Article
Biochemistry & Molecular Biology
Mahiya Farooq, Asha Nabi, Sehla Khursheed, Bilal A. Padder, T. A. Sofi, Khalid Z. Masoodi, Sumaira Hamid, Mehraj D. Shah
Summary: In this study, the genome of Wilsonomyces carpophilus was analyzed, revealing a complex pathogenicity mechanism and a set of specific proteins. Different isolates of the pathogen showed significant morphological variation, but no significant differences in pathogenicity. This study is important for understanding the host-pathogen interaction mechanism.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Microbiology
Hajar El Hamss, M. N. Maruthi, Hadija M. Ally, Christopher A. Omongo, Hua-Ling Wang, Sharon van Brunschot, John Colvin, Helene Delatte
Summary: The composition and diversity of bacterial endosymbionts in Bemisia tabaci populations infesting cassava crops in Uganda changed over time, with higher bacterial diversity in samples collected in 1997 compared to 2017. This coincided with the occurrence of super-abundant cassava-whitefly populations.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Agricultural Engineering
Manyun Zhang, Weijin Wang, Shahla Hosseini Bai, Shaomin Liu, Chen Chen, Zhihong Xu, Xiaomin Guo
Summary: This study found that appropriate phosphorus fertilization can significantly increase camellia fruit yield, but excessive phosphorus fertilization may have impacts on soil environment and microbial community. It is suggested that future phosphorus fertilization in camellia plantations should consider the comprehensive balance among fruit yield, soil, and microbial properties.
INDUSTRIAL CROPS AND PRODUCTS
(2021)
Article
Biology
Taras K. Oleksyk, Walter W. Wolfsberger, Alexandra M. Weber, Khrystyna Shchubelka, Olga T. Oleksyk, Olga Levchuk, Alla Patrus, Nelya Lazar, Stephanie O. Castro-Marquez, Yaroslava Hasynets, Patricia Boldyzhar, Mikhailo Neymet, Alina Urbanovych, Viktoriya Stakhovska, Kateryna Malyar, Svitlana Chervyakova, Olena Podoroha, Natalia Kovalchuk, Juan L. Rodriguez-Flores, Weichen Zhou, Sarah Medley, Fabia Battistuzzi, Ryan Liu, Yong Hou, Siru Chen, Huanming Yang, Meredith Yeager, Michael Dean, Ryan E. Mills, Volodymyr Smolanka
Summary: The collaborative effort aimed to provide genome-wide data for underrepresented populations in Eastern Europe and cross-validate genome sequences and genotypes acquired by different technologies. Results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces.
Article
Biochemistry & Molecular Biology
Laura J. Taylor, K. Fraser Clark, Dounia Daoud, Michael R. van den Heuvel, Spencer J. Greenwood
Summary: In this study, gene expression changes in stage IV larvae of American lobsters exposed to sublethal concentrations of chlorpyrifos were evaluated. The results showed alterations in genes related to stress response, hypoxia response, moulting, and immunity pathways. The most significant changes in gene expression were observed in lobsters exposed to 0.57 mu g/L chlorpyrifos.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2021)
Article
Biotechnology & Applied Microbiology
Yongli Wang, Xia Li, Congsheng Wang, Lu Gao, Yanfang Wu, Xingnan Ni, Jianzhong Sun, Jianxiong Jiang
Summary: This study identified a large number of non-redundant transcripts in Miscanthus sinensis through analyzing its full-length transcriptome data, providing important support for further research and genetic improvement of the species.
Article
Microbiology
Jie Kong, Jingchun Feng, Liwei Sun, Si Zhang
Summary: Benefiting from high-throughput sequencing, research on microbiota has advanced, but there are limitations in amplicon sequencing. This study evaluates the reproducibility of microbiota in deep-sea sediments and finds variations in technical replicates. Despite these variations, amplicon sequencing is still a powerful tool for characterizing microbial diversity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Abrar Akbar, Sabah Al-Momin, Mohamed Kishk, Abdulaziz Al-Ateeqi, Anisha Shajan, Rita Rahmeh
Summary: Food contamination by pathogens causes health problems and economic losses. The use of chemical food preservatives poses a risk to human health. In order to prolong shelf life and prevent spoilage, the dairy sector is exploring natural preservatives such as ribosomally synthesized peptides, bacteriocins. This study presents the draft genome sequence of Enterococcus faecium strain R9, which produces three bacteriocins isolated from raw camel milk. These bacteriocins have valuable technological properties and can help control Listeria monocytogenes in the food industry.
Article
Plant Sciences
Jiaqi Li, Xuhong Ye, Yuling Zhang, Ji Chen, Na Yu, Hongtao Zou
Summary: The results showed that deep burial of straw can increase soil organic matter, improve soil microbial community, and enhance soil fertility, suggesting that deep placement of straw residues could be an effective practice for sustainable cropping systems in the future.
JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION
(2021)
Editorial Material
Biochemistry & Molecular Biology
Yichen Liu, E. Andrew Bennett, Qiaomei Fu
Summary: Ancient DNA techniques have advanced significantly in the past decade, enabling large-scale research independent of human remains. Future directions include expanding research scope and gaining insights into present-day human health.
Article
Oncology
Zongli Xu, Liang Niu, Jack A. Taylor
Summary: Careful selection of robust data preprocessing methods is crucial for DNA methylation array studies. Our evaluations show that ENmix outperformed other pipelines in minimizing experimental variation, improving data quality, and enhancing study power.
CLINICAL EPIGENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Guoshun Xu, Liwen Zhang, Xiaoqing Liu, Feifei Guan, Yuquan Xu, Haitao Yue, Jin-Qun Huang, Jieyin Chen, Ningfeng Wu, Jian Tian
Summary: This study compares the application of different DNA sequencing methods in soil metagenomics research. The results show that combining long-read and short-read data can increase the length of metagenomic sequences and gene pool, and has significant advantages in studying natural product biosynthetic genes in soil microbiomes.
Article
Biodiversity Conservation
Irina Izaguirre, Fernando Unrein, M. Romina Schiaffino, Enrique Lara, David Singer, Vanessa Balague, Josep M. Gasol, Ramon Massana
Summary: A study in lakes at Hope Bay on the Antarctic Peninsula from 1991 to 2007 found a significant contribution of flagellated Chrysophyceae to phytoplankton communities in the oligotrophic lakes. Additional molecular analyses showed an increase in the diversity of Chrysophyceae in these lakes.
Article
Biodiversity Conservation
Danping Xu, Jiayong Li, Tianhui Zhu, Hongjun Yang, Zhihang Zhuo
Summary: The study focused on transcriptomic analysis of Salix cupularis under drought stress, identifying numerous differentially expressed genes (DEGs) between control and stressed seedlings. Through various analytical methods, the study obtained valuable genetic information related to DEGs, laying a theoretical foundation for future research.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Multidisciplinary Sciences
James A. Fellows Yates, Aida Andrades Valtuena, Ashild J. Vagene, Becky Cribdon, Irina M. Velsko, Maxime Borry, Miriam J. Bravo-Lopez, Antonio Fernandez-Guerra, Eleanor J. Green, Shreya L. Ramachandran, Peter D. Heintzman, Maria A. Spyrou, Alexander Huebner, Abigail S. Gancz, Jessica Hider, Aurora F. Allshouse, Valentina Zaro, Christina Warinner
Summary: AncientMetagenomeDir is a collection of annotated metagenomic sample lists from published studies, providing basic, standardized metadata and accession numbers for interdisciplinary ancient metagenomics research. This collection aims to standardize metadata reporting for future studies in this field.
Article
Biochemistry & Molecular Biology
Charles Christian Riis Hansen, Aki Jarl Laruson, Jacob Agerbo Rasmussen, Jesus Adrian Chimal Ballesteros, Mikkel-Holger S. Sinding, Gunnar T. T. Hallgrimsson, Menja von Schmalensee, Robert A. A. Stefansson, Kristinn Haukur Skarphedinsson, Aili Lage Labansen, Madis Leivits, Christian Sonne, Rune Dietz, Kim Skelmose, David Boertmann, Igor Eulaers, Michael D. D. Martin, Agnar S. S. Helgason, M. Thomas P. Gilbert, Snaebjorn Palsson
Summary: Divergence in white-tailed eagle populations across Europe and the North-East Atlantic is observed, with the greatest differentiation between island and mainland populations. The island populations have a common ancestry from a mainland population and show signs of inbreeding and little genetic variation. Temporal differences also indicate persistent regional populations despite potential admixture. These patterns may have been shaped by historical events such as glaciation, colonization, human expansion, and persecution.
Article
Biochemistry & Molecular Biology
Liam Quinn, Genis Garcia-Erill, Cindy Santander, Anna Bruniche-Olsen, Xiaodong Liu, Mikkel-Holger S. Sinding, Michael P. P. Heaton, Timothy P. L. Smith, Patricia Pecnerova, Laura D. D. Bertola, Kristian Hanghoj, Malthe Sebro Rasmussen, Deon de Jager, Hans R. R. Siegismund, Anders Albrechtsen, Rasmus Heller, Ida Moltke
Summary: The iconic Cape buffalo has experienced population declines attributed to multiple factors, including the rinderpest pandemic and recent human activity. This study analyzed whole genome sequencing data to assess genetic diversity in Cape buffalo populations. The results indicate that recent inbreeding and colonialism-associated events have significantly impacted the genetic diversity of the southernmost populations.
Article
Geography, Physical
Jiao Ma, Boyang Sun, Herve Bocherens, Tao Deng
Summary: This study conducted stable isotope analysis to investigate dietary niche turnover of five equid species in the Linxia Basin, northwestern China, during a critical phase in their evolution. The results revealed that Proboscidipparion pater mainly fed on C3 grasses while Cremohipparion licenti and Sivalhippus platyodus may have been mixed feeders. However, Cremohipparion licenti and Sivalhippus platyodus went extinct due to climatic changes. Additionally, Proboscidipparion sinense showed a stronger grazing preference compared to coexisting Equus eisenmannae.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2023)
Article
Multidisciplinary Sciences
Ryan R. Germain, Shaohong Feng, Lucas Buffan, Carlos P. Carmona, Guangii Chen, Gary R. Graves, Joseph A. Tobias, Carsten Rahbek, Fumin Lei, Jon Fjeldsa, Peter A. Hosner, M. Thomas P. Gilbert, Guojie Zhang, David Nogues-Bravo
Summary: By combining morphological, ecological, and life-history trait data with genomic-based estimates of changing effective population size, this study explores the demographic-based shifts in avian functional diversity over the past million years and under pre-anthropogenic climate warming. The results show that functional diversity remained relatively stable over this period, but significant changes occurred in some key areas of trait space due to changing species abundances. Furthermore, the study identifies the vulnerability of different regions of functional space among taxa, enhancing our understanding of losses of biosphere integrity before human disturbances and contemporary biodiversity loss.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Evolutionary Biology
Andrew D. Foote, Alana Alexander, Lisa T. Ballance, Rochelle Constantine, Barbara Galletti Vernazzani Munoz, Christophe Guinet, Kelly M. Robertson, Mikkel-Holger S. Sinding, Mariano Sironi, Paul Tixier, John Totterdell, Jared R. Towers, Rebecca Wellard, Robert L. Pitman, Phillip A. Morin
Summary: Genomic characterization of type D killer whales reveals the severe inbreeding and low recombination rate in this distinct eco/morphotype. Comparison with historical and modern genomes suggests a shared demographic history among geographically dispersed social groups. This study provides insights into the effects of inbreeding on genetic diversity and population health.
JOURNAL OF HEREDITY
(2023)
Article
Multidisciplinary Sciences
Xupeng Bi, Long Zhou, Jin-Jin Zhang, Shaohong Feng, Mei Hu, David N. Cooper, Jiangwei Lin, Jiali Li, Dong-Dong Wu, Guojie Zhang
Summary: Understanding the mechanisms underlying phenotypic innovation is a key goal of comparative genomic studies. By comparing the genomes of 49 primate species, this study identified many novel lineage-specific accelerated regions (LinARs) associated with brain development or disease in humans, and also revealed detailed maps of LinARs in other primate lineages. Functional experimentation showed that gibbon LinARs could be involved in the developmental regulation of their unique limb structures, while some LinARs in the Colobinae were associated with metabolite detoxification, possibly adaptive to their leaf-eating diet. Overall, this study expands our knowledge of the functional roles of LinARs in primate evolution.
Article
Ecology
Chris Baumann, Shumon T. Hussain, Martina Roblickova, Felix Riede, Marcello A. Mannino, Herve Bocherens
Summary: The authors report isotopic data from ravens from Pavlovian archaeological sites, suggesting that ravens had a similar diet to humans at these sites, indicating an early form of synanthropism. The researchers argue that ravens were attracted to human settlements and were potentially captured for feathers and food. The stable isotope analysis also shows that ravens primarily fed on larger herbivores, aligning with the diet of contemporaneous Gravettian foragers.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Ecology
Ryan R. Germain, Shaohong Feng, Guangji Chen, Gary R. Graves, Joseph A. Tobias, Carsten Rahbek, Fumin Lei, Jon Fjeldsa, Peter A. Hosner, M. Thomas P. Gilbert, Guojie Zhang, David Nogues-Bravo
Summary: Using whole-genome sequence data, this study reconstructs the demographic histories of 263 bird species over the past million years and identifies networks of interacting morphological and life history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. The results highlight the direct and indirect effects of key traits representing dispersal, reproduction, and survival on long-term demographic responses to climate change, thus identifying the traits most likely to influence population responses to ongoing climate warming.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Ecology
Sophie G. G. Habinger, Olivier Chavasseau, Stephane Ducrocq, Yaowalak Chaimanee, Jean-Jacques Jaeger, Chit Sein, Aung Naing Soe, Samuel Stern, Herve Bocherens
Summary: By analyzing the fossil mammal assemblage from Pondaung Fm. in Myanmar, this study investigated the ecological characteristics and found ecological differences and various microhabitats within the mammal community. Most primate taxa were found in both described environments, indicating their strong ecological flexibility.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Geochemistry & Geophysics
Maciej T. Krajcarz, Mateusz Baca, Chris Baumann, Herve Bocherens, Tomasz Goslar, Danijela Popovic, Magdalena Sudol-Procyk, Magdalena Krajcarz
Summary: This paper focuses on the Pleistocene deposits in Perspektywiczna Cave, southern Poland, related to cave hyena. Through direct radiocarbon dating, genetic and stable isotope analyses, the paleobiology of this population is inferred. The findings suggest long inhabitation of the region during early MIS 3, with the latest appearance of a cave hyena north to Carpathians around 34,355-33,725 years ago. The genetic structure of the Perspektywiczna Cave hyenas changed, with two different mtDNA haplogroups present.
Article
Multidisciplinary Sciences
Marta Maria Ciucani, Jazmin Ramos-Madrigal, German Hernandez-Alonso, Alberto Carmagnini, Sabhrina Gita Aninta, Xin Sun, Camilla Hjorth Scharff-Olsen, Liam Thomas Lanigan, Ilaria Fracasso, Cecilie G. Clausen, Jouni Aspi, Ilpo Kojola, Laima Baltrunaite, Linas Balciauskas, Jane Moore, Mikael Akesson, Urmas Saarma, Maris Hindrikson, Pavel Hulva, Barbora Cerna Bolfikova, Carsten Nowak, Raquel Godinho, Steve Smith, Ladislav Paule, Sabina Nowak, Robert W. Myslajek, Sabrina Lo Brutto, Paolo Ciucci, Luigi Boitani, Cristiano Vernesi, Hans K. Stenoien, Oliver Smith, Laurent Frantz, Lorenzo Rossi, Francesco Maria Angelici, Elisabetta Cilli, Mikkel-Holger S. Sinding, M. Thomas P. Gilbert, Shyam Gopalakrishnan
Summary: The Sicilian wolf, which lived in isolation on the Sicily island, became extinct in the 1930s-1960s. Genomic analysis of museum specimens revealed that the Sicilian wolf is closely related to the Italian wolf but also carries genetic ancestry from a lineage of Eneolithic and Bronze Age dogs. The Sicilian wolf had lower nucleotide diversity and higher inbreeding compared to the Italian wolf, indicating the effects of a population in a confined island environment.
Article
Biology
Edward Rice, Antton Alberdi, James Alfieri, Giridhar Athrey, Jennifer Balacco, Philippe Bardou, Heath Blackmon, Mathieu Charles, Hans Cheng, Olivier Fedrigo, Steven Fiddaman, Giulio Formenti, Laurent Frantz, M. Thomas Gilbert, Cari Hearn, Erich Jarvis, Christophe Klopp, Sofia Marcos, Andrew Mason, Deborah Velez-Irizarry, Luohao Xu, Wesley Warren
Summary: This research presents a pangenome model for domestic chickens consisting of thirty assemblies from different breeds and research lines. It demonstrates how this model can be used to catalogue structural variants in modern breeds and unravel complex nested variations. The study shows that aligning short reads from diverse wild and domestic chickens to this pangenome reduces reference bias and allows for accurate genotyping of complex structural variants.
Article
Biochemistry & Molecular Biology
German Hernandez-Alonso, Jazmin Ramos-Madrigal, Hein van Grouw, Marta Maria Ciucani, Emily Louisa Cavill, Mikkel-Holger S. Sinding, Shyam Gopalakrishnan, George Pacheco, M. Thomas P. Gilbert
Summary: This study used whole-genome sequencing data to investigate the population structure, domestication history, and taxonomy of the rock dove Columba livia. The results revealed the basal position of the West African subspecies, gene-flow between the rock dove's sister species, and proposed a model for the rock dove's evolution based on the refugia theory. Additionally, the study identified at least one domestication event in the Levant that gave rise to all analyzed domestic breeds.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Fisheries
Mikkel Skovrind, George Pacheco, Emil Aputsiaq Flindt Christensen, Shyam Gopalakrishnan, Katharina Fietz, Tore Hejl Holm-Hansen, Filipe Garrett Vieira, Marcus Anders Krag, Henrik Carl, M. Thomas P. Gilbert, Morten Tange Olsen, Peter Rask Moller
Summary: Environmental variation can lead to local adaptations in wild species. In the case of European perch, a specialised brackish water variant has developed in the Baltic Sea region. However, little is known about the mechanisms underlying the perch’s adaptation to the Baltic Sea. Through genetic analysis, it was found that brackish water perch show distinct genetic differences compared to freshwater perch, with higher levels of gene flow. Selection analysis suggests that genomic adaptation played a role in the perch’s colonization of the Baltic Sea.
FISHERIES RESEARCH
(2023)