Article
Biochemistry & Molecular Biology
Jia Sheng Chian, Jiaheng Li, San Ming Wang
Summary: PALB2 gene variants disrupt DNA repair and increase the risk of genetic diseases. Our evolutionary analysis of PALB2 variants in humans showed that pathogenic variants mostly originated in recent human history.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Marcelo Hernan Cassini
Summary: This study compares the impacts of native and introduced species on human and natural environments in the United States. Surprisingly, it finds that native species cause significantly more damage than introduced species, particularly in agriculture, property, and health and safety. The differences in impacts on biodiversity and natural ecosystems are minor.
Article
Biotechnology & Applied Microbiology
Saoirse Foley, Anna Vlasova, Marina Marcet-Houben, Toni Gabaldon, Veronica F. Hinman
Summary: This study utilizes phylogenomic approaches to identify conserved genes in echinoderms and suggests that the ancestral genes required to form a phylum may be present across broad taxonomic depths.
Article
Microbiology
Ruizhen Wang, Leiming Dong, Yuequ Chen, Shuai Wang, Liangjian Qu
Summary: This study reported a parasitic fungus, Esteya vermicola, that attacks the pinewood nematode causing pine wilt disease. The study also discovered a previously unidentified lineage of endobacteria in Esteya vermicola, which showed efficient gene expression regulation and energy release capabilities.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Cell Biology
Longjun Wu, J. David Lambert
Summary: Clade-specific genes are common and can arise through gene duplication, de novo evolution, or rapid sequence evolution. They have received less attention but play important roles in traits. Attention to these genes is necessary to complement the focus on conserved regulatory toolkit, and their evolution can be further explored.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Immunology
Pattarasuda Puasri, Wilanee Dechkhajorn, Paron Dekumyoy, Tippayarat Yoonuan, Sumate Ampawong, Onrapak Reamtong, Usa Boonyuen, Surachet Benjathummarak, Yaowapa Maneerat
Summary: This study confirmed that G. spinigerum L3 produces EVs and investigated human gene profiles related to the immune response against the larvae. The results showed significant changes in gene expression after co-culturing with the larvae for 1 and 3 days.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biology
Katelyn Mika, Mirna Marinic, Manvendra Singh, Joanne Muter, Jan Joris Brosens, Vincent J. Lynch
Summary: Human pregnancy differs from other mammals in terms of duration and complications, likely due to unique genes involved in placental invasion, blood vessel growth, and immune system control. Analyzing gene expression in the human endometrium during pregnancy reveals human-specific traits and potential contributions to maternal-fetal communication and immune tolerance. Further research on genes unique to human pregnancy may lead to insights on preventing or treating adverse pregnancy outcomes.
Article
Biology
Stephane Peyregne, Janet Kelso, Benjamin M. Peter, Svante Paeaebo
Summary: After the split from Neandertals and Denisovans, modern humans experienced an unusual number of amino acid substitutions in proteins associated with the spindle apparatus. Some of these substitutions may have been positively selected. The KNL1 gene, previously believed to be specific to modern humans, was also found in some Neandertals, suggesting gene flow between these groups.
Article
Biochemistry & Molecular Biology
Doyeon Ha, Donghyo Kim, Inhae Kim, Youngchul Oh, JungHo Kong, Seong Kyu Han, Sanguk Kim
Summary: By investigating the evolutionary divergence of regulatory relationships between transcription factors and target genes, the study finds that the rewiring of gene regulatory networks contributes to phenotypic discrepancies between humans and mice, which may explain the failure of mouse models to accurately mimic human diseases.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Dylan J. M. Bergen, Qiao Tong, Ankit Shukla, Elis Newham, Jan Zethof, Mischa Lundberg, Rebecca Ryan, Scott E. Youlten, Monika Frysz, Peter I. Croucher, Gert Flik, Rebecca J. Richardson, John P. Kemp, Chrissy L. Hammond, Juriaan R. Metz
Summary: Dermal scales possess a strong osteogenic expression profile similar to bone, enriched in genes favoring collagen matrix growth. Despite differences in developmental processes between scale and endoskeleton, zebrafish scales express a subset of evolutionarily conserved genes relevant to human skeletal diseases.
Article
Plant Sciences
Yixiu Yao, Li Jia, Yuan Cheng, Meiying Ruan, Qingjing Ye, Rongqing Wang, Zhuping Yao, Guozhi Zhou, Jia Liu, Jiahong Yu, Peng Zhang, Yuhe Yin, Weiping Diao, Hongjian Wan
Summary: This study identified and analyzed the members of the CCO gene family in pepper and other plants using bioinformatics methods. A total of 158 CCO genes were found, which were further divided into two groups. Results from RNA-seq and qRT-PCR experiments showed that CaCCO genes in pepper responded to H2O2 and other abiotic stresses, indicating their important roles in plant stress responses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Zhengqing Xie, Zhaoran Tian, Fei Wei, Baoming Tian, Fang Wei, Weiwei Chen, Xiaochun Wei, Gangqiang Cao, Gongyao Shi
Summary: As important transcription factors, GRAS family members are crucial for plant development and stress responses. This study provides insights into the evolutionary origin and conservation of GRAS genes in the Brassica genus. The findings highlight the role of gene duplication and purifying selection in the expansion and maintenance of GRAS genes, and suggest their conserved functions in plant development and stress responses.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Ecology
Nashaiman Pervaiz, Hongen Kang, Yiming Bao, Amir Ali Abbasi
Summary: This study investigated the molecular evolutionary history of a subset of MCPH genes in 48 mammalian species, finding that some of these genes have undergone positive selection in eutherian evolutionary history. However, no human-specific adoptive evolution was detected for any of the MCPH genes analyzed in the study.
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Ecology
Ni A. A. An, Jie Zhang, Fan Mo, Xuke Luan, Lu Tian, Qing Sunny Shen, Xiangshang Li, Chunqiong Li, Fanqi Zhou, Boya Zhang, Mingjun Ji, Jianhuan Qi, Wei-Zhen Zhou, Wanqiu Ding, Jia-Yu Chen, Jia Yu, Li Zhang, Shaokun Shu, Baoyang Hu, Chuan-Yun Li
Summary: Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant. The distinctive U1 elements and RNA splice-related sequences drive the origin of de novo genes from lncRNA loci and distinguish them from lncRNAs. The functional new genes acquire functions along with the achievement of their coding potential.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Plant Sciences
Fan Yang, Jiawei Luo, Wenmeng Guo, Yuxin Zhang, Yunxiao Liu, Ze Yu, Yaqiang Sun, Mingjun Li, Fengwang Ma, Tao Zhao
Summary: This study investigates the origin and evolutionary dynamics of SOT genes in the Rosaceae family by analyzing the synteny relationships among PLT genes in various plant lineages. The findings reveal the lineage-specific and synergistic duplications in Amygdaloideae that contribute to the expansion of SOTs in Rosaceae plants.
Article
Multidisciplinary Sciences
Alexander Capraro, Denis O'Meally, Shafagh A. Waters, Hardip R. Patel, Arthur Georges, Paul D. Waters
SCIENTIFIC REPORTS
(2020)
Article
Genetics & Heredity
Sarah L. Whiteley, Clare E. Holleley, Susan Wagner, James Blackburn, Ira W. Deveson, Jennifer A. Marshall Graves, Arthur Georges
Summary: The study found that early developmental cascades differ between genetically driven and thermally driven females in bearded dragons, but converge to the common outcome of ovaries. Genes proposed as regulators of thermosensitive sex determination play a role in temperature sex reversal. This research greatly advances the understanding of how temperature determines sex.
Article
Virology
Emma F. Harding, Alice G. Russo, Grace J. H. Yan, Paul D. Waters, Peter A. White
Summary: Marsupial viruses, particularly the endogenous viral elements (EVEs), are not as well-studied as their eutherian mammal counterparts, but they could play a crucial role in defending against viral infections. This study identified and characterized 200 viral transcripts from Australian marsupials, showing the presence of EVEs from various viral families. The transcription of these ancient EVEs through small non-coding RNA could potentially provide a defense mechanism against vertically transmitted viral integrations in marsupials.
Article
Multidisciplinary Sciences
Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A. M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
Summary: Life on Earth has evolved from simplicity to complexity, with bacteria and archaea excelling in metabolic diversification and eukaryotes displaying morphological innovation. The Earth BioGenome Project proposes sequencing the genomes of all known eukaryotic species to create a digital library of life, which will help address evolutionary and ecological questions and provide insights into speciation, adaptation, and organismal dependencies within ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Paul D. Waters, Hardip R. Patel, Aurora Ruiz-Herrera, Lucia Alvarez-Gonzalez, Nicholas C. Lister, Oleg Simakov, Tariq Ezaz, Parwinder Kaur, Celine Frere, Frank Gruetzner, Arthur Georges, Jennifer A. Marshall Graves
Summary: The study found that microchromosomes, as elements of an ancient animal genome, are highly conserved in birds and share synteny with certain small chromosomes in the chordate amphioxus. Turtles and squamates have independently lost microchromosomes through fusion events, resulting in different fusion patterns in different lineages. Microchromosomes are spatially separated into a central compartment in cells, showing higher interaction between microchromosomes compared to macrochromosomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Laia Marin-Gual, Laura Gonzalez-Rodelas, Gala Pujol, Covadonga Vara, Marta Martin-Ruiz, Soledad Berrios, Raul Fernandez-Donoso, Andrew Pask, Marilyn B. Renfree, Jesus Page, Paul D. Waters, Aurora Ruiz-Herrera
Summary: The study reveals the features of meiotic cell division in marsupials, particularly the strategies of sex chromosome pairing, recombination, and telomere homeostasis. The researchers found that marsupials have non-canonical meiotic strategies, including alternative mechanisms for controlling telomere length in the paternal parent. These findings provide new insights into the diversity of meiotic strategies in mammals.
Article
Ecology
Aurora Ruiz-Herrera, Paul D. Waters
Summary: Sex-linked inheritance is an exception to Mendel's Laws of Heredity, and this article discusses how the evolution of heteromorphic sex chromosomes, specifically the Y chromosome, has been shaped by the intricacies of the meiotic programme. The presence of pseudoautosomal region (PAR) size, meiotic pairing strategies, and Y-borne executioner genes all play a role in explaining the persistence of Y chromosomes in distantly related mammalian phylogroups.
Article
Multidisciplinary Sciences
Li Hu, Juan Long, Yi Lin, Zhongru Gu, Han Su, Xuemin Dong, Zhenzhen Lin, Qian Xiao, Nyambayar Batbayar, Batbayar Bold, Lucia Deutschova, Sergey Ganusevich, Vasiliy Sokolov, Aleksandr Sokolov, Hardip R. Patel, Paul D. Waters, Jennifer Ann Marshall Graves, Andrew Dixon, Shengkai Pan, Xiangjiang Zhan
Summary: The Qinghai-Tibet Plateau presents extreme temperatures, low oxygen levels, and intense UV radiation. Animals in the plateau have adapted to these conditions, with gene flow from Arctic relatives and non-coding genomic changes playing key roles in their adaptation to hypoxia and UV exposure.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Laia Marin-Gual, Laura Gonzalez-Rodelas, Maria M. Garcias, Lukas Kratochvil, Nicole Valenzuela, Arthur Georges, Paul D. Waters, Aurora Ruiz-Herrera
Summary: This study compares the regulation of meiotic prophase I in reptiles by examining four species. The results show that meiosis progression is highly conserved in reptiles, with telomeres clustering forming the bouquet, promoting homologous pairing and synapsis. Low levels of meiotic double strand breaks were also detected in all taxa, providing new insights into reptile meiosis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Paul D. Waters, Jennifer A. Marshall Graves, Sarah L. Whiteley, Arthur Georges, Aurora Ruiz-Herrera
Summary: The molecular mechanism of temperature-dependent sex determination (TSD) is still unknown, particularly how cells transduce thermal signals to affect gene expression. A new hypothesis called 3D-TSD suggests that the genome can remodel in response to temperature by changing 3D chromatin conformation, potentially rewiring enhancer-promoter interactions to alter key sex-determining genes. This hypothesis can explain both monogenic and multigenic thermolabile sex-determining systems and can be integrated with thermal sensing and transduction to the epigenome.
Article
Cell Biology
Jacqueline Smith, James M. Alfieri, Nick Anthony, Peter Arensburger, Giridhar N. Athrey, Jennifer Balacco, Adam Balic, Philippe Bardou, Paul Barela, Yves Bigot, Heath Blackmon, Pavel M. Borodin, Rachel Carroll, Meya C. Casono, Mathieu Charles, Hans Cheng, Maddie Chiodi, Lacey Cigan, Lyndon M. Coghill, Richard Crooijmans, Neelabja Das, Sean Davey, Asya Davidian, Fabien Degalez, Jack M. Dekkers, Martijn Derks, Abigail B. Diack, Appolinaire Djikeng, Yvonne Drechsler, Alexander Dyomin, Olivier Fedrigo, Steven R. Fiddaman, Giulio Formenti, Laurent A. F. Frantz, Janet E. Fulton, Elena Gaginskaya, Svetlana Galkina, Rodrigo A. Gallardo, Johannes Geibel, Almas Gheyas, Cyrill John P. Godinez, Ashton Goodell, Jennifer A. M. Graves, Daren K. Griffin, Bettina Haase, Jian-Lin Han, Olivier Hanotte, Lindsay J. Henderson, Zhuo-Cheng Hou, Kerstin Howe, Lan Huynh, Evans Ilatsia, Erich Jarvis, Sarah M. Johnson, Jim Kaufman, Terra Kelly, Steve Kemp, Colin Kern, Jacob H. Keroack, Christophe Klopp, Sandrine Lagarrigue, Susan J. Lamont, Margaret Lange, Anika Lanke, Denis M. Larkin, Greger Larson, John King N. Layos, Ophelie Lebrasseur, Lyubov P. Malinovskaya, Rebecca J. Martin, Maria Luisa Martin Cerezo, Andrew S. Mason, Fiona M. McCarthy, Michael J. McGrew, Jacquelyn Mountcastle, Christine Kamidi Muhonja, William Muir, Kevin Muret, Terence Murphy, Ismael Ng'ang'a, Masahide Nishibori, Rebecca E. O'Connor, Moses Ogugo, Ron Okimoto, Ochieng Ouko, Hardip R. Patel, Francesco Perini, Maria Ines Pigozzi, Krista C. Potter, Peter D. Price, Christian Reimer, Edward S. Rice, Nicolas Rocos, Thea F. Rogers, Perot Saelao, Jens Schauer, Robert Schnabel, Valerie Schneider, Henner Simianer, Adrian Smith, Mark P. Stevens, Kyle Stiers, Christian Keambou Tiambo, Michele Tixier-Boichard, Anna A. Torgasheva, Alan Tracey, Clive A. Tregaskes, Lonneke Vervelde, Ying Wang, Wesley C. Warren, Paul D. Waters, David Webb, Steffen Weigend, Anna Wolc, Alison E. Wright, Dominic Wright, Zhou Wu, Masahito Yamagata, Chentao Yang, Zhong-Tao Yin, Michelle C. Young, Guojie Zhang, Bingru Zhao, Huaijun Zhou
CYTOGENETIC AND GENOME RESEARCH
(2023)
Article
Cell Biology
Lucia Alvarez-Gonzalez, Cristina Arias-Sarda, Laia Montes-Espuna, Laia Marin-Gual, Covadonga Vara, Nicholas C. Lister, Yasmina Cuartero, Francisca Garcia, Janine Deakin, Marilyn B. Renfree, Terence J. Robinson, Marc A. Marti-Renom, Paul D. Waters, Marta Farre, Aurora Ruiz-Herrera
Summary: This article describes the principles of studying the similarities and differences in genomic interactions between species and presents the patterns of 3D genome folding in vertebrates and lineage-specific patterns of genome reshuffling. By identifying different patterns of chromosome folding, reconstructing ancestral genomes, detecting lineage-specific chromosome rearrangements, and analyzing the dynamics of genome reshuffling, the article explores the interplay between chromatin higher-order organization and therian genome evolution, and proposes a hypothesis to explain the influence of chromatin folding on evolutionary patterns of genome reshuffling.
Article
Biochemistry & Molecular Biology
Nicholas C. Lister, Ashley M. Milton, Benjamin J. Hanrahan, Paul D. Waters
Summary: There are currently nine known examples of transmissible cancers in nature, observed in domestic dog, Tasmanian devil, and six bivalve species. Despite the recognized importance of ncRNAs in these tumours, there have been no studies on their role in this context. The use of CRISPR/Cas system is proposed for studying the RNA biology of transmissible cancers and exploring the role of ncRNAs in the immortality and immune evasion ability of these tumours.
Review
Developmental Biology
Michelle C. Maier, Molly-Rose A. McInerney, Jennifer A. Marshall Graves, Fadi J. Charchar
Summary: Noncoding RNAs on the Y chromosome play a crucial role in sex differentiation, gene expression regulation, and cellular function. They are gradually being recognized for their impact not only on sex development but also on other important clinical phenotypes in humans.
SEXUAL DEVELOPMENT
(2021)
Meeting Abstract
Zoology
H. J. F. Eyck, R. R. Sarma, O. L. Crino, P. D. Waters, M. Crossland, R. Shine, L. A. Rollins
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2020)