Review
Biology
Haeun Lee, Jun Won Min, Seyoung Mun, Kyudong Han
Summary: This review discusses the recently studied and utilized NGS technologies and effective computational approaches for discovering retrotransposons. NGS has provided new perspectives for detecting retrotransposon-mediated SVs and various computational methods have been developed for accurately detecting insertions and deletions in the human genome.
Article
Biochemical Research Methods
Akio Miyao, Utako Yamanouchi
Summary: This study developed a new algorithm, TEF, which can detect transposable elements (TEs) with unknown sequences and determine the sequences of both ends and the insertion positions of transposed TEs by directly comparing the NGS data. This method verifies the genotypes of transpositions by counting the junctions of head and tail, and non-insertion sequences in NGS reads. It is easy to use and independent of any TE library, making it useful for detecting insertions from unknown TEs bypassed by common TE annotation pipelines.
BMC BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Vista Sohrab, Cristina Lopez-Diaz, Antonio Di Pietro, Li-Jun Ma, Dilay Hazal Ayhan
Summary: TEfinder is a simple tool developed for the detection of new TE insertions with minimal software and input file dependencies. The tool has been tested in evolving populations of Fusarium oxysporum and shown to effectively detect new TE insertion events, making it accessible and practical for TE analysis.
Review
Plant Sciences
Yunus Emre Arvas, Sevgi Marakli, Yilmaz Kaya, Ruslan Kalendar
Summary: The use of molecular markers is crucial in various fields of molecular genetics, such as gene identification, plant breeding, and genetic characterization. Transposable elements, particularly retrotransposons, are widely used as molecular markers due to their presence in eukaryotic genomes and ability to integrate into dispersed chromosomal locations. The ongoing development of molecular marker technologies is closely linked to high-throughput genotype sequencing platforms, making this research highly significant.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Camilla Borges Gazolla, Adriana Ludwig, Joana de Moura Gama, Daniel Pacheco Bruschi
Summary: This study investigated the retrotransposons in the genomes of Xenopus tropicalis and Xenopus laevis, and found molecular signatures and conserved domains that distinguish different superfamily elements. The results revealed ancient and more recent amplification waves of these elements, with higher density in the ancestor of X. laevis and recent activity in X. tropicalis and X. laevis. The findings highlight the differential diversity and evolutionary dynamics of retrotransposons in these two species.
G3-GENES GENOMES GENETICS
(2022)
Article
Oncology
Margherita Rimini, Eleonora Loi, Carles Fabregat-Franco, Valentina Burgio, Sara Lonardi, Monica Niger, Mario Scartozzi, Ilario G. Raposelli, Giuseppe Aprile, Francesca Ratti, Federica Pedica, Helena Verdaguer, Mario Rizzato, Federico Nichetti, Eleonora Lai, Alessandro Cappetta, Teresa Macarulla, Matteo Fassan, Filippo De Braud, Andrea Pretta, Francesca Simionato, Francesco De Cobelli, Luca Aldrighetti, Lorenzo Fornaro, Stefano Cascinu, Zavattari Patrizia, Andrea Casadei-Gardini
Summary: This study identified three mutation-based clusters in IDH1-mutated intrahepatic cholangiocarcinomas (IDH1m iCCAs) and demonstrated their prognostic significance.
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Multidisciplinary Sciences
Yung-Heng Chang, Josh Dubnau
Summary: The movement of prion-like proteins between cells is believed to be the cause of neurodegeneration propagation. The co-expression of endogenous retrovirus (ERV) and TDP-43 proteinopathy can reinforce each other, leading to the aggregation of TDP-43 protein. The transmission of ERVs through viral infection triggers TDP-43 pathology in recipient cells, explaining the spread of neurodegenerative effects.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Michael Segel, Blake Lash, Jingwei Song, Alim Ladha, Catherine C. Liu, Xin Jin, Sergei L. Mekhedov, Rhiannon K. Macrae, Eugene V. Koonin, Feng Zhang
Summary: Eukaryotic genomes contain domesticated genes from integrating viruses and mobile genetic elements, including mammalian Gag homologs and PEG10, which can be used for RNA delivery. The development of selective endogenous encapsidation for cellular delivery (SEND) using PEG10 demonstrates its potential as an efficient therapeutic delivery modality.
Article
Mathematics, Applied
Ashaq Hussain Bhat, Tu N. Nguyen, Korhan Cengiz, Puniethaa Prabhu
Summary: The HBEA clustering algorithm uses exact pairwise global alignment algorithm to improve cluster quality and extract cluster representatives. Experimental investigation showed that HBEA produces better operational taxonomic unit (OTU) clusters and computational complexity than other algorithms.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2021)
Review
Plant Sciences
Haoran Peng, Marie Mirouze, Etienne Bucher
Summary: Most plant genomic studies have focused on nuclear chromosomes, neglecting research on extrachromosomal circular DNA (eccDNA). Recent findings show that eccDNAs can originate from various regions of the genome and play a role in stress response and adaptation in plants. This review outlines current technological developments for identifying eccDNA and discusses the functions and future research directions regarding different sources of eccDNA.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Genetics & Heredity
Vinicius A. C. de Abreu, Rafael Moyses Alves, Saura R. Silva, Jesus A. Ferro, Douglas S. Domingues, Vitor F. O. Miranda, Alessandro M. Varani
Summary: The study assembled and compared the mitochondrial genomes of Theobroma cacao and T. grandiflorum, revealing their high plasticity. The plant mitochondrial genes and genomes serve as good markers for phylogenetic, evolutionary, and comparative analyses. The structural differences and specific regions associated with transposable elements may contribute to the divergent evolutionary paths and pressures after species differentiation.
Article
Multidisciplinary Sciences
Marianne Yoth, Stephanie Maupetit-Mehouas, Abdou Akkouche, Nathalie Gueguen, Benjamin Bertin, Silke Jensen, Emilie Brasset
Summary: This study suggests that errantiviruses, although continuously repressed by the piRNA pathway, may retain their ability to infect and transpose, especially when reactivated. Fruit flies restrict the invasion of errantiviruses into their germline by producing piRNAs specifically targeting the invading viruses.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Daniela Moreira Mombach, Tiago Minuzzi Freire da Fontoura Gomes, Elgion Lucio Silva Loreto
Summary: This review explores the regulation of transposable element (TE) expression in Drosophila under stress conditions, and finds that stress does not broadly trigger TE transcription. Furthermore, it proposes an explanation for why TE LTR order is the most highly expressed.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Plant Sciences
Pavel Merkulov, Ekaterina Egorova, Ilya Kirov
Summary: This study demonstrates that nanopore sequencing is a valuable tool for detecting and analyzing eccDNA molecules. The quantity and structure of TE-derived eccDNA vary significantly in response to stress treatments in Arabidopsis plants. Epigenetic stress alone does not lead to eccDNA up-regulation, but when combined with heat stress, it triggers the generation of full-length and various truncated eccDNAs from the ONSEN element.
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
Plant Sciences
I. Kovalchuk, M. Pellino, P. Rigault, R. van Velzen, J. Ebersbach, J. R. Ashnest, M. Mau, M. E. Schranz, J. Alcorn, R. B. Laprairie, J. K. McKay, C. Burbridge, D. Schneider, D. Vergara, N. C. Kane, T. F. Sharbel
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 71, 2020
(2020)
Article
Biochemistry & Molecular Biology
Elena Hamann, Christopher S. Pauli, Zoe Joly-Lopez, Simon C. Groen, Joshua S. Rest, Nolan C. Kane, Michael D. Purugganan, Steven J. Franks
Summary: Abundant evidence suggests rapid evolution in natural populations, with gene expression changes playing a key role in response to environmental fluctuations. The study found that different plant populations showed independent evolutionary trajectories in gene expression changes, with adaptations related to stress responses and flowering time regulation. This highlights the importance of gene expression changes as a mechanism for rapid evolutionary responses and the potential for unique evolutionary trajectories in different populations over time.
Editorial Material
Biochemistry & Molecular Biology
Loren Rieseberg, Emily Warschefsky, Bridget O'Boyle, Pierre Taberlet, Daniel Ortiz-Barrientos, Nolan C. Kane, Benjamin Sibbett
Review
Agronomy
Ziv Attia, Cloe S. Pogoda, Stephan Reinert, Nolan C. Kane, Brent S. Hulke
Summary: The review discusses the effects of climate change on oilseed crops, emphasizing the importance of environmental factors on genetics and yield. It highlights the significance of using genomics and bioinformatics in predicting these effects for breeding of oilseed crops.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Multidisciplinary Sciences
Daniela Vergara, Cellene Feathers, Ezra L. Huscher, Ben Holmes, Jacob A. Haas, Nolan C. Kane
Summary: This study shows that the traditional naming conventions and classification methods for Cannabis may not be suitable for plants based on hybrid lineages. Therefore, a new system is needed to identify variations within Cannabis and provide reliable property identifiers.
Letter
Biochemistry & Molecular Biology
Kyle G. Keepers, Cloe S. Pogoda, James C. Lendemer, Nolan C. Kane, Erin A. Manzitto-Tripp
Article
Plant Sciences
Daniela Vergara, Ezra L. Huscher, Kyle G. Keepers, Rahul Pisupati, Anna L. Schwabe, Mitchell E. McGlaughlin, Nolan C. Kane
Summary: The Cannabis varieties produced by the National Institute on Drug Abuse (NIDA) lack diversity and potency compared to commercially produced Cannabis, and are genetically divergent from those in the private legal market. Research results based on NIDA's varieties are not generalizable due to their lack of diversity in various aspects of the genome, hindering scientific investigation into the effects of Cannabis after consumption.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemical Research Methods
Dustin W. Bailey, Ziv Attia, Stephan Reinert, Brent S. Hulke, Nolan C. Kane
Summary: This article describes a method for extracting high-quality DNA from plant tissue containing secondary metabolites, and provides experimental evidence in the Asteraceae family. The results show that the modified CTAB method on young leaves yielded the highest DNA quantity and sufficient sample purity. There was no significant difference observed between fresh and lyophilized samples, providing a good foundation for DNA extraction from difficult plant samples.
Editorial Material
Biochemistry & Molecular Biology
Loren Rieseberg, Emily Warschefsky, Bridget O'Boyle, Pierre Taberlet, Daniel Ortiz-Barrientos, Nolan C. Kane, Benjamin Sibbett
Article
Biochemistry & Molecular Biology
April M. Goebl, Nolan C. Kane, Daniel F. Doak, Loren H. Rieseberg, Kate L. Ostevik
Summary: Studying conspecific populations living in different microenvironments is important for understanding natural selection. In this study, two sunflower ecotypes in different habitats were investigated to estimate fitness and allele frequency change at different life stages. It was found that habitat- and life stage-specific selection contribute to the maintenance of divergent adaptation between populations.
Article
Fisheries
David Gislason, Daniel Estevez-Barcia, Saemundur Sveinsson, Agneta Hansen, Denis Roy, Margaret Treble, Jesper Boje, Mikko Vihtakari, Bjarki Thor Elvarsson, Kevin Hedges, Elvar H. Hallfredsson, Torild Johansen
Summary: Understanding the genetic differentiation among marine fish populations is challenging due to unknown spawning grounds and difficulties in collecting spawning fish. This study collected juvenile fish from nursery habitats associated with potential spawning grounds and used genotype by sequencing to discover genetic markers for assessing genetic differentiation. The results revealed major genetic differentiation between the northeast and northwest Atlantic, supporting the presence of two primary spawning clusters. Furthermore, genetic differentiation was found among the three northwest Atlantic samples, indicating the existence of more than one spawning area in the northwest.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Review
Evolutionary Biology
Javan K. Carter, Rebecca T. Kimball, Erik R. Funk, Nolan C. Kane, Drew R. Schield, Garth M. Spellman, Rebecca J. Safran
Summary: This review provides an overview of commonly used genomic markers in phylogenomic studies and their applications, as well as a concise outline to efficiently consider key aspects of each type of genetic marker.
JOURNAL OF HEREDITY
(2023)
Article
Ecology
Niamh B. O'Hara, Steven J. Franks, Nolan C. Kane, Silas Tittes, Joshua S. Rest
Summary: This study utilized a historical seed collection of Brassica rapa to investigate the evolutionary changes in disease susceptibility to a necrotrophic fungal pathogen following a drought. The results showed that the well-characterized necrotrophic fungal pathogen response genes have evolved between ancestors and descendants, with the jasmonic acid signaling pathway playing a crucial role in disease susceptibility evolution. Additionally, the study identified genes that respond to drought and evolved between ancestors and descendants, indicating drought as the evolutionary driver and genetic pleiotropy as a possible consequence of increased disease susceptibility.
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Andrew R. Raduski, Adam Herman, Cloe Pogoda, Kevin M. Dorn, David L. Van Tassel, Nolan Kane, Yaniv Brandvain
Summary: Understanding the genetic structure and geography relationship of the North American prairie wildflower, Silphium integrifolium, shows that the species originated in the American Southeast and is divided into three geographic clusters. By incorporating accessions from outside the founding region, breeding programs can be improved to target beneficial agronomic traits.
AMERICAN JOURNAL OF BOTANY
(2021)
Article
Agronomy
Cloe S. Pogoda, Stephan Reinert, Zahirul I. Talukder, Ziv Attia, Erin C. E. Collier-zans, Thomas J. Gulya, Nolan C. Kane, Brent S. Hulke
Summary: This study conducted genome-wide analysis of resistance to two major necrotrophic pathogens in sunflower, uncovering unique QTLs for each pathogen as well as a shared QTL, suggesting strong selection for resistance and a common defense mechanism against these pathogens.
THEORETICAL AND APPLIED GENETICS
(2021)