Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Agronomy
Balakrishnan Marudamuthu, Tamanna Sharma, Supriya Purru, S. K. Soam, Ch. Srinivasa Rao
Summary: Next-generation sequencing (NGS) is a game-changing technology in genomic research, enabling massively parallel sequencing. In agriculture, NGS has transformed enhancement strategies and simplified genetic modification approaches. This review highlights the available NGS platforms and their applications in agricultural genomics.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biology
Maria Guarnaccia, Laura Guarnaccia, Valentina La Cognata, Stefania Elena Navone, Rolando Campanella, Antonella Ampollini, Marco Locatelli, Monica Miozzo, Giovanni Marfia, Sebastiano Cavallaro
Summary: The study developed a targeted next-generation sequencing approach for analyzing genetic variations and chromosomal aberrations in gliomas, which can provide accurate and specific assessment of tumor pathogenesis, prognosis, and treatment response. This has important implications for the diagnosis and treatment of gliomas.
Review
Agronomy
Congwei Sun, Huiting Hu, Yongzhen Cheng, Xi Yang, Qi Qiao, Canguan Wang, Leilei Zhang, Daiying Chen, Simin Zhao, Zhongdong Dong, Feng Chen
Summary: Common wheat contributes to 20% of the total calorie intake in human diet. Recent advances in whole-genome sequencing have provided new opportunities for uncovering genetic variations in wheat traits and accelerating breeding strategies with the assistance of genomics. Combining traditional breeding, marker-assisted selection, and genomic selection with high-density SNP markers can enhance the breeding process and increase genetic gain. Genomics-assisted breeding is becoming the preferred strategy for developing superior wheat cultivars with traits such as high yield, nutritional quality, and climate resilience.
Review
Immunology
Tapoka T. Mkandawire, Adam Sateriale
Summary: This review discusses the significance of using long read DNA and RNA sequencing technologies to provide novel insights into the biology of Cryptosporidium, and highlights that the widespread adoption of these technologies will help fill key gaps in the understanding of Cryptosporidium biology.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Medicine, General & Internal
Cienne Morton, Debashis Sarker, Paul Ross
Summary: Cancers contain numerous mutations, but only a few are critical for malignancy. Targeted therapies and immunotherapy have shown great success in various cancer types. Next-generation sequencing enables the detection of potentially actionable mutations and contributes to the identification of new biomarkers. However, technical challenges and the development of targeted therapies against common genomic aberrations need to be overcome for personalized medicine to become more widely available.
Article
Oncology
Arnaud Bayle, Debora Basile, Simon Garinet, Bastien Rance, Pierre Laurent-Puig, Helene Blons, Julien Taieb, Geraldine Perkins
Summary: This study evaluated the role of NGS targeted panels in digestive oncology, showing that it allows for an exhaustive search for molecular abnormalities and provides patients with more opportunities for targeted therapies. Regular updates and further studies are needed for better analysis of prognostic factors.
Review
Biochemistry & Molecular Biology
Adrian Dockery, Laura Whelan, Pete Humphries, G. Jane Farrar
Summary: Inherited retinal diseases (IRDs) encompass a variety of genetically diverse conditions with phenotypic variations, researchers utilize cutting-edge sequencing techniques to identify elusive causes, providing accurate diagnoses and informed prognoses for family planning and medical interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Pharmacology & Pharmacy
Xiangjun Ji, Baitang Ning, Jinghua Liu, Ruth Roberts, Larry Lesko, Weida Tong, Zhichao Liu, Tieliu Shi
Summary: Pharmacogenomics plays essential roles in optimizing drug responses and avoiding adverse events. Population-specific therapeutic interventions and genotyping can improve clinical outcomes, highlighting the importance of precision medicine strategies. Challenges and regulatory efforts still exist in advancing this field further.
DRUG DISCOVERY TODAY
(2021)
Article
Biochemistry & Molecular Biology
Dario Kringel, Sebastian Malkusch, Eija Kalso, Jorn Lotsch
Summary: The genetic background of pain is being increasingly well understood, leading to the development of a cost-effective next generation sequencing-based pain-genotyping assay that identifies the most representative genes associated with pain.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Christopher Paul Wardell, Cody Ashby, Michael Anton Bauer
Summary: FiNGS is a software developed to improve the precision of variant caller outputs for somatic variants, with demonstrated reliability and better performance than other tools for the same task. It provides researchers with a simple, configurable, and reproducible tool for filtering somatic variants in sequencing data.
BMC BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Payal Ganguly, Bradley Toghill, Shelly Pathak
Summary: This article discusses the importance and research progress of bone marrow aging, explores inflammaging, and the application of next-generation sequencing technology in research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biology
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo, Gulnaz Zaidi, Shravani Rawool, Ritesh P. Thakare, Shahid Banday, Alok K. Mishra, Gautam Das, Sunil K. Malonia
Summary: Next-generation sequencing (NGS) is a powerful tool that can sequence millions of DNA fragments simultaneously, providing detailed information about genomes, genetic variations, gene activity, and changes in gene behavior. Recent advancements have focused on improving sequencing speed and accuracy, reducing costs, and enhancing data analysis. These advancements have great potential for advancing genomics research and improving our understanding of diseases and personalized healthcare.
Article
Biochemistry & Molecular Biology
Yann X. C. Bourgeois, Ben H. Warren
Summary: The continuous improvement of high-throughput sequencing techniques has enabled the production of whole genome data in various species, which in turn provides better tools for integrating selection into historical frameworks. However, the plethora of analytical tools may confuse users and hinder the dissemination of the latest methods.
Article
Pathology
Sarah Benton, Jeffrey Zhao, Bin Zhang, Armita Bahrami, Raymond L. Barnhill, Klaus Busam, Lorenzo Cerroni, Martin G. Cook, Arnaud de la Fouchardiere, David E. Elder, Iva Johansson, Gilles Landman, Alexander Lazar, Philip LeBoit, Lori Lowe, Daniela Massi, Lyn M. Duncan, Jane Messina, Daniela Mihic-Probst, Martin C. Mihm, Michael W. Piepkorn, Birgitta Schmidt, Richard A. Scolyer, Christopher R. Shea, Michael T. Tetzlaff, Victor A. Tron, Xiaowei Xu, Iwei Yeh, Sook Jung Yun, Artur Zembowicz, Pedram Gerami
Summary: The study found that additional genomic information can help improve diagnostic agreement and accuracy among expert pathologists when assessing tumors with Spitzoid features, particularly in diagnosing conventional melanoma and classifying lesions into the Spitz category/WHO Pathway.
AMERICAN JOURNAL OF SURGICAL PATHOLOGY
(2021)
Article
Plant Sciences
Zheng-Zhen Wang, Zi-Xiao Guo, Cai-Rong Zhong, Hao-Min Lyu, Xin-Nian Li, Norman C. Duke, Su-Hua Shi
Summary: Through a study on the mangrove tree, Avicennia marina, we found comprehensive genetic divergence among subspecies, higher than among geographical populations within subspecies. The level of genetic diversity differs significantly among the three subspecies, hinting at a degree of separation among their gene pools.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2022)
Article
Biodiversity Conservation
Dana M. Bergstrom, Barbara C. Wienecke, John van den Hoff, Lesley Hughes, David B. Lindenmayer, Tracy D. Ainsworth, Christopher M. Baker, Lucie Bland, David M. J. S. Bowman, Shaun T. Brooks, Josep G. Canadell, Andrew J. Constable, Katherine A. Dafforn, Michael H. Depledge, Catherine R. Dickson, Norman C. Duke, Kate J. Helmstedt, Andres Holz, Craig R. Johnson, Melodie A. McGeoch, Jessica Melbourne-Thomas, Rachel Morgain, Emily Nicholson, Suzanne M. Prober, Ben Raymond, Euan G. Ritchie, Sharon A. Robinson, Katinka X. Ruthrof, Samantha A. Setterfield, Carla M. Sgro, Jonathan S. Stark, Toby Travers, Rowan Trebilco, Delphi F. L. Ward, Glenda M. Wardle, Kristen J. Williams, Phillip J. Zylstra, Justine D. Shaw
Summary: This study examines the current state and recent trajectories of ecosystem collapse globally, highlighting the pressures from global climate change and human impacts as key drivers. The manifestation of widespread ecosystem collapse serves as a stark warning of the necessity for action to alleviate further degradation. A three-step assessment and management framework is proposed to aid in strategic and effective mitigation to secure our future.
GLOBAL CHANGE BIOLOGY
(2021)
Article
Environmental Sciences
Britta Denise Hardesty, Lauren Roman, Norman C. Duke, Jock R. Mackenzie, Chris Wilcox
Summary: The remote Gulf of Carpentaria is a significant fishing area in Australia, but it is also a hotspot for abandoned fishing gear 'ghost nets'. Despite efforts to combat illegal fishing and clean up the region, the density of ghost nets is increasing. There is a need for improved monitoring and management strategies to address this issue.
MARINE POLLUTION BULLETIN
(2021)
Article
Biochemistry & Molecular Biology
Rufan Zhang, Zixiao Guo, Lu Fang, Cairong Zhong, Norman C. Duke, Suhua Shi
Summary: The study found that the populations of Aegiceras corniculatum are shaped by historical climate changes and sea-level fluctuations, with two main groups identified: Indo-Malayan and Pan-Australasia. Genetic drift in a bottleneck event likely led to the genetic break between the southern and northern South China Sea subgroups of the coastal plant. This case highlights how bottleneck events can promote population subdivision and has implications for other taxa beyond coastal plants.
Biographical-Item
Marine & Freshwater Biology
B. Clough, A. A. Amir, V. C. Chong, N. C. Duke, C. D. Field, B. Kjerfve, S. Y. Lee, A. Sasekumar, S. C. Wong, J. W. H. Yong, W. K. Gong
ESTUARINE COASTAL AND SHELF SCIENCE
(2022)
Article
Evolutionary Biology
Kazumichi Fujiwara, Yosuke Kawai, Toyoyuki Takada, Toshihiko Shiroishi, Naruya Saitou, Hitoshi Suzuki, Naoki Osada
Summary: House mice are an important animal model in biomedical research, and their genetic background at the global level has been investigated in this study. The researchers found that wild house mice consist of three major genetic groups corresponding to three major subspecies, with a higher prevalence of admixture between subspecies in East Asia. In addition, incongruent patterns of genealogies were observed between mitochondrial and autosomal genomes in some samples. The estimated divergence time of the three subspecies was 187,000-226,000 years ago.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Alice Gauthey, Diana Backes, Jeff Balland, Iftakharul Alam, Damien T. Maher, Lucas A. Cernusak, Norman C. Duke, Belinda E. Medlyn, David T. Tissue, Brendan Choat
Summary: Between late 2015 and early 2016, a large-scale die-off of mangrove forests occurred along the northern coastline of Australia, primarily due to the strong El Nino event during that period. The decreased precipitation, lower sea level, and higher temperatures resulted in hydraulic failure and mortality of the dominant species, Avicennia marina. The study found that areas with severe dieback had higher loss of stem hydraulic conductivity, indicating ongoing hydraulic recovery. The species exhibited high resistance to water-stress-induced embolism, suggesting that severe water stress would have been required to cause mortality.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Kazuhiro Konishi, Toshiyuki Yamaji, Chisato Sakuma, Fumio Kasai, Toshinori Endo, Arihiro Kohara, Kentaro Hanada, Naoki Osada
Summary: This study performed a comparative analysis of Vero E6 cell line with other Vero sublines, revealing genetic differences including single nucleotide variants, indels, and copy number variations. The study also identified specific missense variants in Vero E6 that may contribute to its unique response to viral infection compared to other sublines.
FRONTIERS IN GENETICS
(2022)
Article
Ecology
Ziwen He, Xiao Feng, Qipian Chen, Liangwei Li, Sen Li, Kai Han, Zixiao Guo, Jiayan Wang, Min Liu, Chengcheng Shi, Shaohua Xu, Shao Shao, Xin Liu, Xiaomeng Mao, Wei Xie, Xinfeng Wang, Rufan Zhang, Guohong Li, Weihong Wu, Zheng Zheng, Cairong Zhong, Norman C. Duke, David E. Boufford, Guangyi Fan, Chung- Wu, Robert E. Ricklefs, Suhua Shi
Summary: Genomic studies are now exploring whole communities of species. This study focuses on mangroves, a group of about 70 woody plant species that anchor coastal ecosystems. Researchers sequenced the whole genomes of 32 mangroves and combined them with sequences from 30 additional species, providing valuable community-wide genomic data for ecology, evolution, and biodiversity research. The data revealed 27 independent origins of mangroves but showed only slight increases in species number, suggesting common extinction. Factors contributing to extinction include sea-level rises and falls, population fragmentation, and the accumulation of deleterious mutations.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Xinfeng Wang, Ziwen He, Zixiao Guo, Ming Yang, Shaohua Xu, Qipian Chen, Shao Shao, Sen Li, Cairong Zhong, Norman C. Duke, Suhua Shi
Summary: In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). In an alternative view, species may also be delineated by a small set of 'speciation genes' without full RI, a view that has gained broad acceptance. A recent study on two closely related mangrove species (Rhizophora mucronata and R. stylosa) found that despite being sympatric, their genomes remained well delineated with only small introgression blocks. These findings suggest that true 'good species' may continue to exchange genes long after speciation, but detecting such exchanges is challenging.
NATIONAL SCIENCE REVIEW
(2022)
Article
Environmental Sciences
Christine T. Y. Chung, Pandora Hope, Lindsay B. Hutley, Josephine Brown, Norman C. Duke
Summary: The mangroves in the Gulf of Carpentaria, Australia, face risks to their health due to projected changes in sea level variability and increasing maximum daily temperatures.
COMMUNICATIONS EARTH & ENVIRONMENT
(2023)
Article
Ecology
Ziwen He, Xiao Feng, Qipian Chen, Liangwei Li, Sen Li, Kai Han, Zixiao Guo, Jiayan Wang, Min Liu, Chengcheng Shi, Shaohua Xu, Shao Shao, Xin Liu, Xiaomeng Mao, Wei Xie, Xinfeng Wang, Rufan Zhang, Guohong Li, Weihong Wu, Zheng Zheng, Cairong Zhong, Norman C. Duke, David E. Boufford, Guangyi Fan, Chung- Wu, Robert E. Ricklefs, Suhua Shi
Summary: This study sequenced the genomes of 32 mangroves and combined them with sequences of 30 additional species, revealing the origins of mangroves, changes in species number, and factors contributing to mangrove extinction. The findings have significant implications for ecology, evolution, and biodiversity research.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Kazumichi Fujiwara, Marie C. Ranorosoa, Satoshi D. Ohdachi, Satoru Arai, Yuki Sakuma, Hitoshi Suzuki, Naoki Osada
Summary: This study determined the genetic background of the house mouse population in Madagascar and found a close genetic affinity with house mice from the Indian Ocean coastal regions, suggesting that the ancestors of the Madagascar house mice likely colonized the island through human activities.
GENES & GENETIC SYSTEMS
(2022)
Review
Ecology
Martin Zimmer, Gordon N. Ajonina, A. Aldrie Amir, Simon M. Cragg, Stephen Crooks, Farid Dahdouh-Guebas, Norman C. Duke, Sara Fratini, Daniel A. Friess, Veronique Helfer, Mark Huxham, Kandasamy Kathiresan, K. A. Sunanda Kodikara, Nico Koedam, Shing Yip Lee, Mwita M. Mangora, Jurgenne Primavera, Behara Satyanarayana, Jean Wan Hong Yong, Dominic Wodehouse
Summary: Protecting existing mangrove forests is crucial for global conservation, but there is a need for mangrove re-establishment due to historical loss rates. Successful re-establishment requires understanding of site conditions, ecological requirements, and previous barriers, as well as engagement with local communities and stakeholders.
FRONTIERS IN FORESTS AND GLOBAL CHANGE
(2022)
Article
Biotechnology & Applied Microbiology
Yi Cong, Misaki Shintani, Fuga Imanari, Naoki Osada, Toshinori Endo
Summary: Drug repurposing is important for therapeutics innovation in infectious diseases and chronic human diseases. A new approach involving two-stage prediction and machine learning is proposed, which successfully identified 20 potential drug candidates for repurposing.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)