and humans in the local area.
BIOMEDICAL AND ENVIRONMENTAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Sishuo Wang, Haiwei Luo
Summary: The study focuses on elucidating the timescale of Alphaproteobacteria evolution using eukaryotic fossils and suggests that early Rickettsiales lineages had previously established interactions with unicellular eukaryotes. The use of mitochondria-based approach is shown to provide more robustness to uncertainties in calibrations compared to the traditional strategy using cyanobacterial fossils. Further implications include the potential of dating the bacterial tree of life based on endosymbiosis events and the need to revisit previous applications using divergence times of modern hosts of symbiotic bacteria for dating bacterial evolution.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Hongru Su, Eri Onoda, Hitoshi Tai, Hiromi Fujita, Shigetoshi Sakabe, Kentaro Azuma, Shigehiro Akachi, Saori Oishi, Fuyuki Abe, Shuji Ando, Norio Ohashi
Summary: This study conducted a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan, discovering potentially new Ehrlichia species through PCR screening and gene sequencing. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to be variable.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Mengyue Guo, Xiaohui Pang, Yanqin Xu, Wenjun Jiang, Baosheng Liao, Jingsheng Yu, Jiang Xu, Jingyuan Song, Shilin Chen
Summary: This study systematically investigated the phylogeny and evolution of Epimedium using plastid genome data. The findings provide new insights into the relationships and evolution of Epimedium species and contribute to better understanding the classification of this genus.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Immunology
Miao Lu, Yuqi Ji, Hongqing Zhao, Wen Wang, Junhua Tian, Chengyu Duan, Xincheng Qin, Yawen Guo, Gaosong Chen, Fuyu Lei, Chao Meng, Kun Li
Summary: Multiple Rickettsiales species, including some potential human pathogens, have been identified in ticks collected from different locations in Sichuan Province, China. The study reveals the remarkable biodiversity of Rickettsiales in the area and highlights the potential exposure risk to local people.
MICROBIAL PATHOGENESIS
(2023)
Article
Biology
Ahmed J. Saadi, Julian Bibermair, Kevin M. Kocot, Nickellaus G. Roberts, Masato Hirose, Andrew Calcino, Christian Baranyi, Ratcha Chaichana, Timothy S. Wood, Thomas Schwaha
Summary: This study presents the first phylogenomic analysis of the Phylactolaemata class, resolving the interrelationships and estimating divergence time using transcriptomic data and dense taxon sampling. The results show the sister relationship of Stephanellidae and the confirmation of Lophopodidae as the second offshoot within the phylactolaemate tree. The study also highlights the likelihood of cryptic speciation in some species. Divergence time estimates suggest the appearance of Phylactolaemata in the Ediacaran and divergence starting in the Silurian.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Xiaojing Jin, Jiasheng Liao, Qingqing Chen, Junfei Ding, Hongwei Chang, Yong Lyu, Liang Yu, Bohai Wen, Yong Sun, Tian Qin
Summary: In this study, 880 ticks collected from Jinzhai County, Lu'an City, Anhui Province, China in 2021-2022 were examined, revealing extensive diversity of Rickettsiales bacteria. Thirteen Rickettsiales species belonging to three genera were detected, including potential pathogens that may cause unrecognized diseases.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Junyou Wang, John R. Wible, Bin Guo, Sarah L. Shelley, Han Hu, Shundong Bi
Summary: This study reports a well-preserved skull and postcranium of the Middle Jurassic epoch (160 million years ago) haramiyidan Vilevolodon diplomylos, showing intact auditory ossicles. Comparing this fossil with other Mesozoic and extant mammals, the overlapping incudomallear articulation found in various groups of mammals is proposed to have evolved during the transition from dual to single function for the ossicles.
Article
Multidisciplinary Sciences
Kyle D. Brumfield, Michael J. Raupp, Diler Haji, Chris Simon, Joerg Graf, John R. Cooley, Susan T. Janton, Russell C. Meister, Anwar Huq, Rita R. Colwell, Nur A. Hasan
Summary: Periodical cicadas have coevolved with their bacterial symbionts, but little is known about the composition of gut microbial symbionts and their differences among different broods. This study used sequencing to analyze the gut bacterial community of three periodical broods and found similarities in the microbiomes of nymphs from different broods. The study also identified a core microbiome and differences in microbial composition between nymphs and adults. The findings provide valuable insights into the gut microbiome of periodical cicadas.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Xiaodong Xu, Xuexiu Li, Dong Wang
Summary: A robust backbone phylogeny is fundamental for developing a stable classification and is instructive for further research. However, it was still not available for Corydalis DC., a taxonomically notoriously difficult genus. In this study, we constructed backbone phylogeny and estimated the divergence of Corydalis based on plastome data. Our analyses recovered main clades and provided support for the majority of lineages within Corydalis. We also found unusual plastome structural rearrangements, which supported our phylogeny and revealed the unreliability of some diagnostic characters in Corydalis.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Eckart Stolle, Rodrigo Pracana, Federico Lopez-Osorio, Marian K. Priebe, Gabriel Luis Hernandez, Claudia Castillo-Carrillo, Maria Cristina Arias, Carolina Ivon Paris, Martin Bollazzi, Anurag Priyam, Yannick Wurm
Summary: The study investigates the role of supergene regions in Solenopsis fire ants, which determine whether colonies have multiple queens or not. By analyzing genomes, the researchers find that the supergene variant responsible for multiple-queen colonies evolved in one species and spread to other species through introgressive hybridization.
NATURE COMMUNICATIONS
(2022)
Article
Physiology
Sergio Diez-Hermano, Maria D. Ganfornina, Arne Skerra, Gabriel Gutierrez, Diego Sanchez
Summary: This study proposed a novel phylogenetic tree topology for chordate Lipocalins, revealing the evolutionary history of Lipocalins in fish and mammals, and discussing the functional impact of early diverging Lipocalins.
FRONTIERS IN PHYSIOLOGY
(2021)
Review
Immunology
Gertraud Orend, Richard P. Tucker
Summary: Tenascin-C plays important roles in immunity, interacting with Toll-like receptor 4, integrin alpha 9 beta 1, and chemokines. While tenascins predate the appearance of adaptive immunity, the first tenascin-C appears to have evolved in early chordate lineages. Adaptive immunity evolved independently in jawless and jawed vertebrates, with the former using variable lymphocyte receptors and the latter using immunoglobulins.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Daoyuan Yu, Louis Deharveng, Marko Lukic, Yiming Wei, Feng Hu, Manqiang Liu
Summary: Phylogenetic reconstruction of Tomocerinae based on a multi-loci molecular dataset reveals the subfamily originated in the Early Cretaceous and underwent multiple radiation events in the Cretaceous and Eocene. Evolutionary patterns of functional traits suggest multiple ecological divergences during Tomocerinae diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Editorial Material
Biochemistry & Molecular Biology
Mary E. Petrone, Edward C. Holmes, Erin Harvey
Summary: To mitigate the emergence of new pathogenic viruses, public health strategies should conduct long-term surveillance of ecosystems experiencing changes in biodiversity using metagenomic techniques to identify generalist viruses.
Article
Microbiology
Nannan Li, Cixiu Li, Tao Hu, Juan Li, Hong Zhou, Jingkai Ji, Jiangli Wu, Weipeng Kang, Edward C. Holmes, Weifeng Shi, Shufa Xu
Summary: Through meta-transcriptomic sequencing of nearly 2000 samples collected across China, researchers have revealed the diversity and prevalence of honeybee viruses, as well as the existence of novel genetic variants associated with China. The study highlights the widespread distribution and genetic diversity of honeybee viruses, suggesting the importance of understanding and mitigating viral infectious diseases in honeybees.
Article
Virology
Vincenzo A. Costa, David R. Bellwood, Jonathon C. O. Mifsud, Kate Van Brussel, Jemma L. Geoghegan, Edward C. Holmes, Erin Harvey
Summary: The Great Barrier Reef is the largest coral reef ecosystem in the world, supporting over 1,200 fish species with high potential for virus transmission. However, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. The reef has also faced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet.
Article
Virology
Jonathon C. O. Mifsud, Vincenzo A. Costa, Mary E. Petrone, Ezequiel M. Marzinelli, Edward C. Holmes, Erin Harvey
Summary: This article investigates the evolutionary history of the Flaviviridae family and finds that the viruses originated during the early stages of animal evolution approximately 750-800 million years ago. The study also reveals cross-species transmission and co-evolution between different species.
Article
Biochemistry & Molecular Biology
Katherine Eaton, Ravneet K. Sidhu, Jennifer Klunk, Julia A. Gamble, Jesper L. Boldsen, Ann G. Carmichael, Nukhet Varlik, Sebastian Duchene, Leo Featherstone, Vaughan Grimes, Brian Golding, Sharon N. DeWitte, Edward C. Holmes, Hendrik N. Poinar
Summary: By investigating 13 archaeological sites in Denmark, a study found that the plague appeared and evolved continuously in the region from the 14th to the 17th century, with cross-interactions with other European countries, rather than long-term local persistence. This research provides epidemiological links between the plague and the unknown pestilence in medieval and early modern Europe, and demonstrates how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology, paving the way for the next generation of historical disease research.
Article
Evolutionary Biology
Mary E. Petrone, Carolina Lucas, Bridget Menasche, Mallery Breban, Inci Yildirim, Melissa Campbell, Saad B. Omer, Edward C. Holmes, Albert Ko, Nathan D. Grubaugh, Akiko Iwasaki, Craig B. Wilen, Chantal B. F. Vogels, Joseph R. Fauver
Summary: Developing a timely and effective response to emerging SARS-CoV-2 variants of concern is crucial for public health. Global health surveillance relies not only on genomic data but also on methods that utilize genomic data to estimate the epidemiological dynamics of emerging lineages. In this study, the differences in reporting delays among SARS-CoV-2 VOCs were analyzed, indicating that these delays may have delayed the global response to the Mu variant. The nonsystematic biases in the reporting of genomic data could impede the assessment of future emerging variants.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Virology
Robert A. Lopez-Astacio, Oluwafemi F. Adu, Daniel J. Goetschius, Hyunwook Lee, Wendy S. Weichert, Brian R. Wasik, Simon P. Frueh, Brynn K. Alford, Ian E. H. Voorhees, Joseph F. Flint, Sarah Saddoris, Laura B. Goodman, Edward C. Holmes, Susan L. Hafenstein, Colin R. Parrish
Summary: Canine parvovirus (CPV) is a small DNA virus that causes serious diseases in dogs worldwide. In this study, in vitro selection and deep sequencing were used to investigate the escape mutations in CPV induced by two antibodies. The results provide insights into the selection of viral variants and the interactions between antibodies and receptors.
JOURNAL OF VIROLOGY
(2023)
Article
Virology
Peiwen Chen, Ziying Jin, Liuxia Peng, Zuoyi Zheng, Yiu-Man Cheung, Jing Guan, Liming Chen, Yiteng Huang, Xiaohui Fan, Zengfeng Zhang, Dongmei Shi, Jin Xie, Rirong Chen, Boheng Xiao, Chun Hung Yip, David K. Smith, Wenshan Hong, Yongmei Liu, Lifeng Li, Jia Wang, Edward C. Holmes, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan
Summary: A novel H3N8 virus with zoonotic potential has emerged in chickens in China through reassortment with avian H3 and N8 viruses and enzootic H9N2 viruses. This H3N8 virus has independent gene lineages but exchanges internal genes with other H9N2 viruses. Experimental studies show that it is transmissible in ferrets, and serological data suggest a lack of immunological protection in humans.
JOURNAL OF VIROLOGY
(2023)
Article
Plant Sciences
Yuanfei Pan, Mu Liu, Alejandro Sosa, Bo Li, Mang Shi, Xiaoyun Pan
Summary: This study investigates the metacommunities of endophytic fungi in the leaves of an invasive plant and finds that the structure of these fungal communities is influenced by multiple spatial scales and different drivers. These findings are important for understanding the global patterns of fungal diversity.
Article
Virology
Rachel L. Tulloch, Karan Kim, Chisha Sikazwe, Alice Michie, Rebecca Burrell, Edward C. Holmes, Dominic E. Dwyer, Philip N. Britton, Jen Kok, John-Sebastian Eden
Summary: The RAPIDprep assay is a simple and fast protocol for diagnosing infections within 24 hours of sample collection by sequencing ribosomal RNA-depleted total RNA. It effectively depletes human and microbial rRNA and amplifies genomic yield without the need for nucleic acid quantification or quality assessment. This assay can detect known and undiagnosed pathogens, providing valuable information for molecular epidemiological investigations and vaccine design.
Article
Virology
Callum Le Lay, Matthew B. Stott, Mang Shi, Sabrina Sadiq, Edward C. Holmes
Summary: Little is known about the diversity of RNA viruses in geothermal systems. In this study, researchers generated total RNA sequencing data from two hot springs in New Zealand and found that the microbial communities in these hot springs were highly diverse, with different proportions of bacteria, archaea, and eukaryotes. They also detected sequences of 23 RNA viruses from various families in one of the hot springs, some of which were novel and had uncertain host associations.
Article
Virology
Callum Le Lay, Joshua N. Hamm, Timothy J. Williams, Mang Shi, Ricardo Cavicchioli, Edward C. Holmes
Summary: Despite the presence of DNA viruses infecting archaea, no RNA viruses associated with archaea have been identified. In this study, researchers investigated the metatranscriptomes of hypersaline lakes to search for highly divergent RNA viruses. They identified several candidate sequences, but couldn't provide definitive evidence of RNA viruses in archaea.
Article
Virology
Erin Harvey, Jonathon C. O. Mifsud, Edward C. Holmes, Jackie E. Mahar
Summary: This study identified the viral diversity in four Dasyuromorph species using publicly available RNA-seq data. Fifteen new virus sequences were discovered, including five DNA virus families and three RNA virus taxa. Particularly noteworthy was the discovery of a marsupial-specific clade of delta-like viruses and a highly divergent hepacivirus. Understanding the virome of these species is crucial for preventing virus transmission to naive populations, as they are currently being used in translocation efforts.
Article
Virology
Brian R. Wasik, Evin Rothschild, Ian E. H. Voorhees, Stephanie E. Reedy, Pablo R. Murcia, Nicola Pusterla, Thomas M. Chambers, Laura B. Goodman, Edward C. Holmes, James C. Kile, Colin R. Parrish
Summary: This study compares the canine influenza virus (CIV) in dogs and the equine influenza virus (EIV) in horses to reveal their host-specific evolution, determine the sources and connections between outbreaks, and gain insight into the factors controlling their evolutionary fates.
Article
Biochemical Research Methods
Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun
Summary: In this study, we developed VirBot, a simple yet effective RNA virus identification tool based on protein families and adaptive score cutoffs. Compared to seven popular tools for virus identification, VirBot demonstrated high specificity in metagenomic datasets and superior sensitivity in detecting novel RNA viruses on both simulated and real sequencing data.