Article
Multidisciplinary Sciences
Yuan Yuan, Yaolei Zhang, Peijun Zhang, Chang Liu, Jiahao Wang, Haiyu Gao, A. Rus Hoelzel, Inge Seim, Meiqi Lv, Mingli Lin, Lijun Dong, Haoyang Gao, Zixin Yang, Francesco Caruso, Wenzhi Lin, Rute R. da Fonseca, Ding Wang, Xianyan Wang, Marianne H. Rasmussen, Mingming Liu, Jinsong Zheng, Liyuan Zhao, Paula F. Campos, Hui Kang, Maria Iversen, Yue Song, Xinyu Guo, Jiao Guo, Yating Qin, Shanshan Pan, Qiwu Xu, Lingfeng Meng, A. Yunga, Shanshan Liu, Simon Ming-Yuen Lee, Xin Liu, Xun Xu, Huanming Yang, Guangyi Fan, Kun Wang, Songhai Li
Summary: The study generated high-quality genome assemblies of 17 marine mammals, revealing unique and convergent genomic variations associated with the transition to aquatic life in marine mammal lineages. The research advances understanding of the timing, pattern, and molecular changes associated with the evolution of mammalian lineages adapting to aquatic life.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Pedro G. Nachtigall, Luiz A. Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Summary: Despite the differences in heart development among different vertebrate groups, both conserved and group-specific miRNAs play crucial roles in modulating the core and peripheral genes of heart GRNs. Conserved miRNAs have higher expression levels and more targets, while group-specific miRNAs have lower expression levels and fewer targets.
Article
Biochemistry & Molecular Biology
Valentina Rudenko, Eugene Korotkov
Summary: The study presents a method called MSHDTR for searching highly divergent tandem repeats in protein sequences, which is able to detect repeats that significantly evolved over time. By applying this method to the Swiss-Prot database, over 15,000 TR-containing amino acid sequences were identified and classified, and these results have been made accessible through a database accessible over the WWW.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Mohamed Kamel, Kristina Kastano, Pablo Mier, Miguel A. Andrade-Navarro
Summary: This study presents a new web server REP2 for analyzing tandem repeats (TRs) in protein sequences, providing precomputed analyses for 78 UniProt reference proteomes. The data can be used for studying the evolution of TRs using comparative genomics.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Nikolaos Stamidis, Jan Jakub Zylicz
Summary: The failure to repress transcription of repetitive genomic elements can lead to genome instability and human diseases. Multiple parallel mechanisms cooperate to ensure repression and heterochromatinization of these elements, especially during germline development and early embryogenesis. Recent evidence suggests a role of RNA methylation, piRNAs, and other localized satellite RNAs in targeting repressive histone marks and DNA methylation to repetitive elements in mammals.
Article
Genetics & Heredity
Yin Sun, Peishan Zou, Nannan Jiang, Yifu Fang, Guofeng Liu
Summary: This study sequenced the complete chloroplast genomes of six Paphiopedilum species and identified ten highly variable regions that could serve as potential DNA barcodes or phylogenetic markers. The results also demonstrated that chloroplast genome sequencing is an effective means in resolving the complex relationship in Paphiopedilum.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Kyung-Ah Kim, Kyeong-Sik Cheon
Summary: This study aimed to assemble and annotate the chloroplast genome of Adenophora racemosa, an endemic species in Korea, and compare it with genomes of related species. The analysis revealed differences in gene order and nucleotide diversity between A. racemosa and other congeners.
Article
Biochemistry & Molecular Biology
Chun-Hong Nie, Na-An Zhang, Yu-Long Chen, Zhen-Xia Chen, Gui-Ying Wang, Qing Li, Ze-Xia Gao
Summary: Skeletogenesis is a complex process that requires rigorous control at multiple levels during osteogenesis. By constructing a skeletogenesis database, it was found that over 55% of genes are conserved in the six species, with 181 specific genes identified in the human genome.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2021)
Article
Multidisciplinary Sciences
Shenghui Li, Ruochun Guo, Yue Zhang, Peng Li, Fang Chen, Xifan Wang, Jing Li, Zhuye Jie, Qingbo Lv, Hao Jin, Guangyang Wang, Qiulong Yan
Summary: This study analyzed the viral genomes in the human oral cavity and created the Oral Virus Database (OVD), which expands our knowledge of the phylogenetic diversity and host specificity of oral viruses. It also reveals differences in viral diversity and composition related to oral cavity habitats and host properties.
Article
Multidisciplinary Sciences
Shenghui Li, Ruochun Guo, Yue Zhang, Peng Li, Fang Chen, Xifan Wang, Jing Li, Zhuye Jie, Qingbo Lv, Hao Jin, Guangyang Wang, Qiulong Yan
Summary: The human oral cavity is an important reservoir for many unexplored viruses that play a crucial role in maintaining oral health and microbial balance. By analyzing a large dataset of oral metagenomes, the study reveals a wide range of diversity and host specificity in oral viruses, as well as variations in viral composition among different oral habitats.
Article
Biology
Diyan Li, Mengnan He, Qianzi Tang, Shilin Tian, Jiaman Zhang, Yan Li, Danyang Wang, Long Jin, Chunyou Ning, Wei Zhu, Silu Hu, Keren Long, Jideng Ma, Jing Liu, Zhihua Zhang, Mingzhou Li
Summary: The three-dimensional architecture of the genome plays a crucial role in gene expression regulation and conservation across species. This study compares the 3D genomes of fish, chickens, and 10 mammalian species, and reveals that genome size and chromosome length influence the higher hierarchical organization of the genome, while local transcriptional availability is selected through vertebrate evolution. Additionally, conservation of topologically associating domains is associated with modularity of expression profiles, and LINE and SINE transposable elements contribute to heterochromatin and euchromatin organization during genome evolution.
Article
Biochemistry & Molecular Biology
Maxime Policarpo, Julien Fumey, Philippe Lafargeas, Delphine Naquin, Claude Thermes, Magali Naville, Corentin Dechaud, Jean-Nicolas Volff, Cedric Cabau, Christophe Klopp, Peter Rask Moller, Louis Bernatchez, Erik Garcia-Machado, Sylvie Retaux, Didier Casane
Summary: The study found that in cavefishes, the loss of eye-specific genes and nonvisual opsin genes is the largest, and the pseudogenization of eye-specific genes is affected by the level of eye regression, time, and genome ploidy.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Charlotte Tumescheit, Andrew E. Firth, Katherine Brown
Summary: Multiple sequence alignments (MSAs) are critical for biological investigation, but they are often affected by incomplete and divergent sequences. To solve this issue, we have developed a comprehensive and user-friendly MSA trimming tool that offers various visualisation options, allowing users to intervene and understand the removed content.
Article
Cell Biology
Xuanjing Li, Pengcheng Wang, Qi Pan, Gaoming Liu, Weiqiang Liu, Olatunde Omotoso, Juan Du, Zihao Li, Yang Yu, Yun Huang, Pingfen Zhu, Meng Li, Xuming Zhou
Summary: This study generated a high-quality genome of the Asian elephant and identified expanded gene families related to tumor-associated pathways. Comparative genomic analysis revealed genes with positive selection in long-lived mammals, which enhanced the inhibition of tumor cell migration.
Article
Pharmacology & Pharmacy
Mingkun Guo, Shihai Li, Yifan Zhou, Menglong Li, Zhining Wen
Summary: Long-read technologies have advantages in detecting structural variations, but further exploration and comparison are needed. Three commonly used long-read SV detection pipelines show lower performance in tandem repeat regions. Comprehensive evaluation results can assist in choosing appropriate pipelines and complement the research of rare diseases.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Ecology
Benedikt Holtmann, Carlos E. Lara, Eduardo S. A. Santos, Joanne E. Gillum, Neil J. Gemmell, Shinichi Nakagawa
Summary: This study investigated the influence of individual behavioral traits on social relationships and reproductive success in a wild population of dunnocks. The findings suggested that in polygamous groups, cooperative breeding males exhibited differences in behavior, and there was evidence of assortative mating based on behavioral traits for alpha males and females. Additionally, male provisioning significantly impacted reproductive success for both sexes, while female provisioning only correlated with her own reproductive output.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2022)
Article
Evolutionary Biology
Allison K. Miller, Nataliya Timoshevskaya, Jeramiah J. Smith, Joanne Gillum, Saeed Sharif, Shannon Clarke, Cindy Baker, Jane Kitson, Neil J. Gemmell, Alana Alexander
Summary: This study provides a comprehensive analysis of gene flow and population relationships in pouched lamprey in New Zealand, revealing a relatively uniform population structure with ongoing gene flow or recent shared ancestry. The findings can assist managers in population management and conservation measures, and demonstrate the utility of genetic tools in acquiring information about elusive species.
JOURNAL OF HEREDITY
(2022)
Article
Immunology
Kimberly A. Morrissey, Jordan M. Sampson, Megan Rivera, Lijing Bu, Victoria L. Hansen, Neil J. Gemmell, Michael G. Gardner, Terry Bertozzi, Robert D. Miller
Summary: This study investigated the loss of gamma delta T cells in squamate reptiles and found that it is likely caused by large genomic deletions. The tuatara, a close relative of squamates, was identified as the only squamate reptile that retains gamma delta T cells.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Haoyu Cheng, Erich D. Jarvis, Olivier Fedrigo, Klaus-Peter Koepfli, Lara Urban, Neil J. Gemmell, Heng Li
Summary: This paper presents an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to achieve haplotype-resolved genome assembly from single samples without the need for parent sequencing. The algorithm outperforms existing single-sample assembly pipelines and produces assemblies of similar quality to the best pedigree-based assemblies when applied to human and other vertebrate samples.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jean-Francois Doherty, Upendra R. Bhattarai, Sara Ferreira, Robert Poulin, Neil J. Gemmell, Eddy J. Dowle
Summary: Almost every animal trait is strongly associated with parasitic infection or potential exposure to parasites. Accurately determining the status and severity of endoparasitic infection without killing and dissecting the host is a major challenge researchers face. This study demonstrates a noninvasive and minimally stressful method for detecting endoparasitic infection with greater accuracy than dissection alone, improving protocols for live animal studies.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Gert-Jan Jeunen, Eddy Dowle, Jonika Edgecombe, Ulla von Ammon, Neil J. Gemmell, Hugh Cross
Summary: The measurement of biodiversity plays a vital role in life science research. However, the reliability and accuracy of taxonomic assignment in metabarcoding sequencing data greatly depend on the quality and completeness of reference databases. To address this issue, researchers have developed crabs, a software package that allows the creation of curated reference databases for metabarcoding studies.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Gert-Jan Jeunen, Jasmine S. Cane, Sara Ferreira, Francesca Strano, Ulla von Ammon, Hugh Cross, Robert Day, Sean Hesseltine, Kaleb Ellis, Lara Urban, Niall Pearson, Pamela Olmedo-Rojas, Anya Kardailsky, Neil J. Gemmell, Miles Lamare
Summary: Aquatic environmental DNA (eDNA) surveys are revolutionizing marine ecosystem monitoring, but the time-consuming active filtration step remains a bottleneck. This study investigated the similarities and differences between eDNA signals obtained from various sources, including water, filter-feeding organisms, and sponge material. The results showed that vertebrate eDNA signals from water and sponge samples were highly concordant, highlighting the potential of using marine sponges as an additional tool for eDNA-based biodiversity surveys. Caution should be taken to minimize the impact on marine communities during eDNA sampling.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Fisheries
S. Muncaster, A. Goikoetxea, P. M. Lokman, C. E. Moraes, E. L. Damsteegt, J. Edgecombe, N. J. Gemmell, E. V. Todd
Summary: Socially induced sex change is regulated by a combination of genes and epigenetic factors that control sex differentiation and cell fate. The molecular basis for this transformation is still largely unknown. Recent research suggests that both epigenetic effects and genes involved in cell fate are important drivers of sex change.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2023)
Article
Fisheries
Clare I. M. Adams, Gert-Jan Jeunen, Hugh Cross, Helen R. Taylor, Antoine Bagnaro, Kim Currie, Chris Hepburn, Neil J. Gemmell, Lara Urban, Federico Baltar, Michael Stat, Michael Bunce, Michael Knapp
Summary: In response to climate change, efficient monitoring methods are needed for rapidly shifting biodiversity patterns in the oceans. Environmental DNA (eDNA) metabarcoding has emerged as a cost-effective solution. Using eDNA, we detected four community types across a transect in the Southern Hemisphere and found that diversity patterns were mainly driven by planktonic organisms. This technique lays the foundations for multi-trophic environmental monitoring efforts.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Allison K. Miller, Cara L. Brosnahan, Anjali Pande, Cindy F. Baker, Jemma L. Geoghegan, Jane Kitson, Neil J. Gemmell, Edwina J. Dowle
Summary: Infectious diseases have a significant impact on various organisms, and understanding the interactions between hosts and pathogens is crucial for their conservation and management. The use of genomic approaches has made it easier to obtain this knowledge quickly, however, many species still face challenges in accessing appropriate samples and data. Archival materials, such as formalin-fixed paraffin-embedded tissue samples, may provide a valuable resource for studying pathogen emergence and host responses over long periods of time.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Zoology
Kaj Kamstra, Chloe van der Burg, Haylee M. Quertermous, Simon Muncaster, Erica V. Todd, Christine L. Jasoni, Culum Brown, Neil J. Gemmell
Summary: For most vertebrates, sexual fate is genetically determined and remains fixed throughout life. However, for some teleost fishes sex is more plastic. Significant progress has been made in characterising the cellular and molecular processes that underpin gonadal sex change. The brain-mediated mechanisms that underlie and initiate this transformation, however, remain poorly understood.
NEW ZEALAND JOURNAL OF ZOOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Andrew T. M. Bagshaw, Neil J. Gemmell
Summary: In recent years, scientists have shifted their focus from studying the relationships between adjacent nucleotides to exploring the larger scale structure of DNA. A little-known technique called non-denaturing bisulfite modification of genomic DNA in conjunction with high-throughput sequencing has provided valuable insights. This technique has revealed a gradient in reactivity that increases towards the 5' end of poly-dC:dG mononucleotide repeats, suggesting the presence of positive-roll bending not predicted by existing models. Furthermore, these repeats are enriched at positions relative to the nucleosome dyad that bend towards the major groove, providing important information about DNA packaging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Nataliya Timoshevskaya, Kaan Eskut, Vladimir A. Timoshevskiy, Sofia M. C. Robb, Carson Holt, Jon E. Hess, Hugo J. Parker, Cindy F. Baker, Allison K. Miller, Cody Saraceno, Mark Yandell, Robb Krumlauf, Shawn R. Narum, Ralph T. Lampman, Neil J. Gemmell, Jacquelyn Mountcastle, Bettina Haase, Jennifer R. Balacco, Giulio Formenti, Sarah Pelan, Ying Sims, Kerstin Howe, Olivier Fedrigo, Erich D. Jarvis, Jeramiah J. Smith
Summary: Programmed DNA loss is a gene silencing mechanism found in various vertebrate and nonvertebrate lineages. The evolution of somatically eliminated sequences in these species has been difficult to reconstruct due to repetitive and duplicated sequences. However, an improved assembly of the sea lamprey genome has enabled analysis that sheds light on the recruitment of genes to the germline-specific fraction and reveals the roles of segmental duplication and positive selection in the long-term evolution of germline-specific chromosomes.
Meeting Abstract
Zoology
K. A. Morrissey, J. Samson, M. Rivera, L. Bu, V. L. Hansen, N. J. Gemmell, M. G. Gardner, T. Bertozzi, R. D. Miller
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anna C. Clark, Rey Edison, Kevin Esvelt, Sebastian Kamau, Ludovic Dutoit, Jackson Champer, Samuel E. Champer, Philipp W. Messer, Alana Alexander, Neil J. Gemmell
Summary: This manuscript introduces a framework for identifying and evaluating target genes based on biological gene function, gene expression, and results from mouse knockout models. The framework identifies 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other genetic pest control technologies.
MOLECULAR ECOLOGY RESOURCES
(2023)