Article
Biology
Jesper Boman, Goran Arnqvist
Summary: Our understanding of genome size evolution is incomplete and genome size does not reflect organismal complexity. We hypothesized that larger genomes may help organisms cope with environmental variation. Using the seed beetle Callosobruchus maculatus, we conducted experiments exposing populations with different genome sizes to environmental stress and assessed their fitness. We found that populations with larger genomes were better buffered against environmental stress in adult fitness, but not juvenile fitness. The genetic correlation between genome size and adult fitness supports a role for natural selection in genome size evolution.
Review
Chemistry, Multidisciplinary
Duncan J. Kountz, Emily P. Balskus
Summary: The genomic era has revolutionized the discovery and investigation of microbial biochemistry, providing researchers with vast amounts of sequence data to explore biochemical functions and mechanisms, as well as novel enzymes and metabolites. By analyzing genomic context and understanding enzyme mechanisms, new microbial metabolic activities, enzymes, and metabolites can be discovered at an accelerated pace. The canonical organization of microbial genomes into gene clusters presents a unique opportunity for the utilization of genomic data, allowing for effective chemical discovery in microbial systems by leveraging functional and physiological relationships between genes within gene clusters.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Evolutionary Biology
Fernando D. K. Tria, William F. Martin
Summary: Gene duplications in prokaryotic genomes are studied less compared to eukaryotic genomes. Recent findings show that gene duplications are at least 50 times less frequent, and probably 100 times less frequent, than gene acquisitions via lateral gene transfer in prokaryotes. The frequency of gene duplications varies across lineages and functional categories, improving our understanding of genome evolution in prokaryotes.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Irfan Ali Sabir, Muhammad Aamir Manzoor, Iftikhar Hussain Shah, Farhat Abbas, Xunju Liu, Sajid Fiaz, Adnan Noor Shah, Songtao Jiu, Jiyuan Wang, Muhammad Abdullah, Caixi Zhang
Summary: The gibberellin-dioxygenase (GAox) gene family plays a crucial role in regulating plant growth and development. In this study, 399 GAox members were identified in sweet cherry, Japanese apricot, and strawberry. They were further classified into six subgroups based on phylogeny. The analysis reveals their evolutionary process and their tissue-specific expression patterns and hormone response-related functions.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Microbiology
David S. Milner, Luis Javier Galindo, Nicholas A. T. Irwin, Thomas A. Richards
Summary: This article discusses two related topics in evolutionary microbiology: the variation of gene repertoire within species groups and the role of metabolite transporters as accessory proteins. It emphasizes the importance of improved sampling and understanding of eukaryotic microbial pangenome variation and outlines the key factors in gene duplication and transporter gene family evolution. The article also highlights the significance of functional characterization of transporter-encoding genes and analysis of their gain and loss from accessory genomes in revealing information about the ecology and virulence evolution of microbes. It advocates for the systematic study of eukaryotic pangenomes through genome sequencing and functional analysis of genes within the accessory gene repertoire.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Chuya Shinzato, Konstantin Khalturin, Jun Inoue, Yuna Zayasu, Miyuki Kanda, Mayumi Kawamitsu, Yuki Yoshioka, Hiroshi Yamashita, Go Suzuki, Noriyuki Satoh
Summary: By sequencing and comparing the genomes of Acropora species and other related taxa, this study identified genetic features that contribute to the evolutionary success and adaptation of corals, including gene duplications, positive selection of antimicrobial peptides, and symbiosis-related genes. These findings provide insights into the unique adaptations of Acropora to ancient warm marine environments, shedding light on its ability to adjust to rising seawater temperatures in the future.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jean-Francois Gout, Yue Hao, Parul Johri, Olivier Arnaiz, Thomas G. Doak, Simran Bhullar, Arnaud Couloux, Frederic Guerin, Sophie Malinsky, Alexey Potekhin, Natalia Sawka, Linda Sperling, Karine Labadie, Eric Meyer, Sandra Duharcourt, Michael Lynch
Summary: Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages, but the maintenance of WGD-derived paralogs is still debated. The analysis of 13 Paramecium species revealed that gene retention biases and strong selective pressures against post-WGD gene loss play a major role in maintaining duplicate genes. Paramecium is an exceptional model organism in evolutionary cell biology, and this dataset of 13 species sharing an ancestral WGD will be useful for future studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Kirsten Verster, Rebecca L. Tarnopol, Saron M. Akalu, Noah K. Whiteman
Summary: The role of horizontal gene transfer (HGT) in animal evolution, particularly the transfer of toxin genes like cdtB into insect genomes, has been highlighted. Evidence shows that toxin genes transferred through HGT often originate from microbes shared in the same environment, potentially aiding in insect adaptation through evolutionary processes.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Zheng-Feng Wang, Mathieu Rouard, Gaetan Droc, Pat (J S) Heslop-Harrison, Xue-Jun Ge
Summary: This study generated a high-quality chromosome-scale genome assembly of M. beccarii and revealed its genome features and evolution, providing an important genetic resource for studying the genetics of Musaceae plants.
Article
Biochemistry & Molecular Biology
Yue Hao, Makenzie E. Mabry, Patrick P. Edger, Michael Freeling, Chunfang Zheng, Lingling Jin, Robert VanBuren, Marivi Colle, Hong An, R. Shawn Abrahams, Jacob D. Washburn, Xinshuai Qi, Kerrie Barry, Christopher Daum, Shengqiang Shu, Jeremy Schmutz, David Sankoff, Michael S. Barker, Eric Lyons, J. Chris Pires, Gavin C. Conant
Summary: The study investigates the gene loss history after whole-genome triplication (WGT) in Brassiceae tribe members, confirming a two-step formation model with significant temporal gaps. It highlights distinguishable homoeolog loss rates among subgenomes and proposes a mix and match model of allopolyploidy where genes from different subgenomes function together without difficulty.
Article
Horticulture
Salvatore Esposito, Elisa Cappetta, Valentina Tranchida-Lombardo, Giorgia Batelli, Alessandra Ruggiero, Michelina Ruocco, Giorgia Sportelli, Fabrizio Cillo, Monica De Palma
Summary: This study identified and classified 237 GRX genes in tomato, potato, and their wild relatives. The CC-type GRX genes in tomato showed higher diversity, suggesting their important role in GRX evolution. Additionally, the different expression patterns of GRX genes in tomato indicated their specialized functions in developmental, hormonal, and abiotic stress responses.
SCIENTIA HORTICULTURAE
(2023)
Article
Biochemistry & Molecular Biology
Leighton J. Payne, Sean Meaden, Mario R. Mestre, Chris Palmer, Nicolas Toro, Peter C. Fineran, Simon A. Jackson
Summary: Most bacteria and archaea possess multiple antiviral defence systems, and the PADLOC web server provides a convenient resource for analyzing and detecting these systems.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Agriculture, Dairy & Animal Science
Xinwei Xiong, Yousheng Rao, Jinge Ma, Zhangfeng Wang, Qin He, Jishang Gong, Wentao Sheng, Jiguo Xu, Xuenong Zhu, Yuwen Tan, Yanbei Yang
Summary: This study constructed a catalog of microbial genes and genomes in the quail gut using deep metagenomic sequencing. The results showed that the gut microbiome composition and function differed between the two quail breeds. These findings provide an important resource for further research on the quail gut microbiome.
Article
Microbiology
Mary Maranga, Pawel Szczerbiak, Valentyn Bezshapkin, Vladimir Gligorijevic, Chris Chandler, Richard Bonneau, Ramnik J. Xavier, Tommi Vatanen, Tomasz Kosciolek
Summary: In the past decade, there has been rapid accumulation of genomic data from microbial communities due to advancements in high-throughput sequencing technologies. However, the majority of microbial gene functions remain uncharacterized. To address this, a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling, and deep learning-based functional annotations (DeepFRI) has been developed. This workflow significantly improves the annotation coverage and allows for the analysis of the functional potential of individual bacterial species, leading to a better understanding of the human gut microbiome in health and disease.
Article
Evolutionary Biology
Chen Wu, Victoria G. Twort, Richard D. Newcomb, Thomas R. Buckley
Summary: The study found several meiotic genes duplicated in the New Zealand geographic parthenogenetic stick insect, some of which are rare or unique compared to other arthropods. These genes may play important roles in the evolution of reproductive mode.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Oncology
Rashmi Sinha, Jun Chen, Amnon Amir, Emily Vogtmann, Jianxin Shi, Kristin S. Inman, Roberto Flores, Joshua Sampson, Rob Knight, Nicholas Chia
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2016)
Review
Physiology
Andrea G. Braundmeier, Katherine M. Lenz, Kristin S. Inman, Nicholas Chia, Patricio Jeraldo, Marina R. S. Walther-Antonio, Margret E. Berg Miller, Fang Yang, Douglas J. Creedon, Heidi Nelson, Bryan A. White
FRONTIERS IN PHYSIOLOGY
(2015)
Article
Biochemical Research Methods
Helena Mendes-Soares, Michael Mundy, Luis Mendes Soares, Nicholas Chia
BMC BIOINFORMATICS
(2016)
Article
Oncology
Erikka Loftfield, Emily Vogtmann, Joshua N. Sampson, Steven C. Moore, Heidi Nelson, Rob Knight, Nicholas Chia, Rashmi Sinha
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2016)
Letter
Oncology
Rashmi Sinha, Emily Vogtmann, Jun Chen, Amnon Amir, Jianxin Shi, Joshua Sampson, Roberto Flores, Rob Knight, Nicholas Chia
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2016)
Article
Gastroenterology & Hepatology
Gopanandan Parthasarathy, Jun Chen, Xianfeng Chen, Nicholas Chia, Helen M. O'Connor, Patricia G. Wolf, H. Rex Gaskins, Adil E. Bharucha
Article
Biochemical Research Methods
Matthew Thoendel, Patricio R. Jeraldo, Kerryl E. Greenwood-Quaintance, Janet Z. Yao, Nicholas Chia, Arlen D. Hanssen, Matthew P. Abdel, Robin Patel
JOURNAL OF MICROBIOLOGICAL METHODS
(2016)
Article
Genetics & Heredity
Jun Chen, Yoshitaka Toyomasu, Yujiro Hayashi, David R. Linden, Joseph H. Szurszewski, Heidi Nelson, Gianrico Farrugia, Purna C. Kashyap, Nicholas Chia, Tamas Ordog
Article
Microbiology
Patricio Jeraldo, Alvaro Hernandez, Henrik B. Nielsen, Xianfeng Chen, Bryan A. White, Nigel Goldenfeld, Heidi Nelson, David Alhquist, Lisa Boardman, Nicholas Chia
FRONTIERS IN MICROBIOLOGY
(2016)
Article
Multidisciplinary Sciences
Jun Chen, Euijung Ryu, Matthew Hathcock, Karla Ballman, Nicholas Chia, Janet E. Olson, Heidi Nelson
Article
Multidisciplinary Sciences
Jun Chen, Nicholas Chia, Krishna R. Kalari, Janet Z. Yao, Martina Novotna, M. Mateo Paz Soldan, David H. Luckey, Eric V. Marietta, Patricio R. Jeraldo, Xianfeng Chen, Brian G. Weinshenker, Moses Rodriguez, Orhun H. Kantarci, Heidi Nelson, Joseph A. Murray, Ashutosh K. Mangalam
SCIENTIFIC REPORTS
(2016)
Article
Multidisciplinary Sciences
Tina J. Hieken, Jun Chen, Tanya L. Hoskin, Marina Walther-Antonio, Stephen Johnson, Sheri Ramaker, Jian Xiao, Derek C. Radisky, Keith L. Knutson, Krishna R. Kalari, Janet Z. Yao, Larry M. Baddour, Nicholas Chia, Amy C. Degnim
SCIENTIFIC REPORTS
(2016)
Article
Medical Laboratory Technology
Pai C. Kao, Qiao Jun Han, Shuyi Liu, Xiu Jun Li, Kristin S. Inman, Nicholas Chia
ANNALS OF CLINICAL AND LABORATORY SCIENCE
(2016)
Article
Genetics & Heredity
Jaeyun Sung, Vanessa Hale, Annette C. Merkel, Pan-Jun Kim, Nicholas Chia
APPLIED AND TRANSLATIONAL GENOMICS
(2016)
Article
Microbiology
Patricio Jeraldo, Scott A. Cunningham, Daniel Quest, Robert A. Sikkink, Daniel O'Brien, Bruce W. Eckloff, Robin Patel, Nicholas Chia
GENOME ANNOUNCEMENTS
(2015)