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Multidisciplinary Sciences
Bjarni Halldorsson, Hannes P. Eggertsson, Kristjan H. S. Moore, Hannes Hauswedell, Ogmundur Eiriksson, Magnus O. Ulfarsson, Gunnar Palsson, Marteinn T. Hardarson, Asmundur Oddsson, Brynjar O. Jensson, Snaedis Kristmundsdottir, Brynja D. Sigurpalsdottir, Olafur A. Stefansson, Doruk Beyter, Guillaume Holley, Vinicius Tragante, Arnaldur Gylfason, Pall Olason, Florian Zink, Margret Asgeirsdottir, Sverrir T. Sverrisson, Brynjar Sigurdsson, Sigurjon A. Gudjonsson, Gunnar T. Sigurdsson, Gisli H. Halldorsson, Gardar Sveinbjornsson, Kristjan Norland, Unnur Styrkarsdottir, Droplaug N. Magnusdottir, Steinunn Snorradottir, Kari Kristinsson, Emilia Sobech, Helgi Jonsson, Arni J. Geirsson, Isleifur Olafsson, Palmi Jonsson, Ole Birger Pedersen, Christian Erikstrup, Soren Brunak, Sisse Rye Ostrowski, Gudmar Thorleifsson, Frosti Jonsson, Pall Melsted, Ingileif Jonsdottir, Thorunn Rafnar, Hilma Holm, Hreinn Stefansson, Jona Saemundsdottir, Daniel F. Gudbjartsson, Olafur T. Magnusson, Gisli Masson, Unnur Thorsteinsdottir, Agnar Helgason, Hakon Jonsson, Patrick Sulem, Kari Stefansson
Summary: A comprehensive understanding of how diversity in the human genome sequence affects phenotypic diversity relies on a reliable characterization of both sequences and phenotypic variation. In this study, whole-genome sequencing of 150,119 individuals from the UK Biobank was performed, leading to insights into the relationship between sequence variation and phenotypic traits. The analysis revealed rare variants with large effects, which were not previously identified through whole-exome sequencing and/or imputation studies.
Article
Multidisciplinary Sciences
Yongsung Lee, Chung Hyun Cho, Chanyoung Noh, Ji Hyun Yang, Seung In Park, Yu Min Lee, John A. West, Debashish Bhattacharya, Kyubong Jo, Hwan Su Yoon
Summary: We report a multipartite circular mitochondrial genome in the Stylonematophyceae red algae, which encode one or two genes bounded by a specific cassette and a conserved constant region. Visualization using fluorescence microscope and scanning electron microscope confirms the circularity of these minicircles. These highly divergent mitogenomes exhibit reduced gene sets. The newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals the transfer of most mitochondrial ribosomal subunit genes to the nuclear genome. Recombination between minicircles and a unique gene inventory may explain the transition from a typical mitochondrial genome to minicircles. Our findings offer insight into minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Yali Hou, Shilei Zhao, Qi Liu, Xiaolong Zhang, Tong Sha, Yankai Su, Wenming Zhao, Yiming Bao, Yongbiao Xue, Hua Chen
Summary: SARS-CoV-2 is a new RNA virus that has been spreading extensively since its first outbreak in December, 2019. The evolution of the virus and its impact on transmission and pathogenicity in humans are still under debate. Understanding the evolutionary mechanism is essential for predicting the epidemic trend and guiding disease control and treatments.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biology
Rasa A. Muktupavela, Martin Petr, Laure Segurel, Thorfinn Korneliussen, John Novembre, Fernando Racimo
Summary: Ancient genome sequencing technologies allow us to study natural selection in unprecedented detail by directly observing the presence or absence of specific alleles in a particular region during the last 10,000 years. However, a complete understanding of natural selection requires more nuanced statistical methods to model allele frequency changes across space and time.
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Genetics & Heredity
Daren C. Card, Andrew G. Van Camp, Trenten Santonastaso, Michael I. Jensen-Seaman, Nicola M. Anthony, Scott V. Edwards
Summary: The study identified the core MHC genomic region in two squamate species and revealed similarities and differences in the genomic structure and composition of MHC regions between squamates and mammals. The investigation also highlighted unique features of the anole MHC, such as higher proportions of DNA transposons and larger MHC region size. Evolutionary analyses of MHC homologs in squamates and other amniotes demonstrated species-specific relationships and functional relevance of certain codons under diversifying selection.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Jinhua Xiao, Xianqin Wei, Yi Zhou, Zhaozhe Xin, Yunheng Miao, Hongxia Hou, Jiaxing Li, Dan Zhao, Jing Liu, Rui Chen, Liming Niu, Guangchang Ma, Wenquan Zhen, Shunmin He, Jianxia Wang, Xunfan Wei, Weihao Dou, Zhuoxiao Sui, Haikuan Zhang, Shilai Xing, Miao Shi, Dawei Huang
Summary: Figs and fig pollinators exhibit obligate pollination mutualism, with genomic evidence revealing differentiation between pollinators and nonpollinators. Pollinators lack certain genes related to environmental stress and immune activation, while showing streamlined gene repertoires in innate immune system, chemosensory toolbox, and detoxification system. This suggests long-term adaptation to figs has led to gene loss in pollinators.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Infectious Diseases
Klara Janeckova, Christian Roos, Pavla Fedrova, Nikola Tom, Darina Cejkova, Simone Lueert, Julius D. Keyyu, Idrissa S. Chuma, Sascha Knauf, David Smajs
Summary: Our study found no significant differences between the genomes of TPE strains that infect nonhuman primates and those that infect humans. Although interspecies transmission in nonhuman primates is rare and evidence for current spillover events is lacking, the presence of the yaws bacterium in nonhuman primates is demonstrated. It is important to continue yaws surveillance in areas where nonhuman primates are naturally infected with TPE, even if yaws is successfully eliminated in humans.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Microbiology
Peng Wu, Wenqi Xiao, Yingyong Luo, Zhuang Xiong, Xiaodie Chen, Jing He, Ajia Sha, Mingying Gui, Qiang Li
Summary: This study investigated the codon bias of 12 mitochondrial core protein-coding genes in 9 Ganoderma species. The results showed that the codons of all Ganoderma strains preferred to end in A/T, and correlations were identified between codon base composition and codon adaptation index, codon bias index, and frequency of optimal codons. The study also revealed variations in base bias indicators between and within Ganoderma strains. Additionally, the study provided insights into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Haiqing Xu, Jianzhi Zhang
Summary: The study examines the impact of the nonrandom structure of the standard genetic code (SGC) on biological processes, suggesting that the frameshift-robustness of SGC may be a byproduct of its mismatch-robustness rather than direct selection.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Kamil S. Jaron, Darren J. Parker, Yoann Anselmetti, Patrick Tran Van, Jens Bast, Zoe Dumas, Emeric Figuet, Clementine M. Francois, Keith Hayward, Victor Rossier, Paul Simion, Marc Robinson-Rechavi, Nicolas Galtier, Tanja Schwander
Summary: This study investigated the genome evolution of parthenogenetic species in the stick insect genus Timema and found that parthenogenesis leads to a significant reduction in heterozygosity and often results in genetically uniform populations. Additionally, the study revealed that parthenogenetic species experience less effective positive selection, indicating that sex is prevalent in natural populations due to its facilitation of rapid adaptation. The study also observed no increased accumulation of transposable elements in parthenogenetic species, likely due to the low TE activity in the genus. Overall, these findings provide empirical support for the negative consequences of parthenogenesis as predicted by theory.
Article
Evolutionary Biology
Jianlong Zhu, Ben J. Evans
Summary: In most eukaryotes, aerobic respiration requires interactions between autosomally encoded genes (N-interact genes) and mitochondrial DNA, RNA, and protein. In species where females are philopatric, contrasting distributions of genetic variation in mitochondrial and nuclear genomes create variation in mitonuclear interactions that may be subject to natural selection. Our study on macaque monkeys suggests that natural selection on mitonuclear interactions could have influenced several aspects of macaque societies including species diversity, ecological breadth, female-biased adult sex ratio and demography, sexual dimorphism, and mitonuclear phylogenomics.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Yu Fu, Fasheng Liang, Congjun Li, Alan Warren, Mann Kyoon Shin, Lifang Li
Summary: This study analyzed the macronuclear genome of ciliates and calculated several indices to investigate codon usage bias and its influencing factors. The results showed that ciliates preferred using codons ending with A or T, and codon usage bias was affected by gene mutation and natural selection.
Article
Multidisciplinary Sciences
Andrew W. Lo, Ruixun Zhang
Summary: Bayes' rule is a fundamental principle that can help humans make adaptive decisions in stochastic environments, which emerges purely through the forces of evolution rather than conscious individual actions. The emergence of finite memory is influenced by specific environmental factors, providing a reasonable explanation for certain phenomena in human cognition.
Article
Genetics & Heredity
Yanqiong Yang, Jiajia Wang, Renhuai Dai, Xianyi Wang
Summary: In this study, the mitochondrial genomes of four Krisna species were sequenced and compared, revealing similar characteristics in base composition, gene size, and codon usage patterns. The analysis of substitution rates showed variations in the evolution rates of different genes. Thirteen protein-coding genes were identified as suitable markers for phylogenetic studies within Krisna, and genes with high nucleotide diversity may be potential markers for population genetics and species delimitation.
Article
Genetics & Heredity
Alexandre Hassanin
Summary: The study analyzed the synonymous nucleotide composition (SNC) of Sarbecovirus genomes and identified eight groups based on specific nucleotide compositional features. The SARS-CoV-2 virus showed unique nucleotide composition compared to other sarbecoviruses. The findings suggest that bats and pangolins played an important role in the evolution of the virus.