Article
Biochemistry & Molecular Biology
Evelien de Greef, Anthony L. Einfeldt, Patrick J. O. Miller, Steven H. Ferguson, Colin J. Garroway, Kyle J. Lefort, Ian G. Paterson, Paul Bentzen, Laura J. Feyrer
Summary: This study provides valuable insights into the genetic structure, demographic history, and adaptations of the northern bottlenose whale. The presence of genetic subdivision and evidence of inbreeding highlight the vulnerability of the endangered Scotian Shelf population. The decline in effective population size poses risks to genetic diversity, emphasizing the importance of protecting habitat and promoting gene flow.
Article
Multidisciplinary Sciences
Jedediah F. Brodie, Sara Williams, Brittany Garner
Summary: Biodiversity is declining globally, primarily driven by habitat loss and harvest activities. Herbivores and frugivores are particularly vulnerable to declines from hunting and habitat loss, with significant implications for plant communities and nutrient cycling. While globally phylogenetically unique species do not have an elevated risk of decline, in certain areas they are more likely to be threatened.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Luyao Wang, Jin Han, Kening Lu, Menglin Li, Mengtao Gao, Zeyi Cao, Ting Zhao, Xue Chen, Xiaoyuan Tao, Quanjia Chen, Xueying Guan
Summary: An evolutionary model using diploid and allotetraploid cotton species found that 80% of non-coding transcripts in allotetraploid cotton are uniquely activated compared to its diploid ancestors. The function of activated lncRNAs in allotetraploid cotton is largely unknown. Transcriptome analysis revealed that lncRNA expression is preferentially associated with flanking PCGs, and a low-throughput functional screening identified lncRNAs related to plant height and stress tolerance. The study suggests that lncRNAs are more active under abiotic stresses, such as temperature stress, and may play a cis-regulatory role in response to environmental stimuli.
Article
Biochemistry & Molecular Biology
Emily Humble, Jane Hosegood, Gary Carvalho, Mark de Bruyn, Simon Creer, Guy M. W. Stevens, Amelia Armstrong, Ramon Bonfil, Mark Deakos, Daniel Fernando, Niv Froman, Lauren R. Peel, Stephen Pollett, Alessandro Ponzo, Joshua D. Stewart, Sabine Wintner, Rob Ogden
Summary: Understanding population connectivity and genetic diversity is crucial for conservation, but it remains challenging for globally threatened marine megafauna. This study uses a comparative framework to investigate the genetic differentiation and diversity of manta rays, revealing higher connectivity and heterozygosity in oceanic manta rays. The findings also emphasize the potential impact of fisheries on population dynamics.
Editorial Material
Agriculture, Dairy & Animal Science
J. Kor Oldenbroek
Summary: The conservation of genetic diversity is a costly process, but genomic information is now essential for making choices in conservation. Genomics can accurately measure genetic distances and detect valuable rare alleles and haplotypes, aiding in the conservation of genomic regions.
Article
Biochemistry & Molecular Biology
Ellie E. Armstrong, Anubhab Khan, Ryan W. Taylor, Alexandre Gouy, Gili Greenbaum, Alexandre Thiery, Jonathan T. Kang, Sergio A. Redondo, Stefan Prost, Gregory Barsh, Christopher Kaelin, Sameer Phalke, Anup Chugani, Martin Gilbert, Dale Miquelle, Arun Zachariah, Udayan Borthakur, Anuradha Reddy, Edward Louis, Oliver A. Ryder, Yadvendradev Jhala, Dmitri Petrov, Laurent Excoffier, Elizabeth Hadly, Uma Ramakrishnan
Summary: Species conservation can benefit from understanding evolutionary and genetic history. Tigers, especially Indian tigers with high genomic diversity, may experience recent inbreeding events due to connectivity loss in fragmented habitats. Demographic models suggest subspecies divergence within the last 20,000 years, with Amur and Sumatran tigers showing different patterns of selection for metabolic and body size regulation genes. Further investigation on local adaptation is recommended prior to genetic rescue efforts.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Aurelie Labarre, David Lopez-Escard, Francisco Latorre, Guy Leonard, Francois Bucchini, Aleix Obiol, Corinne Cruaud, Michael E. Sieracki, Olivier Jaillon, Patrick Wincker, Klaas Vandepoele, Ramiro Logares, Ramon Massana
Summary: The study utilized single-cell genomics to analyze the genomes of 15 MAST species from marine surface plankton, revealing their potential for phagocytosis and ability to thrive in the photic ocean with the presence of rhodopsin genes. The complexity of phagocytosis machinery in microbial eukaryotes was highlighted, contrasting with the well-defined set of genes for photosynthesis, providing essential insights into the ecophysiology of uncultured species and the function of rhodopsins in stramenopiles.
Article
Food Science & Technology
Lijun You, Ruirui Lv, Hao Jin, Teng Ma, Zhixin Zhao, Lai-Yu Kwok, Zhihong Sun
Summary: The study conducted a comparative genomics analysis of 384 L. rhamnosus genomes, revealing a large and open pan-genome with a core-gene phylogenetic tree containing five branches, showing a random distribution of dairy and gut-associated isolates. Gut-associated isolates exhibited more metabolic pathway and carbohydrate-active enzyme genes. Intra-species diversification was observed among cheese-originated isolates, with significant differences in metabolism-related genes across clades.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Food Science & Technology
Xin Su, Lixia Zhao, Qin Liu, Weicheng Li, Bilige Menghe, Wenjun Liu
Summary: In this study, Leuconostoc mesenteroides was analyzed by comparative genomics, revealing its genomic characteristics and population genetic diversity in different environments. The results showed that Leu. mesenteroides has great genomic plasticity and high adaptability, providing a solid genetic foundation for its subsequent development and use.
Article
Biochemistry & Molecular Biology
Michael Westbury, Diana Le Duc, David A. Duchene, Arunkumar Krishnan, Stefan Prost, Sereina Rutschmann, Jose H. Grau, Love Dalen, Alexandra Weyrich, Karin Noren, Lars Werdelin, Fredrik Dalerum, Torsten Schoeneberg, Michael Hofreiter
Summary: During the Miocene, the highly diverse family of Carnivora, Hyaenidae, has been reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage was found, with high levels of genetic diversity and stable population sizes seen in the spotted hyena and aardwolf.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Plant Sciences
Sariel Huebner
Summary: Graph-based pangenomes can provide a comprehensive platform to study diversity in populations or species, but still face challenges in species with large complex genomes. However, with advancing technology, the graph-pangenome is expected to become a central platform in genomics studies and applications.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Anne-Christine Monnet, Kevin Cilleros, Frederic Medail, Marwan Cheikh Albassatneh, Juan Arroyo, Gianluigi Bacchetta, Francesca Bagnoli, Zoltan Barina, Manuel Cartereau, Nicolas Casajus, Panayotis Dimopoulos, Gianniantonio Domina, Aggeliki Doxa, Marcial Escudero, Bruno Fady, Arndt Hampe, Vlado Matevski, Stephen Misfud, Toni Nikolic, Daniel Pavon, Anne Roig, Estefania Santos Barea, Ilaria Spanu, Arne Strid, Giovanni Giuseppe Vendramin, Agathe Leriche
Summary: Trees are crucial in ecosystems worldwide, but the biodiversity of Mediterranean trees is not well understood. The WOODIV database provides reliable data on occurrences, functional traits, and genetic information for 210 Euro-Mediterranean tree species, benefiting research in conservation, biogeography, and community ecology.
Review
Genetics & Heredity
Pushpendra Kumar Gupta
Summary: The Earth Biogenome Project aims to provide high-quality genome sequences for all named eukaryote species. The project is divided into three phases, with the goal of sequencing all species' genomes by 2030. This article briefly discusses the current status, future plans, and challenges of the project.
TRENDS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Gabriel Damasco, Christopher Baraloto, Alberto Vicentini, Douglas C. Daly, Bruce G. Baldwin, Paul V. A. Fine
Summary: This study reveals that the commonly found species Protium heptaphyllum in the Amazon may actually consist of eight separately evolving lineages, each adapted to different geographic and climate conditions. Some of the newly discovered species are rare and facing rapid deforestation in their habitats, emphasizing the urgent need for improved sampling and species discovery methods to avoid oversimplifying assumptions regarding diversity and rarity in the tropics.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Marvin Choquet, Felix Lenner, Arianna Cocco, Gaelle Toullec, Erwan Corre, Jean-Yves Toullec, Andreas Wallberg
Summary: This study used comparative genomics to investigate the genetic variation and adaptation potential of 20 krill species collected from different oceans. The results showed that Antarctic krill species had lower levels of genetic variation and evolutionary rates, indicating a potentially lower adaptive potential to rapid climate change. Additionally, the study identified several candidate genes associated with adaptive evolution in Antarctic krill.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Qichao Chai, Xiaoguang Shang, Shuang Wu, Guozhong Zhu, Chaoze Cheng, Caiping Cai, Xinyu Wang, Wangzhen Guo
Article
Biotechnology & Applied Microbiology
Guozhong Zhu, Weixi Li, Feng Zhang, Wangzhen Guo
Article
Biochemistry & Molecular Biology
Erli Niu, Shuai Fang, Xiaoguang Shang, Wangzhen Guo
MOLECULAR GENETICS AND GENOMICS
(2018)
Article
Biotechnology & Applied Microbiology
Jun Xu, Xinyu Wang, Yongqing Li, Jianguo Zeng, Guilin Wang, Chaoyang Deng, Wangzhen Guo
PLANT BIOTECHNOLOGY JOURNAL
(2018)
Article
Biotechnology & Applied Microbiology
Guilin Wang, Jun Xu, Lechen Li, Zhan Guo, Qingxin Si, Guozhong Zhu, Xinyu Wang, Wangzhen Guo
PLANT BIOTECHNOLOGY JOURNAL
(2020)
Article
Biochemistry & Molecular Biology
Xiaoguang Shang, Lijie Zhu, Yujia Duan, Wangzhen Guo
MOLECULAR GENETICS AND GENOMICS
(2020)
Article
Plant Sciences
Xiujuan Su, Guozhong Zhu, Xiaohui Song, Haijiang Xu, Weixi Li, Xinzhu Ning, Quanjia Chen, Wangzhen Guo
Article
Plant Sciences
Weixi Li, Xinyue Mi, Xuanxiang Jin, Daiwei Zhang, Guozhong Zhu, Xiaoguang Shang, Dayong Zhang, Wangzhen Guo
Summary: By analyzing the transcriptional changes and co-expression analysis of cotton root tissues under abiotic and biotic stress conditions, this study identified common stress-responsive genes and stress metabolism pathways. Thiamine metabolism was found to be an important intersection between abiotic and biotic stresses, and exogenous thiamine application enhanced stress tolerance in cotton by increasing calcium signal transduction and activating downstream stress-responsive genes.
Article
Plant Sciences
Guilin Wang, Xinyu Wang, Jian Song, Haitang Wang, Chaofeng Ruan, Wenshu Zhang, Zhan Guo, Weixi Li, Wangzhen Guo
Summary: The plasma membrane is a key battlefield between plants and attacking microbes. Necrosis-and-ethylene-inducing peptide 1 (NLP)-like proteins, produced by bacterial, fungal, and oomycete species, can target and damage lipid membranes causing cell death. In this study, it was discovered that cotton produces an enzyme called lysophospholipase (GhLPL2) which blocks the virulence of a NLP produced by the pathogen Verticillium dahliae. This discovery highlights the potential of lysophospholipase overexpression as a strategy for breeding crops with high resistance to NLP-producing pathogens.
Article
Plant Sciences
Yujia Duan, Xiaoguang Shang, Qingfei He, Lijie Zhu, Weixi Li, Xiaohui Song, Wangzhen Guo
Summary: This study reveals that a lipid transfer protein, GhLTP4, promotes fiber cell elongation in cotton by increasing ceramides content and activating auxin-responsive pathways. A transcription factor, GhbHLH105, is identified to be involved in the expression of GhLTP4. These findings provide insights into the complex interactions between lipids and auxin-signaling pathways to promote plant cell elongation.
Article
Plant Sciences
Xuanxiang Jin, Qichao Chai, Chuchu Liu, Xin Niu, Weixi Li, Xiaoguang Shang, Aixing Gu, Dayong Zhang, Wangzhen Guo
Summary: This study identified a novel pathway mediated by GhNAC4 that promotes secondary cell wall biosynthesis, enhances secondary wall development, and regulates the expression of ribosomal protein-encoding genes, ultimately enhancing drought tolerance in cotton.
Article
Plant Sciences
Jun Xu, Guilin Wang, Jing Wang, Yongqing Li, Liangliang Tian, Xinyu Wang, Wangzhen Guo
Article
Biotechnology & Applied Microbiology
Caiping Cai, Guozhong Zhu, Tianzhen Zhang, Wangzhen Guo
Article
Genetics & Heredity
Dayong Zhang, Chuan Chen, Haitang Wang, Erli Niu, Peiyue Zhao, Shuai Fang, Guozhong Zhu, Xiaoguang Shang, Wangzhen Guo
Summary: This study identified a PPR protein GhImA in allotetraploid cotton that regulates fiber development by impacting mitochondrial RNA splicing, respiratory metabolism, ATP supply, and ROS balance. GhImA and its homolog GhImD act dose-dependently in controlling Complex I activities and cellular response processes in cotton fibers.