Article
Biochemical Research Methods
Runzhou Yu, Dehan Cai, Yanni Sun
Summary: RNA viruses mutate constantly, but accurate assembly of viral genomes is crucial for studying virus evolution and understanding the relationship between genotypes and virus properties. A new tool called AccuVIR has been developed for viral genome assembly and polishing using error-prone long reads. It can distinguish sequencing errors from true variants, resulting in more accurate viral genomes compared to other tools.
Review
Fisheries
Li Lian Wong, Siti Aisyah Razali, Zulaikha Mat Deris, Muhd Danish-Daniel, Min Pau Tan, Siti Azizah Mohd Nor, Hongyu Ma, Wang Min, Liang Yantao, Md Asaduzzaman, Yeong Yik Sung, Zhanjiang Liu, Patrick Sorgeloos, Yves Van de Peer, Nor Afiqah-Aleng
Summary: High-throughput sequencing technologies have been widely applied in aquaculture research, providing important data support for disease management, breeding programs, etc.
Article
Oncology
Marios Gavrielatos, Konstantinos Kyriakidis, Demetrios A. Spandidos, Ioannis Michalopoulos
Summary: Genome assemblers are computational tools used for de novo genome assembly, evaluating quality based on contiguity and misassembly occurrences. The advancement in sequencing technologies has led to the development of novel strategies aiming to address weaknesses and create complete genome maps. Different assembly strategies were benchmarked in this study, showing that HiFi sequencing enables the rise of new algorithms and may democratize genome assembly projects for smaller labs with limited resources.
MOLECULAR MEDICINE REPORTS
(2021)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Ecology
Zi-Wen Yang, Yu Men, Jing Zhang, Zhi-Hui Liu, Jiu-Yang Luo, Yan-Hui Wang, Wen-Jun Li, Qiang Xie
Summary: The study found that air dried preservation method had poor effects on insect microbiome samples, while RNAlater was not suitable for longer field works. CTAB and ethanol were recommended as more effective and cost-efficient preservatives. Additionally, NGS sequencing of the V4 region of the 16S rRNA gene had lower resolution compared to TGS sequencing, potentially leading to misestimations of microbial community compositions.
Article
Immunology
Xiao-guang Cao, Shu-sheng Zhou, Chun-yan Wang, Kui Jin, Hua-dong Meng
Summary: This study demonstrates that NGS is accurate and efficient in diagnosing sepsis, and the combination of NGS and ALB for early screening is more effective. NGS and ALB are identified as independent prediction factors for sepsis, with the combined diagnostic approach being more accurate.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Environmental Sciences
Ruchika Sharma, Chandragouda Patil, Jaseela Majeed, Subodh Kumar, Geeta Aggarwal
Summary: Medicinal plants have been widely used as traditional herbal medicines for various diseases. The increased demand for these plants emphasizes the need for conservation, especially for endangered species. Next-generation sequencing (NGS) technologies have made significant advancements in medicinal plant research, making it more cost-effective and time-efficient. NGS systems allow for high-throughput whole genome sequencing, RNA sequencing, and transcriptome analysis, providing valuable data for various areas of study.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
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)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Review
Medicine, General & Internal
Syahzuwan Hassan, Rosnah Bahar, Muhammad Farid Johan, Ezzeddin Kamil Mohamed Hashim, Wan Zaidah Abdullah, Ezalia Esa, Faidatul Syazlin Abdul Hamid, Zefarina Zulkafli
Summary: Thalassemia is a highly heterogeneous disease with over a thousand recorded mutation types worldwide. Conventional PCR-based DNA analysis for thalassemia diagnosis is time-consuming and resource-intensive due to phenotype variability, disease complexity, and test limitations. Advanced molecular techniques such as next-generation sequencing (NGS) and third-generation sequencing (TGS) offer more suitable and valuable options for DNA analysis of thalassemia. The continuous improvement of sequencing methods and bioinformatics tools, particularly for identifying copy number variations and homologous genes, will lead to more accurate thalassemia detection.
Article
Biotechnology & Applied Microbiology
Elena Espinosa, Rocio Bautista, Ivan Fernandez, Rafael Larrosa, Emilio L. Zapata, Oscar Plata
Summary: The recent advent of long-read sequencing technologies has improved sequencing accuracy and computational cost. However, de novo whole-genome assembly remains challenging. This study evaluates the assembly reconstruction using different sequencing platforms and tools, finding that PacBio high-fidelity long-reads play a crucial role in haplotype construction and combining it with high-fidelity ONT datasets or short-reads improves assembly correctness.
Article
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Review
Biochemistry & Molecular Biology
Natsuko Aida, Akiko Saito, Toshifumi Azuma
Summary: The development of next-generation sequencing (NGS) has greatly improved the speed and capacity of genetic analysis, expanding its applications to include genome, epigenome, metagenome, and transcriptome analyses. Bone tissue, as a crucial unit supporting the body, is susceptible to genetic diseases. The relationship between age-related bone fragility and genetic factors has recently gained attention.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Elisabetta Notario, Grazia Visci, Bruno Fosso, Carmela Gissi, Nina Tanaskovic, Maria Rescigno, Marinella Marzano, Graziano Pesole
Summary: The 16S rRNA amplicon-based sequencing approach is commonly used and cost-effective for microbiome profiling. This study compared different methods and found that the full-length approach has the best discriminatory power for microbiome taxonomic characterization.
Review
Obstetrics & Gynecology
M. D. Kilby
Summary: This paper reviews the role of NGS in investigating fetal malformations, emphasizing the importance of prospective case selection and informative pre-test counseling, as well as the crucial role of regulated laboratory sequencing and bioinformatic pathways in clinical practice.
BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY
(2021)
Article
Plant Sciences
Tao Fujiwara, Hongmei Liu, Esteban Meza-Torres, Rita E. Morero, Alvaro J. Vega, Zhenlong Liang, Atsushi Ebihara, Ilia J. Leitch, Harald Schneider
Summary: By recording parameters related to genome size and chromosome number, we demonstrated the importance of genome diversity and disparity in shaping fern species diversity.
Article
Biochemistry & Molecular Biology
Pol Fernandez, Ilia J. Leitch, Andrew R. Leitch, Oriane Hidalgo, Maarten J. M. Christenhusz, Lisa Pokorny, Jaume Pellicer
Summary: Giant genomes are rare in the plant kingdom, with most research focusing on angiosperms and gymnosperms. However, a study on ferns reveals differences in genome organization and dynamics. The genus Tmesipteris has two species with giant genomes, which exhibit high repeat diversity compared to small-genome taxa.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Jiri Macas, Laura Avila Robledillo, Jonathan Kreplak, Petr Novak, Andrea Koblizkova, Iva Vrbova, Judith Burstin, Pavel Neumann
Summary: In this study, the assembly and analysis of the pea metapolycentromere, a unique type of centromere that represents an intermediate stage between monocentric and holocentric organizations, is reported. The results reveal the sequence organization and potential mechanisms for the formation of the metapolycentromere. It is found that the metapolycentromere is formed through the expansion of centromeric chromatin and the accumulation of novel satellite repeats. Furthermore, genetic experiments demonstrate that centromere evolution involving chromosomal translocations and centromere repositioning also contribute to the formation of metapolycentromeres.
Article
Evolutionary Biology
Roberta Gargiulo, Robin S. Waples, Adri K. Grow, Richard P. Shefferson, Juan Viruel, Michael F. Fay, Tiiu Kull
Summary: Estimating effective population size (N-e) is important, but it remains challenging for organisms with complex life-history traits. In this study, we examined how clonal versus sexual reproduction affected N-e in two populations of the orchid Cypripedium calceolus. The results showed that N-e in partially clonal plants cannot be predicted solely based on the number of genets generated by sexual reproduction.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Agronomy
Antonia Diakostefani, Rania Velissaris, Emilia Cvijanovic, Robin Bulgin, Andriana Pantelides, Ilia J. Leitch, Sahr Mian, Joseph A. Morton, Marybel Soto Gomez, Mark A. Chapman
Summary: Underutilised crops have great potential for breeding programmes in the face of climate change and population growth due to their improved stress tolerance and/or nutrition. Therefore, developing genome resources for these crops can enhance their use by providing insights into population structure, phylogeny, candidate genes, and linkage mapping. In this study, we sequenced and assembled the nuclear and plastid genomes of five underutilised legumes and developed a pipeline to identify thousands of markers that can be used in other species. Our findings provide valuable information for genomic and population genetic studies of these crops and offer approaches for investigating other important yet underutilised crops.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Evolutionary Biology
Rowena Hill, Quentin Levicky, Frances Pitsillides, Amy Junnonen, Elena Arrigoni, J. Miguel Bonnin, Anthony Kermode, Sahr Mian, Ilia J. Leitch, Alan G. Buddie, Richard J. A. Buggs, Ester Gaya
Summary: The Ascomycota, the largest phylum in the fungal kingdom, exhibit diverse lifestyles, including associations with plants. This study focuses on the relatively understudied endophytic ascomycetes, which are asymptomatic inhabitants of plants. By sequencing and assembling genomes for 15 endophytic ascomycete strains and using phylogenetic analysis, the researchers refined the classification of taxa and provided valuable insights into plant-fungal interactions. They also demonstrated the importance of cytometric genome size estimates in assessing assembly completeness.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Theo Llewellyn, Sahr Mian, Rowena Hill, Ilia J. Leitch, Ester Gaya
Summary: Lichen-forming fungi are important symbionts with diverse genomes. Accurate genome size measurements can be obtained from lichen thalli and used to assess the completeness of metagenome-derived assemblies.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Murukarthick Jayakodi, Agnieszka A. Golicz, Jonathan Kreplak, Lavinia Fechete, Deepti Angra, Petr Bednar, Elesandro Bornhofen, Hailin Zhang, Raphael Boussageon, Sukhjiwan Kaur, Kwok Cheung, Jana Cizkova, Heidrun Gundlach, Asis Hallab, Baptiste Imbert, Gabriel Keeble-Gagnere, Andrea Koblizkova, Lucie Kobrlova, Petra Krejci, Troels W. Mouritzen, Pavel Neumann, Marcin Nadzieja, Linda Kaergaard Nielsen, Petr Novak, Jihad Orabi, Sudharsan Padmarasu, Tom Robertson-Shersby-Harvie, Laura Avila Robledillo, Andrea Schiemann, Jaakko Tanskanen, Petri Toronen, Ahmed O. Warsame, Alexander H. J. Wittenberg, Axel Himmelbach, Gregoire Aubert, Pierre-Emmanuel Courty, Jaroslav Dolezel, Liisa U. Holm, Luc L. Janss, Hamid Khazaei, Jiri Macas, Martin Mascher, Petr Smykal, Rod J. Snowdon, Nils Stein, Frederick L. Stoddard, Jens Stougaard, Nadim Tayeh, Ana M. Torres, Bjorn Usadel, Ingo Schubert, Donal Martin O'Sullivan, Alan H. Schulman, Stig Uggerhoj Andersen
Summary: Increasing the proportion of locally produced plant protein in diets could reduce greenhouse gas emissions and loss of biodiversity. However, plant protein production is hindered by the lack of a cool-season legume equivalent to soybean. This study presents a high-quality genome assembly of faba bean and demonstrates its potential for sustainable protein production.
Article
Multidisciplinary Sciences
Pavel Neumann, Ludmila Oliveira, Tae-Soo Jang, Petr Novak, Andrea Koblizkova, Veit Schubert, Andreas Houben, Jiri Macas
Summary: The transition from monocentric to holocentric organization in Cuscuta was associated with loss or truncation of kinetochore-related genes, disruption of centromeric localization of kinetochore proteins, and degeneration of the spindle assembly checkpoint. This indicates that holocentric Cuscuta species lack a standard kinetochore and do not employ the SAC to control microtubule attachment to chromosomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Yi-Tzu Kuo, Amanda Souza Camara, Veit Schubert, Pavel Neumann, Jiri Macas, Michael Melzer, Jianyong Chen, Jorg Fuchs, Simone Abel, Evelyn Klocke, Bruno Huettel, Axel Himmelbach, Dmitri Demidov, Frank Dunemann, Martin Mascher, Takayoshi Ishii, Andre Marques, Andreas Houben
Summary: This study reveals the holocentric characteristics of the lilioid plant Chionographis japonica, showing that its centromeres consist of evenly spaced units and differ from other known holocentric species. The study also finds that C. japonica forms clustered centromeres similar to monocentric species, but the large-scale chromatin arrangement is different. The formation of holocentromeres from interphase centromere clusters was simulated using polymer simulations.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Anne Edwards, Isaac Njaci, Abhimanyu Sarkar, Zhouqian Jiang, Gemy George Kaithakottil, Christopher Moore, Jitender Cheema, Clare E. M. Stevenson, Martin Rejzek, Petr Novak, Marielle Vigouroux, Martin Vickers, Roland H. M. Wouters, Pirita Paajanen, Burkhard Steuernagel, Jonathan D. Moore, Janet Higgins, David Swarbreck, Stefan Martens, Colin Y. Kim, Jing-Ke Weng, Sagadevan Mundree, Benjamin Kilian, Shiv Kumar, Matt Loose, Levi Yant, Jiri Macas, Trevor L. Wang, Cathie Martin, Peter M. F. Emmrich
Summary: Grass pea is a protein-rich crop cultivated in several countries as an insurance crop for food security in a changing climate. However, its cultivation has been limited due to a lack of genetic resources and its association with a disease called neurolathyrism. In this study, researchers have sequenced the genome of grass pea and identified the biosynthetic pathway for the neurotoxin beta-L-oxalyl-2,3-diaminopropionic acid (beta-L-ODAP), which causes the disease. This finding provides valuable insights for developing varieties with reduced toxin production.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Jacopo Calevo, Maarten J. M. Christenhusz, Michael F. Fay
Summary: Orchis patens was previously believed to have three disjunct populations in northern Italy, Algeria/Tunisia, and the Canary Islands. While the population in the Canary Islands is commonly referred to as O. canariensis, there has been doubt about the name for the Italian taxon because the type specimen of O. patens is from the Algerian populations. In this study, we reviewed the taxonomic literature and provided a key based on recently published molecular data for these three taxa in the Orchis section Robustocalcare. We concluded that Orchis patens subsp. brevicornis is the correct name for the Italian taxon.
Article
Plant Sciences
Andrew R. Leitch, Lu Ma, Steven Dodsworth, Joerg Fuchs, Andreas Houben, Ilia J. Leitch
Summary: Angiosperm genomes consist of genes and their regulatory regions, repeats, semi-degraded repeats, and "dark matter". This study compares the histone modifications associated with chromatin packaging of these different genomic components in two species with significantly different genome sizes. The results reveal distinct associations between certain histone marks and different genomic features, providing insights into epigenetic profiles and chromatin organization.
Review
Ecology
Wencai Wang, Xianzhi Zhang, Sonia Garcia, Andrew R. Leitch, Ales Kovarik
Summary: The classical model of concerted evolution states that rDNA units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected. However, advanced sequencing techniques have revealed that rDNA homogenization in many organisms is not complete. This work summarizes the variation in rDNAs across different taxa and discusses the factors contributing to this incomplete concerted evolution.
