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
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
Biotechnology & Applied Microbiology
Thomas Roder, Simone Oberhaensli, Noam Shani, Remy Bruggmann
Summary: OpenGenomeBrowser is a self-hostable, open-source platform for managing access to genomic data and simplifying comparative genomics analyses. It offers a wide range of features, including generation of phylogenetic trees, comparison of gene loci, browsing of biochemical pathways, and execution of BLAST searches.
Article
Biology
Stephan Majda, Daniela Beisser, Jens Boenigk
Summary: The study shows that heterotrophic taxa have a reduced genome size and higher GC content compared to phototrophic taxa, with a large pan genome but a small core genome indicating different specialization among lineages. Despite this, the pan genome of mixotrophs and heterotrophs together covers the complete functionality of phototrophic strains, suggesting a random reduction of genes.
COMMUNICATIONS BIOLOGY
(2021)
Article
Agricultural Engineering
Bingchao Wu, Jie Zhu, Xixi Ma, Jiyuan Jia, Dan Luo, Qiong Ding, Xiaoshan Wang, Linkai Huang
Summary: By comparing the chloroplast genomes of upland and lowland ecotypes of switchgrass, this study reveals conservation in terms of repetitive sequences, codon usage, and the identification of a lowland-specific hotspot. The phylogenetic analysis also highlights the complexity of the evolutionary process of switchgrass.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Microbiology
Yvonne O. Ogaji, Robert C. Lee, Tim I. Sawbridge, Benjamin G. Cocks, Hans D. Daetwyler, Sukhjiwan Kaur
Summary: This study used Oxford Nanopore long-read sequencing to generate high-quality genome and mitochondrial genome assemblies for 18 isolates of the Australian Ascochyta Blight (AB) complex, revealing differences and similarities between the pathogens. It was found that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic.
Article
Plant Sciences
Qiyu Chen, Chunling Chen, Bo Wang, Zehuan Wang, Wenfen Xu, Yuan Huang, Qingwen Sun
Summary: This study assembled and analyzed the chloroplast genomes of the genus Sabia, revealing a relatively conserved genome structure with multiple variable loci. Phylogenetic analysis indicated that the two sections of Sabia did not form separate monophyletic groups. Divergence time calculations showed that the evolutionary branches of Sabia and Meliosma began approximately 85.95 million years ago, with species within Sabia diverging around 7.65 million years ago.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Roman Martin, Hagen Dressler, Georges Hattab, Thomas Hackl, Matthias G. Fischer, Dominik Heider
Summary: MOSGA 2 is an accessible and easy-to-use analysis tool for eukaryotic genome annotations, developed with advanced analyses to improve annotation quality. By validating and ensuring genome data quality, integrating comparative genomics methods, and extending established applications, MOSGA 2 provides a broader genomic view and comprehensive genome analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Plant Sciences
Kwanjeera Wanichthanarak, Intawat Nookaew, Phongthana Pasookhush, Thidathip Wongsurawat, Piroon Jenjaroenpun, Namkhang Leeratsuwan, Songsak Wattanachaisaereekul, Wonnop Visessanguan, Yongyut Sirivatanauksorn, Narong Nuntasaen, Chutima Kuhakarn, Vichai Reutrakul, Pravech Ajawatanawong, Sakda Khoomrung
Summary: In this study, we successfully outlined the complete chloroplast genome of Ventilago harmandiana using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the genome were confirmed with PCR amplifications and investigation of coverage depth. The phylogenetic trees reconstructed using prevalent methods were topologically similar.
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
Biochemistry & Molecular Biology
Iago Rodrigues Blanco, Lucas Jose Luduverio Pizauro, Joao Victor dos Anjos Almeida, Carlos Miguel Nobrega Mendonca, Alessandro de Mello Varani, Ricardo Pinheiro de Souza Oliveira
Summary: This study compared the genomes of P. pentosaceus available in the public GenBank database, focusing on their pediocin-like bacteriocin repertoire. The analysis revealed a temporal signal in the pattern of gene gain and loss, indicating that the complete genetic repertoire of this bacterial group is still unknown. Thirteen bacteriocin genes from Class II and III were predicted, and four pediocin-like bacteriocins and their accompanying immunity genes were highlighted. In silico modeling showed differences in the helix motif compared to physically determined pediocin-like structures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Genetics & Heredity
Yinggu Wu, Yuyang Lian, Sihua Peng, Aqiang Wang, Heming Yang, Jinlei Li, Shuyan Yang, Shihao Zhou
Summary: Zeugodacus cucurbitae, Bactrocera dorsalis, and Ceratitis capitata are important pests of fruit and vegetable crops, and their rapid reproduction rate and egg production make them difficult to control. This study investigates the key genes regulating reproduction in these three fruit fly species and finds that they have different specific genes enriched in immune system, cell growth and differentiation, and degradation and metabolism pathways. Z. cucurbitae may have a stronger immune system, B. dorsalis has a faster developmental and reproductive rate, and C. capitata has a higher detoxification capacity.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Mikkel-Holger S. Sinding, Shyam Gopalakrishnan, Jazmin Ramos-Madrigal, Marc de Manuel, Vladimir V. Pitulko, Lukas Kuderna, Tatiana R. Feuerborn, Laurent A. F. Frantz, Filipe G. Vieira, Jonas Niemann, Jose A. Samaniego Castruita, Christian Caroe, Emilie U. Andersen-Ranberg, Peter D. Jordan, Elena Y. Pavlova, Pavel A. Nikolskiy, Aleksei K. Kasparov, Varvara V. Ivanova, Eske Willerslev, Pontus Skoglund, Merete Fredholm, Sanne Eline Wennerberg, Mads Peter Heide-Jorgensen, Rune Dietz, Christian Sonne, Morten Meldgaard, Love Dalen, Greger Larson, Bent Petersen, Thomas Sicheritz-Ponten, Lutz Bachmann, Oystein Wiig, Tomas Marques-Bonet, Anders J. Hansen, M. Thomas P. Gilbert
Article
Biotechnology & Applied Microbiology
Javier U. Chicote, Marcos Lopez-Sanchez, Tomas Marques-Bonet, Jose Callizo, Luis A. Perez-Jurado, Antonio Garcia-Espana
Article
Biochemistry & Molecular Biology
Aitor Serres-Armero, Brian W. Davis, Inna S. Povolotskaya, Carlos Morcillo-Suarez, Jocelyn Plassais, David Juan, Elaine A. Ostrander, Tomas Marques-Bonet
Summary: Genomic research on domestic dog breeds explores extreme phenotypic diversity and the impact of copy number variation on breed-specific traits. Through whole genome CNV maps and GWAS, 96 loci with CNV differences across breeds were identified, potentially influencing breed-specific phenotypes and disease susceptibilities.
Article
Evolutionary Biology
Martin Kuhlwilm, Claudia Fontsere, Sojung Han, Marina Alvarez-Estape, Tomas Marques-Bonet
Summary: Modern human contamination is a common issue in ancient DNA studies, and it is also present in studies on great apes. A simple method called HuConTest has been proposed to detect human contamination in short-read sequencing data from different species. This method is particularly useful for more complex samples with smaller amounts of endogenous DNA.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Mara K. N. Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques Bonet, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katharina J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose Victor Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Francoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guojie Zhang, He Zhang, Harris A. Lewin, Stephen Richards
Summary: The Earth BioGenome Project (EBP) is a global international initiative that requires agreement and coordination on standards. To ensure rapid progress towards its goals, EBP has established five technical standards committees and made the current versions of the standards documents available on its website.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Mareike C. Janiak, Felipe E. Silva, Robin M. D. Beck, Dorien de Vries, Lukas F. K. Kuderna, Nicole S. Torosin, Amanda D. Melin, Tomas Marques-Bonet, Ian B. Goodhead, Mariluce Messias, Maria N. F. da Silva, Iracilda Sampaio, Izeni P. Farias, Rogerio Rossi, Fabiano R. de Melo, Joao Valsecchi, Tomas Hrbek, Jean P. Boubli
Summary: Mitochondrial DNA is an important tool in molecular ecology, particularly for species that are difficult to sample. In this study, we assembled 205 new mitochondrial genomes for platyrrhine primates and used them to evaluate the riverine barrier hypothesis. Our results suggest that the effects of riverine barriers vary among different clades and that other evolutionary mechanisms may have played a role in the diversification of platyrrhines.
Article
Biochemistry & Molecular Biology
Irune Ruiz-Gartzia, Esther Lizano, Tomas Marques-Bonet, Joanna L. Kelley
Summary: Wet specimens from museum collections can serve as a new source of DNA for scientific studies, but the overall condition of the specimens is crucial for obtaining high-quality genomic DNA.
MOLECULAR ECOLOGY RESOURCES
(2022)
Editorial Material
Multidisciplinary Sciences
Jasmin Rees, Aida Andres
Article
Genetics & Heredity
Harvinder Pawar, Harrison J. Ostridge, Joshua M. Schmidt, Aida M. Andres
Summary: Chimpanzees have evolved to reduce the pathogenicity of Simian Immunodeficiency Virus (SIV) and become semi-natural hosts. Genes involved in SIV/HIV cell entry and immune response show evidence of positive selection in central and eastern chimpanzees, supporting the hypothesis that the population first infected by SIV experienced strong selective pressure to control the virus.
Review
Genetics & Heredity
David Juan, Gabriel Santpere, Joanna L. Kelley, Omar E. Cornejo, Tomas Marques-Bonet
Summary: Primate genomics is crucial for understanding human evolution and disease. Currently, there is limited data available on genetic diversity and functional genomics of primate species. Efforts are being made to characterize primate genomes, genetic variation, and functional landscapes. These data sets will provide insights into the genetics of primate traits and human diseases. This review discusses existing genome assemblies, genetic variation, and challenges in sample acquisition. It also explores how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will enhance our understanding of primate biology.
NATURE REVIEWS GENETICS
(2023)
Article
Evolutionary Biology
Barbara D. Bitarello, Debora Y. C. Brandt, Diogo Meyer, Aida M. Andres
Summary: Identifying genomic regions and genes under natural selection is important in evolutionary genetics. While methods for detecting positive selection have been established, methods for identifying balancing selection targets are still developing. Balancing selection is recognized as a key driver of diversity within populations, and understanding its role in evolution requires identifying its signatures in genomes.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Marc Palmada-Flores, Joseph D. Orkin, Bettina Haase, Jacquelyn Mountcastle, Mads F. Bertelsen, Olivier Fedrigo, Lukas F. K. Kuderna, Erich D. Jarvis, Tomas Marques-Bonet
Summary: Researchers have generated a new high-quality reference genome assembly for the ring-tailed lemur, which is of great significance for the study of this species and related species.
Article
Biology
Pere Renom, Toni de-Dios, Sergi Civit, Laia Llovera, Alejandro Sanchez-Gracia, Esther Lizano, Juan Carlos Rando, Tomas Marques-Bonet, Gael J. Kergoat, Isaac Casanovas-Vilar, Carles Lalueza-Fox
Summary: Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, with gigantism and dwarfism occurring in originally small and large species respectively. Canariomys bravoi is placed within the African grass rat clade, with island endemic rodents showing faster evolutionary rates compared to non-insular mammals.
Meeting Abstract
Anthropology
Alfie Gleeson, Aida Andres, Aida Gomez-Robles
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY
(2021)
Article
Genetics & Heredity
Gargi Dayama, Weichen Zhou, Javier Prado-Martinez, Tomas Marques-Bonet, Ryan E. Mills
NAR GENOMICS AND BIOINFORMATICS
(2020)