Article
Plant Sciences
Yichao Wang, Shuya Liu, Jing Wang, Yanxin Yao, Yang Chen, Qing Xu, Zengxia Zhao, Nansheng Chen
Summary: Mitochondrial genomes can be used as super barcodes to distinguish diatom species with higher resolution compared to common molecular markers. Comparative analysis of mitochondrial genomes revealed extensive genome rearrangement events and showed their value in evolutionary studies.
FRONTIERS IN PLANT SCIENCE
(2022)
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
Plant Sciences
Qingqing Zhou, Yang Ni, Jingling Li, Linfang Huang, Husheng Li, Haimei Chen, Chang Liu
Summary: In this study, we assembled the complete plastome and mitogenome of Caragana spinosa and explored the multiple configurations of the organelle genomes. The analysis of the plastome and mitogenome provides valuable information for understanding the molecular characteristics of C. spinosa and can serve as a reference for studying other Caragana species.
Article
Biotechnology & Applied Microbiology
Yisong Li, Zhong-Zhi Sun, Jin-Cheng Rong, Bin-Bin Xie
Summary: The study revealed high intraspecies genomic diversity of M. luteus and highlighted that gene gain/loss events and extensive recombination events played key roles in the genome evolution. As a free-living species, some lineages have recently developed or are developing a mammal-associated lifestyle.
Article
Biochemistry & Molecular Biology
Giovanni Pascarella, Chung Chau Hon, Kosuke Hashimoto, Annika Busch, Joachim Luginbuhl, Callum Parr, Wing Hin Yip, Kazumi Abe, Anton Kratz, Alessandro Bonetti, Federico Agostini, Jessica Severin, Shigeo Murayama, Yutaka Suzuki, Stefano Gustincich, Martin Frith, Piero Carninci
Summary: This study reveals the somatic recombination of repeat elements, such as Alu and L1, in the human genome. It also identifies tissue-specific non-allelic homologous recombination hallmarks and retroelements as potential recombination hotspots. The study further shows that neuron-specific recombination of repeat elements accompanies chromatin changes during cell-fate determination. Moreover, somatic recombination profiles are altered in Parkinson's and Alzheimer's disease, indicating a link between retroelement recombination and genomic instability in neurodegeneration.
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
Microbiology
Margaret D. Weinroth, James L. Bono
Summary: This study investigates the genomic diversity of Escherichia coli O55:H7, a human foodborne pathogen. By analyzing closed genomes and newly sequenced genomes, the researchers found significant diversity within the strain, including different sequence types and prophage compositions. The study also identified a large number of insertion sequences and plasmids within each strain.
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
Biology
Shiqian Feng, Andrea Pozzi, Vaclav Stejskal, George Opit, Qianqian Yang, Renfu Shao, Damian K. Dowling, Zhihong Li
Summary: "Contrary to expectations, this study found that mt-genome fragmentation is not correlated with the increase in mt-genome rearrangements in a genus of booklice, Liposcelis. The researchers proposed that fragmentation of the mt-genome may be a consequence of recombination errors between mt-genome copies, which is linked to a heightened mutation rate in clades exhibiting mt-fragmentation. Furthermore, the study showed that species with fragmented mt-genomes diverge more rapidly, despite experiencing strong purifying selection."
Article
Genetics & Heredity
Jie Huang, Zhaocen Lu, Chunrui Lin, Weibin Xu, Yan Liu
Summary: Limestone karsts are known for their high species richness and endemism. The genus Aspidistra, which is widely distributed in karst areas, is an ideal group for studying the evolutionary mechanisms of karst plants. In this study, the chloroplast genomes of seven Aspidistra species were reported, and a comprehensive comparative analysis was conducted. Eight divergent hotspot regions were identified as potential molecular markers. The findings enrich the resources of plastid genomes of karst plants and provide new perspectives on the taxonomy, phylogeny, and evolution of Aspidistra species.
Editorial Material
Multidisciplinary Sciences
Martha I. Nelson, Elodie Ghedin
Summary: The evolutionary steps taken by the 1918 flu pandemic virus have been revealed through the analysis of lung samples stored in medical archives. Three genomes of the influenza A virus responsible for the global pandemic have been obtained, showing mutations that may have triggered the devastating second wave.
Article
Plant Sciences
Jun Chen, Yu Zang, Shuai Shang, Shuo Liang, Meiling Zhu, Ying Wang, Xuexi Tang
Summary: Seagrasses are marine flowering plants found in tropical and sub-tropical areas that evolved from terrestrial monocotyledons, providing insight into plant adaptation to sea environments. The analysis of chloroplast genomes of Zostera species revealed conserved structures, candidate DNA barcodes, and positively selected genes for seagrass adaptation. Additionally, seagrasses were found to have a higher rate of evolution than terrestrial monocotyledons, indicating greater environmental pressure and potential key roles of specific genes in seagrass adaptation.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Liping Yan, Wentian Xu, Dong Zhang, Junqing Li
Summary: Flesh flies play vital roles in ecosystem, economic, forensic, and evolutionary studies due to their diverse habits as larvae. Phylogenetic studies have reached convergence, offering the opportunity to elucidate the evolution of these fast-evolving insects from the perspective of mitochondrial genome.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Environmental Sciences
Kuiyan Liu, Yang Chen, Zongmei Cui, Shuya Liu, Qing Xu, Nansheng Chen
Summary: Thalassiosira is a species-rich genus in Bacillariophyta with significant ecological contributions, but can also have negative impacts through harmful algal blooms. This study constructed complete chloroplast genomes of six Thalassiosira strains and compared them with other diatoms, revealing conventional quadripartite structure but with some exceptions. Endosymbiotic gene transfers were found in the evolution of Thalassiosira cpDNAs, with highly variable genomic regions that could be used for molecular markers and phylogenetic analysis. Thalassiosira species appeared around 51 million years ago and diversified 17-28 million years ago, making their cpDNAs valuable for evolutionary and functional analysis.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Cheng Sun, Jiaxing Huang, Yun Wang, Xiaomeng Zhao, Long Su, Gregg W. C. Thomas, Mengya Zhao, Xingtan Zhang, Irwin Jungreis, Manolis Kellis, Saverio Vicario, Igor Sharakhov, Semen M. Bondarenko, Martin Hasselmann, Chang N. Kim, Benedict Paten, Luca Penso-Dolfin, Li Wang, Yuxiao Chang, Qiang Gao, Ling Ma, Lina Ma, Zhang Zhang, Hongbo Zhang, Huahao Zhang, Livio Ruzzante, Hugh M. Robertson, Yihui Zhu, Yanjie Liu, Huipeng Yang, Lele Ding, Quangui Wang, Dongna Ma, Weilin Xu, Cheng Liang, Michael W. Itgen, Lauren Mee, Gang Cao, Ze Zhang, Ben M. Sadd, Matthew W. Hahn, Sarah Schaack, Seth M. Barribeau, Paul H. Williams, Robert M. Waterhouse, Rachel Lockridge Mueller
Summary: Bumblebees are globally important pollinators facing threats such as pathogen transmission, habitat loss, pesticide usage, and global climate change. By de novo sequencing and assembling genomes of 17 species, researchers have identified genetic and genomic variations potentially linked to key ecological and behavioral traits. This study provides insights into the evolutionary processes of bumblebee genes and genomes across phylogeny and their adaptations for survival.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Yannis Nevers, Tamsin E. M. Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codo, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Pilizota, Cristina Guijarro-Clarke, Wataru Iwasaki, Odile Lecompte, Erik Sonnhammer, David S. Roos, Toni Gabaldon, David Thybert, Paul D. Thomas, Yanhui Hu, David M. Emms, Elspeth Bruford, Salvador Capella-Gutierrez, Maria J. Martin, Christophe Dessimoz, Adrian Altenhoff
Summary: The Orthology Benchmark Service is a valuable resource for evaluating orthology inference methods in comparative genomics and phylogenetic analysis. It is supported and maintained by the Quest for Orthologs consortium and provides a standard dataset and common procedures for comparing different methods.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Jesse R. Willis, Ester Saus, Susana Iraola-Guzman, Ewa Ksiezopolska, Luca Cozzuto, Luis A. Bejarano, Nuria Andreu-Somavilla, Miriam Alloza-Trabado, Andrea Blanco, Anna Puig-Sola, Elisabetta Broglio, Carlo Carolis, Julia Ponomarenko, Jochen Hecht, Toni Gabaldon
Summary: The human oral microbiome plays a significant role in human health, with factors such as age, chronic health disorders, smoking, and presence of yeasts in the oral cavity influencing its composition. Relatives and even classmates tend to have more similar oral microbiomes, indicating that multiple intrinsic and extrinsic factors collectively shape the oral microbiome.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Review
Biochemistry & Molecular Biology
Miquel Angel Schikora-Tamarit, Toni Gabaldon
Summary: Fungal pathogens pose a threat to human health, food security, and ecosystem diversity. Understanding the genetic basis of virulence and drug resistance traits is crucial for tackling fungal infections. Genomics approaches, including comparative genomics, population genomics, and directed evolution studies, have played a key role in uncovering the mechanisms behind these traits. Different types of genomic mutations contribute to intraspecific differences in virulence or drug resistance. Challenges in the field and future directions are also discussed in this review.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Correction
Biochemistry & Molecular Biology
Laia Carrete, Ewa Ksiezopolska, Cinta Pegueroles, Emilia Gomez-Molero, Ester Saus, Susana Iraola-Guzman, Damian Loska, Oliver Bader, Cecile Fairhead, Toni Gabaldon
Article
Immunology
Hrant Hovhannisyan, Antonio Rodriguez, Ester Saus, Mario Vaneechoutte, Toni Gabaldon
Summary: The study focuses on the challenges of analyzing transcriptomic interactions between host and pathogen RNA in in vivo conditions. The researchers successfully designed pan-Candida target capture probes to enrich protein-coding and non-coding transcriptomes in order to enhance transcriptomic analysis in four major Candida species. The probe-based enrichment approach showed better fidelity of expression levels, enabling species multiplexing and capturing of lncRNAs, and demonstrated robust genotype-based identification of the infecting strain present in the sample.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Ahmed Ibrahem Hafez, Beatriz Soriano, Aya Allah Elsayed, Ricardo Futami, Raquel Ceprian, Ricardo Ramos-Ruiz, Genis Martinez, Francisco Jose Roig, Miguel Angel Torres-Font, Fernando Naya-Catala, Josep Alvar Calduch-Giner, Lucia Trilla-Fuertes, Angelo Gamez-Pozo, Vicente Arnau, Jose Maria Sempere-Luna, Jaume Perez-Sanchez, Toni Gabaldon, Carlos Llorens
Summary: The GPRO suite is an ongoing bioinformatic project for the analysis of -omics data. It introduces a client- and server-side solution for comparative transcriptomics and variant analysis. The client-side includes two Java applications, RNASeq and VariantSeq, which manage pipelines and workflows using common command line tools. The server-side, named GPRO Server-Side, hosts all dependencies and requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The solution offers both desktop and web applications, with step-by-step and pipeline modes for execution. It also features an experimental support system called GENIE, with a chatbot assistant and expert system for troubleshooting and recommendations.
Article
Oncology
Olfat Khannous-Lleiffe, Jesse R. Willis, Ester Saus, Victor Moreno, Sergi Castellvi-Bel, Toni Gabaldon
Summary: Colorectal cancer (CRC) is a global healthcare challenge influenced by genetic and environmental factors. This study used 16S rRNA sequencing to analyze FIT samples and found that the gut microbiome has predictive potential and undergoes changes during the progression from healthy tissue to carcinoma. These findings have implications for understanding the role of microbes in adenoma to carcinoma progression and improving CRC screening programs.
Article
Biology
Veronica Mixao, Juan Carlos Nunez-Rodriguez, Valentina del Olmo, Ewa Ksiezopolska, Ester Saus, Teun Boekhout, Attila Gacser, Toni Gabaldon
Summary: This study analyzed the genomic sequences of 55 hybrid strains of pathogenic yeast and found that genetic drift is the main force shaping LOH patterns in these genomes, and LOH patterns are likely the result of acute episodes rather than continuous accumulation of sporadic events.
Article
Biology
Irene Julca, Pablo Vargas, Toni Gabaldon
Summary: The evolutionary history of the Olea europaea complex involves hybridization and polyploidization events, leading to the formation of new subspecies. The genetic diversity of the species is crucial for its management and preservation of genetic resources.
Article
Biochemistry & Molecular Biology
Efe Aydin, Ester Saus, Uciel Chorostecki, Toni Gabaldon
Summary: Long noncoding RNAs (lncRNAs) have potential as prognostic biomarkers or therapeutic targets in cancer. Somatic mutations in lncRNAs have been associated with tumor relapse, but their underlying mechanisms are unknown. In this study, a recurrent A > G point mutation in NEAT1 was found to alter its structure and affect the binding of miRNAs. Differential expression analysis showed upregulation of Vimentin, consistent with previous findings. This study proposes a pipeline to explore the functional effects of lncRNA somatic mutations.
Correction
Plant Sciences
Mara Baudena, Victor M. M. Santana, M. Jaime Baeza, Susana Bautista, Maarten B. B. Eppinga, Lia Hemerik, Angeles Garcia Mayor, Francisco Rodriguez, Alejandro Valdecantos, V. Ramon Vallejo, Ana Vasques, Max Rietkerk
Article
Microbiology
Borja Aldeguer-Riquelme, Josefa Anton, Fernando Santos
Summary: Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. This study analyzes the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, and proposes the name of Palauibacterales order. The findings suggest that Palauibacterales could have a key role as a thiamine supplier in the marine environment, expanding the understanding of the ecological roles of Gemmatimonadota.
Article
Mathematics
Carlos Julio Mayorga, Maria Angeles Castro, Antonio Sirvent, Francisco Rodriguez
Summary: In this work, the authors propose a method to directly obtain expressions for the fundamental solutions of linear delay differential equations. These expressions can be used to derive exact numerical schemes for arbitrary initial functions and may also facilitate obtaining explicit exact solutions.
Article
Mathematics, Applied
M. Angeles Castro, Carlos J. J. Mayorga, Antonio Sirvent, Francisco Rodriguez
Summary: In this work, we present an exact numerical solution for the second order delay differential equation x(t)=ax(t)+bx(t-tau), with general initial condition x(t)=f(t) for -tau <= t <= 0 by utilizing special functions. Based on this exact solution, we propose a family of nonstandard finite difference methods that possess both high order accuracy and efficient computational properties. We also demonstrate that the numerical solutions obtained using these new schemes exhibit consistent asymptotic stability properties with the exact solutions.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2023)
Article
Biology
Miguel A. Naranjo-Ortiz, Manu Molina, Diego Fuentes, Veronica Mixao, Toni Gabaldon
Summary: Certain genomic features in genome sequencing and assembly can lead to low-quality assemblies. This study presents Karyon, a Python-based toolkit that assesses parameters and generates informative plots to identify noncanonical genomic traits. Testing on 35 highly fragmented fungal assemblies, it was found that 10 assemblies displayed unusual genomic configurations.