Article
Multidisciplinary Sciences
Taylorlyn Stephan, Shawn M. Burgess, Hans Cheng, Charles G. Danko, Clare A. Gill, Erich D. Jarvis, Klaus-Peter Koepfli, James E. Koltes, Eric Lyons, Pamela Ronald, Oliver A. Ryder, Lynn M. Schriml, Pamela Soltis, Sue VandeWoude, Huaijun Zhou, Elaine A. Ostrander, Elinor K. Karlsson
Summary: Genomics research has primarily focused on humans and a limited number of species, resulting in a lack of understanding about the genomes of the majority of species. However, a broad view that encompasses the vast diversity of life is necessary to comprehend how genomes function and how genetic variation shapes phenotypes. Integrating comparative genomics with other fields is crucial for scientific discovery and the protection of ourselves and our world.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Food Science & Technology
Qinghua Ye, Yuting Shang, Moutong Chen, Rui Pang, Fan Li, Chufang Wang, Xinran Xiang, Baoqing Zhou, Shuhong Zhang, Jumei Zhang, Shi Wu, Liang Xue, Yu Ding, Qingping Wu
Summary: This study used whole-genome analysis to identify new serovar-specific genes for the most common serogroup B Salmonella serovars in China, and designed specific PCR primer sets for validation. PCR successfully detected all target Salmonella serovars in different types of food samples, with high analytical sensitivity. The findings highlight the value of whole-genome analysis in identifying new serovar-specific targets for developing rapid and accurate molecular detection methods.
Article
Biochemistry & Molecular Biology
Benedikt Kirsch-Gerweck, Leonard Bohnenkaemper, Michel T. Henrichs, Jarno N. Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Joachim Burger, Jens Stoye, Yoan Diekmann
Summary: We developed an efficient haplotype-based approach to detect positive selection in large genomic datasets. By combining pattern matching and model-based inference, our method achieves high sensitivity and specificity with low computational resource requirements. Evaluation using UK Biobank data indicates scalability to population genomic datasets with millions of individuals. Our approach serves as an algorithmic blueprint for big data genomics, combining a combinatorial core with statistical inference in closed form.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Ran Brosh, Jon M. Laurent, Raquel Ordonez, Emily Huang, Megan S. Hogan, Angela M. Hitchcock, Leslie A. Mitchell, Sudarshan Pinglay, John A. Cadley, Raven D. Luther, David M. Truong, Jef D. Boeke, Matthew T. Maurano
Summary: Big-IN is a versatile platform for targeted integration of large DNAs into mammalian cells, enabling functional analysis and verification of engineered stem cells. This approach allows for the integration of constructs into cells, providing the potential for systematic analysis of disease-related genomic loci.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Tiffany N. Batarseh, Sarah N. Batarseh, Abraham Morales-Cruz, Brandon S. Gaut
Summary: In this study, the genetic diversity of 'Candidatus Liberibacter' species was examined using comparative genomics. The analysis revealed that the 'Ca. Liberibacter solanacearum' species has the highest intraspecific diversity and the largest plant host range.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Leonardo C. J. Corvalan, Mariane B. Sobreiro, Larissa R. Carvalho, Renata O. Dias, Ramilla S. Braga-Ferreira, Cintia P. Targueta, Carlos M. e Silva-Neto, Bianca W. Berton, Ana Maria S. Pereira, Jose A. F. Diniz-filho, Mariana P. C. Telles, Rhewter Nunes
Summary: Serjania erecta is an important genetic resource with medicinal properties. We sequenced and analyzed its chloroplast genome, identifying differences between species and potential molecular markers.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Richard J. Edwards, Matt A. Field, James M. Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D. Rosen, Gary S. Johnson, Edward S. Rice, La Deanna Hillier, Jillian M. Hammond, Samuel G. Towarnicki, Arina Omer, Ruqayya Khan, Ksenia Skvortsova, Ozren Bogdanovic, Robert A. Zammit, Erez Lieberman Aiden, Wesley C. Warren, J. William O. Ballard
Summary: The study presents high-quality de novo assemblies of Basenji genomes and compares them with Boxer and German Shepherd Dog genomes. The choice of reference genome significantly impacts read mapping and variant detection in canid variant analyses. The Basenji's unique phylogeny and genome structure make it suitable for targeted variant analysis, while a pangenome approach may be more appropriate for comprehensive analyses across the canid family.
Article
Biology
Qiong Liu, Yuhua Deng, An Song, Yifan Xiang, De Chen, Lai Wei
Summary: Liu et al. conducted a comparative analysis of 15 genomes from mites, identifying genetic signatures for diet specialisation. Different gene families and selective pressures were revealed for herbivorous, haematophagous and fat-feeding species.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Jun Chen, Yu Zang, Shuo Liang, Song Xue, Shuai Shang, Meiling Zhu, Ying Wang, Xuexi Tang
Summary: This study sequenced and compared the mitochondrial genomes of Zostera japonica and Phyllospadix iwatensis, providing new evidence of genome size reduction, gene loss, and adaptive evolution in seagrasses. It found a large number of repeat sequences and extensive loss of ribosomal protein genes in seagrass species. Additionally, it identified positive selection genes associated with seagrass adaptation to the marine environment.
Article
Biochemistry & Molecular Biology
Giacomo Potente, Etienne Leveille-Bourret, Narjes Yousefi, Rimjhim Roy Choudhury, Barbara Keller, Seydina Issa Diop, Daniel Duijsings, Walter Pirovano, Michael Lenhard, Peter Szovenyi, Elena Conti
Summary: The study presented the first chromosome-scale genome assembly of Primula veris, revealing the evolution of the S locus via multiple gene duplications and independent translocations. A new whole-genome duplication specific to the Primula lineage in Ericales was also discovered. The study proposed a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination and provided insights into the evolution of supergenes and genome architecture.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Letter
Biochemistry & Molecular Biology
Sofia N. Barreira, Anh-Dao Nguyen, Mark T. Fredriksen, Tyra G. Wolfsberg, R. Travis Moreland, Andreas D. Baxevanis
Summary: The study developed a pipeline for generating de novo assemblies of proteomes from 100 animal species across 21 phyla, creating the Animal Proteome Database (AniProtDB) to provide open access to this collection. This solution addresses the issue of limited availability of high-quality proteomic data and enables the utilization of data from nontraditional research organisms for biomedical research.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Cameron M. Nugent, Tony Kess, Matthew K. Brachmann, Barbara L. Langille, Steven J. Duffy, Sarah J. Lehnert, Brendan F. Wringe, Paul Bentzen, Ian R. Bradbury
Summary: Despite the absence of physical barriers and the presence of pelagic stages in many marine taxa, environmental variation is widely recognized as a significant factor driving diversity in marine species. However, understanding the genomic and ecological processes that shape populations remains inadequate for most marine species, which often hinders management and conservation efforts.
Article
Biotechnology & Applied Microbiology
Mengjia Zhang, Nansheng Chen
Summary: This study constructed the complete chloroplast genomes of seven Thalassionema strains, revealing genetic differences within and between species. Additionally, the study identified genomic differences between Thalassionema species and other diatoms. The study also provided insights into the phylogenetic position and emergence time of Thalassionema species.
Article
Plant Sciences
Kuan Liu, Rong Wang, Xiu-Xiu Guo, Xue-Jie Zhang, Xiao-Jian Qu, Shou-Jin Fan
Summary: This study sequenced and analyzed the chloroplast genomes of 13 Eragrostideae species, identifying useful molecular markers for phylogenetic analysis. The study revealed Enneapogon as the earliest diverging lineage, Eragrostis as the sister to Uniola including Harpachne, and discussed the classification of Harpachne harpachnoides based on morphological and molecular evidence.
Article
Immunology
Xiao-Yong Zhan, Gao-Feng Zha, Yulong He
Summary: The ongoing outbreak of human monkeypox (hMPX) in 2022 is a serious global threat. Understanding the evolution of the monkeypox virus (MPXV) at the gene level may provide insights into the unique aspects of the current outbreak, including human-to-human transmission. Analysis of MPXV coding genes revealed that while most genes were subjected to negative selection, there were a few genes that showed evidence of positive Darwinian selection, which may play a crucial role in viral adaptation, virulence, and transmission.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Eddie Luidy Imada, Diego Fernando Sanchez, Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Aleksey Stupnikov, Francisco Lobo-Pereira, Chi-Wai Yip, Kayoko Yasuzawa, Naoto Kondo, Masayoshi Itoh, Harukazu Suzuki, Takeya Kasukawa, Chung-Chau Hon, Michiel J. L. de Hoon, Jay W. Shin, Piero Carninci, Andrew E. Jaffe, Jeffrey T. Leek, Alexander Favorov, Gloria R. Franco, Ben Langmead, Luigi Marchionni
Article
Microbiology
Rodrigo Araujo Lima Rodrigues, Amina Cherif Louazani, Agnello Picorelli, Graziele Pereira Oliveira, Francisco Pereira Lobo, Philippe Colson, Bernard La Scola, Jonatas Santos Abrahao
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Carolina O. de C. Lima, Aline B. M. Vaz, Giovanni M. De Castro, Francisco Lobo, Ricardo Solar, Cristine Rodrigues, Luiz Roberto Martins Pinto, Luciana Vandenberghe, Gilberto Pereira, Andrea Miura da Costa, Raquel Guimaraes Benevides, Vasco Azevedo, Ana Paula Trovatti Uetanabaro, Carlos Ricardo Soccol, Aristoteles Goes-Neto
Summary: The study analyzed the variation of microbial community structure during the fermentation of cocoa beans and recommended the use of specific microbial species in the fermentation of fine cocoa beans. Significant changes in microbial community structures were observed at different time points, correlating with factors such as temperature, acidity, and pH.
Article
Microbiology
Marcela Franca Dias, Giovanni Marques de Castro, Magna Cristina de Paiva, Mariana de Paula Reis, Susanne Facchin, Anderson Oliveira do Carmo, Marta Salgueiro Alves, Maria Luiza Suhadolnik, Amanda de Moraes Motta, Isabel Henriques, Evanguedes Kalapothakis, Francisco Pereira Lobo, Andrea Maria Amaral Nascimento
Summary: Freshwater ecosystems provide a conducive environment for the acquisition and dissemination of antibiotic resistance genes (ARGs), with integrons playing a crucial role in this process. This study in the Velhas River, Brazil, revealed a diverse range of putative environmental integron-cassettes and their potential bacterial hosts through deep sequencing of intI-attC and 16S rRNA amplicons. The results indicated the presence of various ORFs related to different biological processes, particularly ARGs-cassettes associated with class 1 mobile integrons carried by pathogenic Gammaproteobacteria. Additionally, taxonomic and functional profiling identified Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla, with Betaproteobacteria, Alphaproteobacteria, and Actinobacteria classes being the main contributors to KEGG orthologs associated with resistance. Overall, these findings highlight the role of environmental integrons as a reservoir for resistance determinants beyond clinical settings and provide insights into the bacterial community in the Velhas River.
BRAZILIAN JOURNAL OF MICROBIOLOGY
(2021)
Article
Environmental Sciences
Maria Luiza S. Suhadolnik, Patricia S. Costa, Giovanni M. Castro, Francisco P. Lobo, Andrea M. A. Nascimento
Summary: The meta-analysis revealed the widespread presence of arsenic and iron redox genes in various environmental conditions, with specific genes playing important roles in different environments. The diversity and taxonomy of gene carriers were also found to be extensive. However, almost all AsRGs and FeRGs were not carried by plasmid sequences.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Biochemical Research Methods
Giovanni Marques de Castro, Zandora Hastenreiter, Thiago Augusto Silva Monteiro, Thieres Tayroni Martins da Silva, Francisco Pereira Lobo
Summary: This article presents and validates a machine learning strategy to predict essential genes in insects using sequence-based intrinsic attributes and transcriptomic data. Even models trained using only intrinsic attributes can predict genes in other insect species, including lineage-specific essential genes. Furthermore, the inclusion of RNA-Seq data contributes to increased classifier performance.
Article
Microbiology
Paula Luize Camargos Fonseca, Demetra Skaltsas, Felipe Ferreira da Silva, Rodrigo Bentes Kato, Giovanni Marques de Castro, Glen Jasper Yupanqui Garcia, Gabriel Quintanilha-Peixoto, Thairine Mendes-Pereira, Anderson Oliveira do Carmo, Eric Roberto Guimaraes Rocha Aguiar, Daniel Santana de Carvalho, Diogo Henrique Costa-Rezende, Elisandro Ricardo Drechsler-Santos, Fernanda Badotti, Alice Ferreira-Silva, Guilherme Oliveira, Priscila Chaverri, Aline Bruna Martins Vaz, Aristoteles Goes-Neto
Summary: This study investigates the fungal community of the rubber tree using in silico approaches and experimental methods. The results reveal specific phyllospheric fungal communities in the rubber tree and uncover the hierarchical structure of the core fungal communities. Additionally, the study provides insights into the high abundance of insect parasite-pathogens and anaerobic fungi in a case study of an adult rubber tree.
Article
Surgery
Luigi Marchionni, Francisco Pereira Lobo, Rumen Kostadinov, Anna Serra, Federico Genzano Besso, Silvia Deaglio, Piero Stratta, Monica Berrino, Claudio Zanettini, Eddie Luidy Imada, Mohamed N. Omar, Gianluca Gaidano, Benedetto Bruno, Giuseppe Saglio, Antonio Amoroso
Summary: We report a case of transmission of AML from a self-donor to two kidney and one liver recipients. The recipients showed donor chimerism and distinct clonal evolution, providing a potential molecular explanation for tumor escape.
AMERICAN JOURNAL OF TRANSPLANTATION
(2022)
Article
Microbiology
Carolina O. de C. Lima, Giovanni M. De Castro, Ricardo Solar, Aline B. M. Vaz, Francisco Lobo, Gilberto Pereira, Cristine Rodrigues, Luciana Vandenberghe, Luiz Roberto Martins Pinto, Andrea Miura da Costa, Maria Gabriela Bello Koblitz, Raquel Guimaraes Benevides, Vasco Azevedo, Ana Paula Trovatti Uetanabaro, Carlos Ricardo Soccol, Aristoteles Goes-Neto
Summary: This study used high-throughput sequencing technologies to investigate the microbial community during the fermentation of cocoa beans. The results showed that there was a succession of microbial community during fermentation, and different genes were dominant at different time points. The findings provide insights for improving cocoa processing practices to ensure the production of more stable quality end products.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Jorge Augusto Hongo, Giovanni Marques de Castro, Alison Pelri Albuquerque Menezes, Agnello Cesar Rios Picorelli, Thieres Tayroni Martins da Silva, Eddie Luidy Imada, Luigi Marchionni, Luiz-Eduardo Del-Bem, Anderson Vieira Chaves, Gabriel Magno de Freitas Almeida, Felipe Campelo, Francisco Pereira Lobo
Summary: This article introduces a phylogeny-aware comparative genomics tool called CALANGO, which is used to find homologous regions and biological roles associated with quantitative phenotypes across species. Through two case studies, CALANGO has identified both known and previously unidentified genotype-phenotype associations, providing new directions for research in ecology and agriculture.