Journal articles: 'Genetics and Genome Biology'

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Pennisi, E. "Genetics: From Genes to Genome Biology." Science 272, no. 5269 (June 21, 1996): 1736–38. http://dx.doi.org/10.1126/science.272.5269.1736.

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Pegoraro, Mirko, and Gareth D. Weedall. "Malaria in the ‘Omics Era’." Genes 12, no. 6 (May 30, 2021): 843. http://dx.doi.org/10.3390/genes12060843.

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Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth—the number of Plasmodium species’ genomes sequenced—and in depth—massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.

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Smýkal, P. "Pea (Pisum sativum L.) in biology prior and after Mendel's discovery." Czech Journal of Genetics and Plant Breeding 50, No. 2 (June 12, 2014): 52–64. http://dx.doi.org/10.17221/2/2014-cjgpb.

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Pea (Pisum sativum L.) has been extensively used in early hybridization studies and it was the model organism of choice for Mendel’s discovery of the laws of inheritance, making pea part of the foundation of modern genetics. Pea has also been used as model for experimental morphology and physiology. However, subsequent progress in pea genomics has lagged behind many other plant species, largely as a consequence of its genome size and low economic significance. The availability of the genome sequences of five legume species (Medicago truncatula, Lotus japonicus, Glycine max, Cajanus cajan and Cicer aerietinum) offers opportunities for genome wide comparison. The combination of a candidate gene and synteny approach has allowed the identification of genes underlying agronomically important traits such as virus resistances and plant architecture. Useful genomic resources already exist and include several types of molecular marker sets as well as both transcriptome and proteome datasets. The advent of greater computational power and access to diverse germplasm collections enable the use of association mapping to identify genetic variation related to desirable agronomic traits. Current genomic knowledge and technologies can facilitate the allele mining for novel traits and their incorporation from wild Pisum sp. into elite domestic backgrounds. Fast neutron and targeting-induced local lesions in genomes (TILLING) pea mutant populations are available for reverse genetics approaches, BAC libraries for positional gene cloning as well as transgenic and in vitro regeneration for proof of function through gene silencing or over-expression. Finally, recently formed International Pea Genome Sequencing Consortium, holds promise to provide the pea genome sequence by 2015, a year of 150 anniversary of Mendel’s work.

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Teterina, Anastasia A., John H. Willis, and Patrick C. Phillips. "Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization." Genetics 214, no. 4 (February 28, 2020): 769–80. http://dx.doi.org/10.1534/genetics.119.303018.

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The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of interchromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species.

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Beacon, Tasnim H., James R. Davie, and Michael J. Hendzel. "Introduction: Genome Biology." Genome 64, no. 4 (April 2021): v—vii. http://dx.doi.org/10.1139/gen-2021-0003.

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Totikov, Azamat, Andrey Tomarovsky, Dmitry Prokopov, Aliya Yakupova, Tatiana Bulyonkova, Lorena Derezanin, Dmitry Rasskazov, et al. "Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology." Genes 12, no. 9 (August 28, 2021): 1336. http://dx.doi.org/10.3390/genes12091336.

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Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

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Bult, C. J. "The Mouse Genome Database (MGD): integrating biology with the genome." Nucleic Acids Research 32, no. 90001 (January 1, 2004): 476D—481. http://dx.doi.org/10.1093/nar/gkh125.

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Shiloh, Y. "Cancer genetics: Tumor biology and genome technology converge." European Journal of Cancer 29 (January 1993): S9. http://dx.doi.org/10.1016/0959-8049(93)90650-5.

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Wixon, Jo. "Meeting Highlights: Genome Sequencing and Biology 2001." Comparative and Functional Genomics 2, no. 4 (2001): 243–51. http://dx.doi.org/10.1002/cfg.97.

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We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.

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Sung, Bong Hyun, Donghui Choe, Sun Chang Kim, and Byung-Kwan Cho. "Construction of a minimal genome as a chassis for synthetic biology." Essays in Biochemistry 60, no. 4 (November 30, 2016): 337–46. http://dx.doi.org/10.1042/ebc20160024.

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Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput ‘-omics’ research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300–500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis. Current size-reduced genomes are not perfect minimal genomes, but chemically synthesized genomes have just been constructed. Some minimal genomes provide various desirable functions for bioindustry, such as improved genome stability, increased transformation efficacy and improved production of biomaterials. The minimal genome as a chassis genome for synthetic biology can be used to construct custom-designed genomes for various practical and industrial applications.

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Volkman, Sarah K., Daniel E. Neafsey, Stephen F. Schaffner, Daniel J. Park, and Dyann F. Wirth. "Harnessing genomics and genome biology to understand malaria biology." Nature Reviews Genetics 13, no. 5 (April 12, 2012): 315–28. http://dx.doi.org/10.1038/nrg3187.

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Deakin, Janine E., Sally Potter, Rachel O’Neill, Aurora Ruiz-Herrera, Marcelo B. Cioffi, Mark D. B. Eldridge, Kichi Fukui, et al. "Chromosomics: Bridging the Gap between Genomes and Chromosomes." Genes 10, no. 8 (August 20, 2019): 627. http://dx.doi.org/10.3390/genes10080627.

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The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term ‘chromosomics’ as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.

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Chen, Xiao-Guang, Xuanting Jiang, Jinbao Gu, Meng Xu, Yang Wu, Yuhua Deng, Chi Zhang, et al. "Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution." Proceedings of the National Academy of Sciences 112, no. 44 (October 19, 2015): E5907—E5915. http://dx.doi.org/10.1073/pnas.1516410112.

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The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits a number of human viral diseases, including dengue and Chikungunya fevers. This species has a large genome with significant population-based size variation. The complete genome sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes from southeastern China, a region within the historical range of the origin of the species. The genome comprises 1,967 Mb, the largest mosquito genome sequenced to date, and its size results principally from an abundance of repetitive DNA classes. In addition, expansions of the numbers of members in gene families involved in insecticide-resistance mechanisms, diapause, sex determination, immunity, and olfaction also contribute to the larger size. Portions of integrated flavivirus-like genomes support a shared evolutionary history of association of these viruses with their vector. The large genome repertory may contribute to the adaptability and success of Ae. albopictus as an invasive species.

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McCartney, Michael A., Sophie Mallez, and Daryl M. Gohl. "Genome projects in invasion biology." Conservation Genetics 20, no. 6 (September 11, 2019): 1201–22. http://dx.doi.org/10.1007/s10592-019-01224-x.

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Totikov, Azamat, Andrey Tomarovsky, Lorena Derezanin, Olga Dudchenko, Erez Lieberman-Aiden, Klaus Koepfli, and Sergei Kliver. "Chromosome-Level Genome Assemblies: Expanded Capabilities for Conservation Biology Research." Proceedings 76, no. 1 (November 2, 2020): 10. http://dx.doi.org/10.3390/iecge-07149.

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Genome assemblies are becoming increasingly important for understanding genetic diversity in threatened species. However, due to limited budgets in the area of conservation biology, genome assemblies, when available, tend to be highly fragmented with tens of thousands of scaffolds. The recent advent of high throughput chromosome conformation capture (Hi-C) makes it possible to generate more contiguous assemblies containing scaffolds that are length of entire chromosomes. Such assemblies greatly facilitate analyses and visualization of genome-wide features. We compared genetic diversity in seven threatened species that had both draft genome assemblies and newer chromosome-level assemblies available. Chromosome-level assemblies allowed better estimation of genetic diversity, localization, and, especially, visualization of low heterozygosity regions in the genomes.

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Bailey, E. "Reaping the benefits of an equine genome map." Proceedings of the British Society of Animal Science 2005 (2005): 241. http://dx.doi.org/10.1017/s1752756200011522.

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Genetics has not been a usual academic pursuit in the study of horses. Nutrition, exercise physiology and veterinary topics related to infectious diseases or mechanical defects are more traditional scientific pursuits. Genetics has been left to the realm of horse breeders. Indeed, horse breeders are historically credited with being the leading practitioners of the art and certainly have the longest pedigree records including the Weatherby Studbook and the oral tradition of Arabian horse breeding.On the other hand, modern animal breeder need not yield ground in the area of genetics to horse breeders. Rightfully, our quantitative geneticists can point to the remarkable genetic gains and genetic predictions that have been made with Dairy cattle and since the 1940s,... without benefit of molecular biology!

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Bhadauria, Vijai, Sabine Banniza, Yangdou Wei, and You-Liang Peng. "Reverse Genetics for Functional Genomics of Phytopathogenic Fungi and Oomycetes." Comparative and Functional Genomics 2009 (2009): 1–11. http://dx.doi.org/10.1155/2009/380719.

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Sequencing of over 40 fungal and oomycete genomes has been completed. The next major challenge in modern fungal/oomycete biology is now to translate this plethora of genome sequence information into biological functions. Reverse genetics has emerged as a seminal tool for functional genomics investigations. Techniques utilized for reverse genetics like targeted gene disruption/replacement, gene silencing, insertional mutagenesis, and targeting induced local lesions in genomes will contribute greatly to the understanding of gene function of fungal and oomycete pathogens. This paper provides an overview on high-throughput reverse genetics approaches to decode fungal/oomycete genomes.

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Blake, Judith A., Richard Baldarelli, James A. Kadin, Joel E. Richardson, Cynthia L. Smith, Carol J. Bult, Anna V. Anagnostopoulos, et al. "Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology." Nucleic Acids Research 49, no. D1 (November 24, 2020): D981—D987. http://dx.doi.org/10.1093/nar/gkaa1083.

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Abstract The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. MGD is the authoritative source for biological reference data related to mouse genes, gene functions, phenotypes and mouse models of human disease. MGD is the primary source for official gene, allele, and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. MGD’s biocuration scientists curate information from the biomedical literature and from large and small datasets contributed directly by investigators. In this report we describe significant enhancements to the content and interfaces at MGD, including (i) improvements in the Multi Genome Viewer for exploring the genomes of multiple mouse strains, (ii) inclusion of many more mouse strains and new mouse strain pages with extended query options and (iii) integration of extensive data about mouse strain variants. We also describe improvements to the efficiency of literature curation processes and the implementation of an information portal focused on mouse models and genes for the study of COVID-19.

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Daniels, Jan-Peter, Keith Gull, and Bill Wickstead. "Cell Biology of the Trypanosome Genome." Microbiology and Molecular Biology Reviews 74, no. 4 (December 2010): 552–69. http://dx.doi.org/10.1128/mmbr.00024-10.

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SUMMARY Trypanosomes are a group of protozoan eukaryotes, many of which are major parasites of humans and livestock. The genomes of trypanosomes and their modes of gene expression differ in several important aspects from those of other eukaryotic model organisms. Protein-coding genes are organized in large directional gene clusters on a genome-wide scale, and their polycistronic transcription is not generally regulated at initiation. Transcripts from these polycistrons are processed by global trans-splicing of pre-mRNA. Furthermore, in African trypanosomes, some protein-coding genes are transcribed by a multifunctional RNA polymerase I from a specialized extranucleolar compartment. The primary DNA sequence of the trypanosome genomes and their cellular organization have usually been treated as separate entities. However, it is becoming increasingly clear that in order to understand how a genome functions in a living cell, we will need to unravel how the one-dimensional genomic sequence and its trans-acting factors are arranged in the three-dimensional space of the eukaryotic nucleus. Understanding this cell biology of the genome will be crucial if we are to elucidate the genetic control mechanisms of parasitism. Here, we integrate the concepts of nuclear architecture, deduced largely from studies of yeast and mammalian nuclei, with recent developments in our knowledge of the trypanosome genome, gene expression, and nuclear organization. We also compare this nuclear organization to those in other systems in order to shed light on the evolution of nuclear architecture in eukaryotes.

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Mardis, Elaine R. "Advances in Genome biology and Technology." Pharmacogenomics 5, no. 4 (June 2004): 355–56. http://dx.doi.org/10.1517/14622416.5.4.355.

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Heraghty, Sam D., John M. Sutton, Meaghan L. Pimsler, Janna L. Fierst, James P. Strange, and Jeffrey D. Lozier. "De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii." G3: Genes|Genomes|Genetics 10, no. 8 (June 25, 2020): 2585–92. http://dx.doi.org/10.1534/g3.120.401437.

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Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 – 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species.

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Schmidt, Hanno, Sören Lukas Hellmann, Ann-Marie Waldvogel, Barbara Feldmeyer, Thomas Hankeln, and Markus Pfenninger. "A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera)." G3: Genes|Genomes|Genetics 10, no. 4 (February 14, 2020): 1151–57. http://dx.doi.org/10.1534/g3.119.400710.

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Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Making use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species, and the respective recombination rate among the first insect recombination rates at all. The genome assembly and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in particular. The estimated recombination rate will help evolutionary biologists gaining a better understanding of commonalities and differences of genomic patterns in insects.

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Farré, Marta, and Aurora Ruiz-Herrera. "The Plasticity of Genome Architecture." Genes 11, no. 12 (November 27, 2020): 1413. http://dx.doi.org/10.3390/genes11121413.

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Smith, Mike U. "It’s Not Your Grandmother’s Genetics Anymore!" American Biology Teacher 76, no. 4 (April 1, 2014): 224–29. http://dx.doi.org/10.1525/abt.2014.76.4.2.

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Genetics is perhaps the most rapidly growing field of science today. Recent findings such as those of the Human Genome Project have led to new understandings of basic genetic phenomena and even to increased confusion about some basic genetic ideas, such as the nature of the gene. These developments directly influence how we should teach genetics. This article considers eight claims typically made by introductory biology teachers and considers how they differ from current understandings.

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Clarke, Angus. "Genetic imprinting in clinical genetics." Development 108, Supplement (April 1, 1990): 131–39. http://dx.doi.org/10.1242/dev.108.supplement.131.

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Genetic, and indeed genomic, imprinting does occur in humans. This is manifest at the level of the genome, the individual chromosome, subchromosomal region or fragile site, or the single locus. The best evidence at the single gene level comes from a consideration of familial tumour syndromes. Chromosomal imprinting effects are revealed when uniparental disomy occurs, as in the Prader-Willi syndrome and doubtless other sporadic, congenital anomaly syndromes. Genomic imprinting is manifest in the developmental defects of hydatidiform mole, teratoma and triploidy. Fragile (X) mental retardation shows an unusual pattern of inheritance, and imprinting can account for these effects. Future work in clinical genetics may identify congenital anomalies and growth disorders caused by imprinting: the identification of imprinting effects for specific chromosomal regions in mice will allow the examination of the homologous chromosomal region in humans.

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Domazet-Lošo, Tomislav. "mRNA Vaccines: Why Is the Biology of Retroposition Ignored?" Genes 13, no. 5 (April 20, 2022): 719. http://dx.doi.org/10.3390/genes13050719.

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The major advantage of mRNA vaccines over more conventional approaches is their potential for rapid development and large-scale deployment in pandemic situations. In the current COVID-19 crisis, two mRNA COVID-19 vaccines have been conditionally approved and broadly applied, while others are still in clinical trials. However, there is no previous experience with the use of mRNA vaccines on a large scale in the general population. This warrants a careful evaluation of mRNA vaccine safety properties by considering all available knowledge about mRNA molecular biology and evolution. Here, I discuss the pervasive claim that mRNA-based vaccines cannot alter genomes. Surprisingly, this notion is widely stated in the mRNA vaccine literature but never supported by referencing any primary scientific papers that would specifically address this question. This discrepancy becomes even more puzzling if one considers previous work on the molecular and evolutionary aspects of retroposition in murine and human populations that clearly documents the frequent integration of mRNA molecules into genomes, including clinical contexts. By performing basic comparisons, I show that the sequence features of mRNA vaccines meet all known requirements for retroposition using L1 elements—the most abundant autonomously active retrotransposons in the human genome. In fact, many factors associated with mRNA vaccines increase the possibility of their L1-mediated retroposition. I conclude that is unfounded to a priori assume that mRNA-based therapeutics do not impact genomes and that the route to genome integration of vaccine mRNAs via endogenous L1 retroelements is easily conceivable. This implies that we urgently need experimental studies that would rigorously test for the potential retroposition of vaccine mRNAs. At present, the insertional mutagenesis safety of mRNA-based vaccines should be considered unresolved.

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Karczewski, Konrad J., and Alicia R. Martin. "Analytic and Translational Genetics." Annual Review of Biomedical Data Science 3, no. 1 (July 20, 2020): 217–41. http://dx.doi.org/10.1146/annurev-biodatasci-072018-021148.

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Understanding the influence of genetics on human disease is among the primary goals for biology and medicine. To this end, the direct study of natural human genetic variation has provided valuable insights into human physiology and disease as well as into the origins and migrations of humans. In this review, we discuss the foundations of population genetics, which provide a crucial context to the study of human genes and traits. In particular, genome-wide association studies and similar methods have revealed thousands of genetic loci associated with diseases and traits, providing invaluable information into the biology of these traits. Simultaneously, as the study of rare genetic variation has expanded, so-called human knockouts have elucidated the function of human genes and the therapeutic potential of targeting them.

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Sharma, Archana, and T. Satyanarayana. "Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology." Genomics Insights 6 (January 2013): GEI.S12732. http://dx.doi.org/10.4137/gei.s12732.

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With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

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Grigoriev, Igor V., Richard D. Hayes, Sara Calhoun, Bishoy Kamel, Alice Wang, Steven Ahrendt, Sergey Dusheyko, et al. "PhycoCosm, a comparative algal genomics resource." Nucleic Acids Research 49, no. D1 (October 26, 2020): D1004—D1011. http://dx.doi.org/10.1093/nar/gkaa898.

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Abstract Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other ‘omics’ data. PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.

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Berner, Daniel, Marius Roesti, Steven Bilobram, Simon K. Chan, Heather Kirk, Pawan Pandoh, Gregory A. Taylor, Yongjun Zhao, Steven J. M. Jones, and Jacquelin DeFaveri. "De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries." Genes 10, no. 6 (June 3, 2019): 426. http://dx.doi.org/10.3390/genes10060426.

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The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7).

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Dymond, Jessica S., Lisa Z. Scheifele, Sarah Richardson, Pablo Lee, Srinivasan Chandrasegaran, Joel S. Bader, and Jef D. Boeke. "Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course." Genetics 181, no. 1 (November 17, 2008): 13–21. http://dx.doi.org/10.1534/genetics.108.096784.

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Brandolini, A., P. Vaccino, G. Boggini, H. Özkan, B. Kilian, and F. Salamini. "Quantification of genetic relationships among A genomes of wheats." Genome 49, no. 4 (April 1, 2006): 297–305. http://dx.doi.org/10.1139/g05-110.

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The genetic relationships of A genomes of Triticum urartu (Au) and Triticum monococcum (Am) in polyploid wheats are explored and quantified by AFLP fingerprinting. Forty-one accessions of A-genome diploid wheats, 3 of AG-genome wheats, 19 of AB-genome wheats, 15 of ABD-genome wheats, and 1 of the D-genome donor Ae. tauschii have been analysed. Based on 7 AFLP primer combinations, 423 bands were identified as potentially A genome specific. The bands were reduced to 239 by eliminating those present in autoradiograms of Ae. tauschii, bands interpreted as common to all wheat genomes. Neighbour-joining analysis separates T. urartu from T. monococcum. Triticum urartu has the closest relationship to polyploid wheats. Triticum turgidum subsp. dicoccum and T. turgidum subsp. durum lines are included in tightly linked clusters. The hexaploid spelts occupy positions in the phylogenetic tree intermediate between bread wheats and T. turgidum. The AG-genome accessions cluster in a position quite distant from both diploid and other polyploid wheats. The estimates of similarity between A genomes of diploid and polyploid wheats indicate that, compared with Am, Au has around 20% higher similarity to the genomes of polyploid wheats. Triticum timo pheevii AG genome is molecularly equidistant from those of Au and Am wheats.Key words: A genome, Triticum, genetic relationships, AFLP.

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Lu, J., E. Peatman, Q. Yang, S. Wang, Z. Hu, J. Reecy, H. Kucuktas, and Z. Liu. "The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish." Nucleic Acids Research 39, Database (October 8, 2010): D815—D821. http://dx.doi.org/10.1093/nar/gkq765.

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Ferrier, David E. K., and Shunsuke Sogabe. "Genome Biology: Unconventional DNA Repair in an Extreme Genome." Current Biology 28, no. 20 (October 2018): R1208—R1210. http://dx.doi.org/10.1016/j.cub.2018.09.004.

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Singh, Rama S. "Darwin to DNA, molecules to morphology: the end of classical population genetics and the road ahead." Genome 46, no. 6 (December 1, 2003): 938–42. http://dx.doi.org/10.1139/g03-118.

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Molecular reductionism has permeated all of biology and because of successive new technical breakthroughs it has succeeded in unraveling the structural details of genes and genomes. The molecular revolution has reached its reductionist limit, i.e., the study of component parts in isolation, and is ready to come full circle through genomics, proteomics, and gene expression studies back to the phenotype and bring evolutionary biology to confront the Darwinian paradigm, the relationship between gene, organism, and environment. Classical experimental population genetics, dealing with genetic polymorphism and estimation of selection coefficients on a gene-by-gene basis, is coming to an end and a new era of interdisciplinary and interactive biology focusing on dynamic relationships among gene, organism, and environment has begun. In the new population genetics, there will be a shift in focus from single genes to gene networks, from gene-structure to gene-regulation, from additivity to epistasis, and from simple phenotypes to gene-interaction networks and the evolution of complex and modular systems.Key words: genome sequencing, population genetics, gene regulation, gene expression, speciation, norm of reaction, phenotypic plasticity.

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Henry, Robert J. "Progress in Plant Genome Sequencing." Applied Biosciences 1, no. 2 (July 4, 2022): 113–28. http://dx.doi.org/10.3390/applbiosci1020008.

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The genome sequence of any organism is key to understanding the biology and utility of that organism. Plants have diverse, complex and sometimes very large nuclear genomes, mitochondrial genomes and much smaller and more highly conserved chloroplast genomes. Plant genome sequences underpin our understanding of plant biology and serve as a key platform for the genetic selection and improvement of crop plants to achieve food security. The development of technology that can capture large volumes of sequence data at low costs and with high accuracy has driven the acceleration of plant genome sequencing advancements. More recently, the development of long read sequencing technology has been a key advance for supporting the accurate sequencing and assembly of chromosome-level plant genomes. This review explored the progress in the sequencing and assembly of plant genomes and the outcomes of plant genome sequencing to date. The outcomes support the conservation of biodiversity, adaptations to climate change and improvements in the sustainability of agriculture, which support food and nutritional security.

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Munn, Maureen, Peggy O’Neill Skinner, Lane Conn, H. Geraldine Horsma, and Paula Gregory. "The Involvement of Genome Researchers in High School Science Education." Genome Research 9, no. 7 (July 1, 1999): 597–607. http://dx.doi.org/10.1101/gr.9.7.597.

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The rapid accumulation of genetic information generated by the Human Genome Project and related research has heightened public awareness of genetics issues. Education in genome science is needed at all levels in our society by specific audiences and the general public so that individuals can make well-informed decisions related to public policy and issues such as genetic testing. Many scientists have found that an effective vehicle for reaching a broad sector of society is through high school biology courses. From an educational perspective, genome science offers many ways to meet emerging science learning goals, which are influencing science teaching nationally. To effectively meet the goals of the science and education communities, genome education needs to include several major components—accurate and current information about genomics, hands-on experience with DNA techniques, education in ethical decision-making, and career counseling and preparation. To be most successful, we have found that genome education programs require the collaborative efforts of science teachers, genome researchers, ethicists, genetic counselors, and business partners. This report is intended as a guide for genome researchers with an interest in participating in pre-college education, providing rationale for their involvement and recommendations for ways they can contribute, and highlighting a few exemplary programs. World Wide Web addresses for all of the programs discussed in this report are given in Table 1. We are developing a database of outreach programs offering genetics education (http://genetics-education.mbt.washington.edu/database) and request that readers submit an entry describing their programs. We invite researchers to contact us for more information about activities in their local area.

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Gojobori, T., and W. Martin. "Welcome to Genome Biology and Evolution." Genome Biology and Evolution 1 (May 13, 2010): 1. http://dx.doi.org/10.1093/gbe/evp004.

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Adams, David J., and Louise van der Weyden. "Contemporary approaches for modifying the mouse genome." Physiological Genomics 34, no. 3 (August 2008): 225–38. http://dx.doi.org/10.1152/physiolgenomics.90242.2008.

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The mouse is a premiere experimental organism that has contributed significantly to our understanding of vertebrate biology. Manipulation of the mouse genome via embryonic stem (ES) cell technology makes it possible to engineer an almost limitless repertoire of mutations to model human disease and assess gene function. In this review we outline recent advances in mouse experimental genetics and provide a “how-to” guide for those people wishing to access this technology. We also discuss new technologies, such as transposon-mediated mutagenesis, and resources of targeting vectors and ES cells, which are likely to dramatically accelerate the pace with which we can assess gene function in vivo, and the progress of forward and reverse genetic screens in mice.

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Blake, Damer P., Kate Worthing, and Mark C. Jenkins. "Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities." Genes 11, no. 9 (September 21, 2020): 1103. http://dx.doi.org/10.3390/genes11091103.

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Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control.

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Najafi, Ali, Gholamreza Bidkhori, Joseph Bozorgmehr, Ina Koch, and Ali Masoudi-Nejad. "Genome Scale Modeling in Systems Biology: Algorithms and Resources." Current Genomics 15, no. 2 (April 2014): 130–59. http://dx.doi.org/10.2174/1389202915666140319002221.

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Fraser-Liggett, C. M. "Insights on biology and evolution from microbial genome sequencing." Genome Research 15, no. 12 (December 1, 2005): 1603–10. http://dx.doi.org/10.1101/gr.3724205.

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GILLEARD, J. S., and R. N. BEECH. "Population genetics of anthelmintic resistance in parasitic nematodes." Parasitology 134, no. 8 (July 3, 2007): 1133–47. http://dx.doi.org/10.1017/s0031182007000066.

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SUMMARYA key aim of anthelmintic resistance research is to identify molecular markers that could form the basis of sensitive and accurate diagnostic tests. These would provide powerful tools to study the origin and spread of anthelmintic resistance in the field and to monitor strategies aimed at preventing and managing resistance. Molecular markers could also form the basis of routine diagnostic tests for use in surveillance and clinical veterinary practice. Much of the research conducted to date has focused on the investigation of possible associations of particular candidate genes with the resistance phenotype. In the future, as full parasite genome sequences become available, there will be an opportunity to apply genome-wide approaches to identify the genetic loci that underlie anthelmintic resistance. Both the interpretation of candidate gene studies and the application of genome-wide approaches require a good understanding of the genetics and population biology of the relevant parasites as well as knowledge of how resistance mutations arise and are selected in populations. Unfortunately, much of this information is lacking for parasitic nematodes. This review deals with a number of aspects of genetics and population biology that are pertinent to these issues. We discuss the possible origins of resistance mutations and the likely effects of subsequent selection on the genetic variation at the resistance-conferring locus. We also review some of the experimental approaches that have been used to test associations between candidate genes and anthelmintic resistance phenotypes and highlight implications for future genome-wide studies.

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Newman, Catherine E., T. Ryan Gregory, and Christopher C. Austin. "The dynamic evolutionary history of genome size in North American woodland salamanders." Genome 60, no. 4 (April 2017): 285–92. http://dx.doi.org/10.1139/gen-2016-0166.

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The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5–20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.

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Ishii, Takashige, and Koichiro Tsunewaki. "Chloroplast genome differentiation in Asian cultivated rice." Genome 34, no. 5 (October 1, 1991): 818–26. http://dx.doi.org/10.1139/g91-126.

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Restriction endonuclease analysis of chloroplast DNA was carried out to clarify the chloroplast genome differentiation between Asian varieties of Oryza sativa. Based on the restriction fragment patterns obtained with six endonucleases, i.e., EcoRI, HindIII, PstI, PvuII, SmaI, and XhoI, chloroplast genomes of 68 local varieties from 15 Asian countries could be classified into five types (types 1, 3, 10, 11, and 12). Among these types, four length mutations and two base substitutions were found; these changes were located on the PstI physical map of rice chloroplast DNA. In a dendrogram showing genetic relationships among five chloroplast genomes, they are mainly divided into two groups, which we have named as the Japonica (types 1, 11, and 12) and Indica (types 3 and 10) chloroplast genome groups. Both groups are distributed widely in Asian countries. The Japonica isozyme group classified by J.C. Glaszmann (1985. Rice Genetics. International Rice Research Institute, Manila, Philippines, pp. 83–90) carries only the Japonica chloroplast genome, whereas the Indica isozyme group contains both Japonica and Indica chloroplast genomes.Key words: Oryza sativa, Asian varieties, chloroplast DNA, restriction endonuclease analysis, chloroplast genome differentiation.

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Cann, Isaac K. O., and Yoshizumi Ishino. "Archaeal DNA Replication: Identifying the Pieces to Solve a Puzzle." Genetics 152, no. 4 (August 1, 1999): 1249–67. http://dx.doi.org/10.1093/genetics/152.4.1249.

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Abstract Archaeal organisms are currently recognized as very exciting and useful experimental materials. A major challenge to molecular biologists studying the biology of Archaea is their DNA replication mechanism. Undoubtedly, a full understanding of DNA replication in Archaea requires the identification of all the proteins involved. In each of four completely sequenced genomes, only one DNA polymerase (Pol BI proposed in this review from family B enzyme) was reported. This observation suggested that either a single DNA polymerase performs the task of replicating the genome and repairing the mutations or these genomes contain other DNA polymerases that cannot be identified by amino acid sequence. Recently, a heterodimeric DNA polymerase (Pol II, or Pol D as proposed in this review) was discovered in the hyperthermophilic archaeon, Pyrococcus furiosus. The genes coding for DP1 and DP2, the subunits of this DNA polymerase, are highly conserved in the Euryarchaeota. Euryarchaeotic DP1, the small subunit of Pol II (Pol D), has sequence similarity with the small subunit of eukaryotic DNA polymerase δ. DP2 protein, the large subunit of Pol II (Pol D), seems to be a catalytic subunit. Despite possessing an excellent primer extension ability in vitro, Pol II (Pol D) may yet require accessory proteins to perform all of its functions in euryarchaeotic cells. This review summarizes our present knowledge about archaeal DNA polymerases and their relationship with those accessory proteins, which were predicted from the genome sequences.

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Chia, Na-Yu, and Huck-Hui Ng. "Stem cell genome-to-systems biology." Wiley Interdisciplinary Reviews: Systems Biology and Medicine 4, no. 1 (April 11, 2011): 39–49. http://dx.doi.org/10.1002/wsbm.151.

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Verhey, S. D. "Integrated cell biology/biochemistry/molecular genetics laboratories: the cytoplasmic genome projects." Journal of Industrial Microbiology and Biotechnology 24, no. 5 (May 1, 2000): 339–44. http://dx.doi.org/10.1038/sj.jim.2900802.

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Kucukyildirim, Sibel, Megan Behringer, Emily M. Williams, Thomas G. Doak, and Michael Lynch. "Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species Haloferax volcanii." Genetics 215, no. 4 (June 8, 2020): 1107–16. http://dx.doi.org/10.1534/genetics.120.303299.

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Organisms adapted to life in extreme habitats (extremophiles) can further our understanding of the mechanisms of genetic stability, particularly replication and repair. Despite the harsh environmental conditions they endure, these extremophiles represent a great deal of the Earth’s biodiversity. Here, for the first time in a member of the archaeal domain, we report a genome-wide assay of spontaneous mutations in the halophilic species Haloferax volcanii using a direct and unbiased method: mutation accumulation experiments combined with deep whole-genome sequencing. H. volcanii is a key model organism not only for the study of halophilicity, but also for archaeal biology in general. Our methods measure the genome-wide rate, spectrum, and spatial distribution of spontaneous mutations. The estimated base substitution rate of 3.15 × 10−10 per site per generation, or 0.0012 per genome per generation, is similar to the value found in mesophilic prokaryotes (optimal growth at ∼20–45°). This study contributes to a comprehensive phylogenetic view of how evolutionary forces and molecular mechanisms shape the rate and molecular spectrum of mutations across the tree of life.

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Gassanov, Z., D. Kaidarova, A. Zhylkaidarova, and B. Ongarbayev. "Prostate cancer genetics and biology." Oncologia i radiologia Kazakhstana 58, no. 4 (December 31, 2020): 56–59. http://dx.doi.org/10.52532/2521-6414-2020-4-58-56-59.

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Relevance: Despite a high survival with localized prostate cancer, metastatic prostate cancer remains virtually incurable even after intensive multimodal therapy. Death in advanced stages of the disease is caused by the lack of therapeutic regimens able to produce a long-term tumor reaction due to its extreme genetic and cellular heterogeneity. According to epidemiological studies, a family history of prostate cancer significantly increases the risk. Clinical diagnosis is often based on a single biopsy made to determine the molecular status of a particular cancer case. Pathological and genomic heterogeneity can lead to bias in diagnosis. Therefore, the use of genetic research technologies is highly relevant. The purpose wasto justify the use of genetic profiling technologies for patients with prostate cancer. Results: Many cases lack an understanding of the multifactorial impact of current treatment methods on the patient’s immune system. Combination therapy efficacy and tolerability depend on the choice of an optimal treatment regimen. Approaches to prioritizing the types of combination therapy should be developed. Cancer genome affects the disease course and progression. Simulation of these interactions in a genetic model allows predicting the treatment outcome and effectiveness. Conclusions: The conducted systematic review shows that a deep understanding of prostate cancer biology and genetics and genetic profiling can save and improve the lives of many patients with serious diseases.

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Journal articles on the topic 'Genetics and Genome Biology'

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