Article
Evolutionary Biology
Nelson J. R. Fagundes, Rafael Bisso-Machado, Pedro I. C. C. Figueiredo, Maikel Varal, Andre L. S. Zani
Summary: The concept of junk DNA, although undermined by the discovery of biochemical functions in traditionally considered junk DNA elements, is still valid. The authors highlight the inadequate concept of biological function and the need to consider two dimensions of discussion - horizontal and vertical - when discussing biological functions.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Alison H. Nguyen, Weixiang Wang, Emily Chong, Kamalakar Chatla, Doris Bachtrog
Summary: By studying the Y chromosomes in fruit flies, it was found that the differences between Y chromosomes are mainly caused by a few active transposable elements, which have recently expanded on the largest Y chromosome. Different elements are responsible for the expansion of Y on differently sized chromosomes.
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
Kelly E. Miller, Clotilde Cadart, Rebecca Heald
Summary: Genome size and cell size in frogs are strongly correlated, and this correlation affects developmental rate. However, it is unclear how the relationship between cell size and ploidy is established during embryonic development. By studying different polyploid frogs, researchers discovered that cell size is primarily determined by egg size, while nuclear size is correlated with genome size. At the subcellular level, nuclear size is more strongly correlated with genome size, while mitotic spindle size scales with cell size. These findings demonstrate the relationship between cell size and ploidy in frogs and reveal different size scaling mechanisms during embryogenesis, suggesting that Xenopus development is consistent across a wide range of genome and egg sizes.
Article
Multidisciplinary Sciences
Ho-Yon Hwang, Jiou Wang
Summary: Genetic mapping is crucial in narrowing down candidate mutations and genes corresponding to mutant phenotypes. This study introduces a mapping toolkit for use in Caenorhabditis elegans, utilizing insertion-deletion polymorphisms for efficient and cost-effective mapping. The method minimizes the need for large populations of mutants and showcases its strengths and weaknesses through mapping of known and unknown mutations.
SCIENTIFIC REPORTS
(2021)
Article
Evolutionary Biology
Leonardo G. de Lima, Francisco J. Ruiz-Ruano
Summary: This study conducted a comprehensive analysis of SatDNA in 37 species from the genus Drosophila, revealing the diversity and variation of SatDNA sequences in the genome. The study also identified shared SatDNA families among closely related species and the emergence of species-specific SatDNA families. Additionally, the study found a positive correlation between genome size and the category of repetitive elements.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Yong Sheng, Hengyu Wang, Yixin Ou, Yingying Wu, Wei Ding, Meifeng Tao, Shuangjun Lin, Zixin Deng, Linquan Bai, Qianjin Kang
Summary: CRISPR-Cas immunity systems protect prokaryotic genomes by inhibiting the invasion of mobile genetic elements. The authors demonstrate that insertion sequences can insert into cas genes, thereby inactivating CRISPR defenses and increasing bacterial susceptibility to foreign DNA invasion.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Amalia Ibiapino, Miguel A. Garcia, Bruno Amorim, Mariana Baez, Mihai Costea, Sasa Stefanovic, Andrea Pedrosa-Harand
Summary: Karyotypes of Cuscuta plants exhibit high diversity in terms of chromosome number and genome size. The prevalent evolutionary processes in this genus include genome duplications and dysploidy. The expansion of genome size in Cuscuta may be associated with its parasitic lifestyle. The position of rDNA sites varies, especially in species with multiple sites in the same karyotype.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Computer Science, Information Systems
Ziyang Lu, Yiwei Zhang
Summary: This study focuses on deletion and insertion errors in DNA-based storage and communication systems. An upper bound on the size of binary codes that can correct a (t, s)-burst error is provided, demonstrating the minimum redundancy required for such codes. An explicit construction for binary (t, s)-burst correcting codes for the case where t = 2s is also presented.
IEEE TRANSACTIONS ON INFORMATION THEORY
(2023)
Article
Biotechnology & Applied Microbiology
Shanshan Huang, Huiying Li, Liyuan Ma, Rui Liu, Yiran Li, Hongmei Wang, Xiaolu Lu, Xinping Huang, Xinhong Wu, Xueduan Liu
Summary: This study analyzed the distribution and evolution of insertion sequences (IS) in 36 Acidithiobacillus genomes and found significant differences in IS distribution and copy number among different species. ISs can enhance the resistance of Acidithiobacillus to heavy metals and improve their adaptation to extreme acidic environments by utilizing sulfur.
Article
Biochemistry & Molecular Biology
Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose, Tal Pupko
Summary: The article discusses the evolutionary events of insertions and deletions of short DNA segments, proposes the phenomenon of border-induced selection, and develops corresponding dynamic models to explore the topic.
Article
Mathematics, Applied
Qing Li, Songtao Li, Yanling Zhang, Xiaojie Chen, Shuo Yang
Summary: Social norms play a significant role in the emergence of fairness in the dictator game. However, there are limited studies on how social norms influence the evolution of fairness through indirect reciprocity. This study proposes an indirect reciprocal model and finds that specific dominant norms can lead to high levels of fairness in reputation-based role assignment.
Article
Genetics & Heredity
Basdeo Kushwaha, Naresh S. Nagpure, Shreya Srivastava, Manmohan Pandey, Ravindra Kumar, Sudhir Raizada, Suyash Agarwal, Mahender Singh, Valaparamail S. Basheer, Rahul G. Kumar, Paramananda Das, Sofia P. Das, Siddhi Patnaik, Amrita Bit, Satish Kumar Srivastava, Achchhe L. Vishwakarma, Chaitanya G. Joshi, Dinesh Kumar, Joy K. Jena
Summary: Precise estimation of genome size is crucial for various genomic studies. This study estimated the genome size of 51 freshwater teleosts and explored the relationship between genome size, chromosome number, and body length. The findings provide valuable information for fish genomics, molecular ecology, and evolutionary conservation genetics.
Article
Biochemistry & Molecular Biology
Michal Gala, Peter Pristas, Gabriel Zoldak
Summary: This paper examined the impact of opening and formation of subdomain interfaces during the evolution of Heat shock proteins 70 (Hsp70). It found that indel events, such as insertions and deletions, in specific regions disrupt the mechanical balance of the protein and cause dysfunction. The study highlights the importance of considering the balance between structural elements in the rational design of functional allosteric machines.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Kaixuan Luo, Jianling Zhong, Alexias Safi, Linda K. Hong, Alok K. Tewari, Lingyun Song, Timothy E. Reddy, Li Ma, Gregory E. Crawford, Alexander J. Hartemink
Summary: In this study, we developed a method called TF Occupancy Profiler (TOP) that allows comprehensive observation and quantification of the binding of multiple transcription factors (TFs) in the genome using data from chromatin accessibility experiments. TOP enables the study of how TF occupancy changes across different cell types, exposure to hormones, and genetic backgrounds of individuals.
Article
Oncology
Sharadha Sakthikumar, Ingegerd Elvers, Jaegil Kim, Maja L. Arendt, Rachael Thomas, Jason Turner-Maier, Ross Swofford, Jeremy Johnson, Steven E. Schumacher, Jessica Alfoldi, Erik Axelsson, C. Guillermo Couto, William C. Kisseberth, Mats E. Pettersson, Gad Getz, Jennifer R. S. Meadows, Jaime F. Modiano, Matthew Breen, Marcin Kierczak, Karin Forsberg-Nilsson, Voichita D. Marinescu, Kerstin Lindblad-Toh
Article
Genetics & Heredity
Mats E. Pettersson, Patric Jern
Article
Multidisciplinary Sciences
Ievgeniia A. Tiukova, Mats E. Pettersson, Marc P. Hoeppner, Remi-Andre Olsen, Max Kaller, Jens Nielsen, Jacques Dainat, Henrik Lantz, Jonas Soderberg, Volkmar Passoth
Article
Multidisciplinary Sciences
Jason Hill, Erik D. Enbody, Mats E. Pettersson, C. Grace Sprehn, Dorte Bekkevold, Arild Folkvord, Linda Laikre, Gunnar Kleinau, Patrick Scheerer, Leif Andersson
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Mats E. Pettersson, Christina M. Rochus, Fan Han, Junfeng Chen, Jason Hill, Ola Wallerman, Guangyi Fan, Xiaoning Hong, Qiwu Xu, He Zhang, Shanshan Liu, Xin Liu, Leanne Haggerty, Toby Hunt, Fergal J. Martin, Paul Flicek, Ignas Bunikis, Arild Folkvord, Leif Andersson
Article
Multidisciplinary Sciences
Nima Rafati, Junfeng Chen, Amaury Herpin, Mats E. Pettersson, Fan Han, Chungang Feng, Ola Wallerman, Carl-Johan Rubin, Sandrine Peron, Arianna Cocco, Marten Larsson, Christian Troetschel, Ansgar Poetsch, Kai Korsching, Wolfgang Boenigk, Heinz G. Koerschen, Florian Berg, Arild Folkvord, U. Benjamin Kaupp, Manfred Schartl, Leif Andersson
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biology
Fan Han, Minal Jamsandekar, Mats E. Pettersson, Leyi Su, Angela P. Fuentes-Pardo, Brian W. Davis, Dorte Bekkevold, Florian Berg, Michele Casini, Geir Dahle, Edward D. Farrell, Arild Folkvord, Leif Andersson
Article
Biochemistry & Molecular Biology
Robert Gustafsson, Ulrich Eckhard, Weihua Ye, Erik D. Enbody, Mats Pettersson, Per Jemth, Leif Andersson, Maria Selmer
Article
Genetics & Heredity
Erik Axelsson, Ingrid Ljungvall, Priyasma Bhoumik, Laura Bas Conn, Eva Muren, Asa Ohlsson, Lisbeth Hoier Olsen, Karolina Engdahl, Ragnvi Hagman, Jeanette Hanson, Dmytro Kryvokhyzha, Mats Pettersson, Olivier Grenet, Jonathan Moggs, Alberto Del Rio-Espinola, Christian Epe, Bruce Taillon, Nilesh Tawari, Shrinivas Mane, Troy Hawkins, Ake Hedhammar, Philippe Gruet, Jens Haggstrom, Kerstin Lindblad-Toh
Summary: Selective breeding in controlled populations has led to a diverse range of canine morphology and behaviors, but also a loss of genetic variation and random trapping of disease alleles. Recent breeding practices may have increased genetic load, as evidenced by a relative rise in deleterious genetic variation in specific breeds such as the cavalier King Charles spaniel. Candidate risk alleles linked to the common veterinary care cause in certain breeds identified through whole genome sequencing suggest a potential predisposition to heart disease.
Article
Biology
Junfeng Chen, Huijuan Bi, Mats E. Pettersson, Daiki X. Sato, Angela P. Fuentes-Pardo, Chunheng Mo, Shady Younis, Ola Wallerman, Patric Jern, Gregorio Moles, Ana Gomez, Gunnar Kleinau, Patrick Scheerer, Leif Andersson
Summary: This study reveals that TSHR alleles associated with reproductive timing in Atlantic herring show differences in cAMP signaling between spring-spawning and autumn-spawning individuals, with both coding and non-coding variants in the TSHR locus potentially regulating seasonal reproduction.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Mette Lillie, Jason Hill, Mats E. Pettersson, Patric Jern
Summary: Endogenous retroviruses (ERVs) have been preserved in host genomes for millions of years, providing insights into the interaction between retroviruses and hosts. The identification of a recently expanded ERV lineage called phaCin-beta in koalas suggests the presence of a possibly still existing phaCin-beta retrovirus. The use of genomics approaches to search for novel retroviruses in host species is highly valuable.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Ananya Roy, Sharadha Sakthikumar, Sergey V. Kozyrev, Jessika Nordin, Raphaela Pensch, Suvi Makelainen, Mats Pettersson, Elinor K. Karlsson, Kerstin Lindblad-Toh, Karin Forsberg-Nilsson
Summary: Current knowledge of cancer genomics is biased against noncoding mutations. This study assessed mutations in conserved positions in the genome to identify genes enriched in noncoding constraint mutations (NCCMs). The comparison of two types of tumors showed different frequencies of NCCMs. These newly identified NCCMs in different molecular pathways may aid in patient stratification and personalized treatment options.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Virology
Mats E. Pettersson, Patric Jern
Summary: Retroviruses have infiltrated vertebrate germlines for millions of years as inherited endogenous retroviruses (ERVs), contributing to genomic innovation and evolution. ZBED6 may play a key role in utilizing ERVs as platforms for genomic innovation and evolution.
Article
Virology
Mats E. Pettersson, Patric Jern
Summary: Endogenous retroviruses and transposable elements play a crucial role in genomic innovation and evolution in mammalian genomes. ZBED6, derived from DNA transposons, may contribute to extended regulatory roles in genomic expression by utilizing ERVs as platforms.
Article
Biotechnology & Applied Microbiology
Sharadha Sakthikumar, Ananya Roy, Lulu Haseeb, Mats E. Pettersson, Elisabeth Sundstrom, Voichita D. Marinescu, Kerstin Lindblad-Toh, Karin Forsberg-Nilsson