Editorial Material
Biochemical Research Methods
Yafei Mao, Guojie Zhang
Summary: The release of the first telomere-to-telomere human genome sequence is a significant milestone in human genomics research, offering potential insights for evolutionary genomics. This article describes the advances of this new genome assembly and discusses the challenges of applying this sequencing strategy to various extant species.
Article
Biochemistry & Molecular Biology
Maria Eduarda Ferraz, Tiago Ribeiro, Mariela Sader, Thiago Nascimento, Andrea Pedrosa-Harand
Summary: Structural karyotype changes in Phaseolus species, specifically in the Leptostachyus group, are associated with ectopic recombination events involving repetitive DNA. Differences in the abundance and distribution of repeat sequences among species within the Leptostachyus group may contribute to the observed high rates of structural rearrangements.
CHROMOSOME RESEARCH
(2023)
Article
Entomology
Liliana M. Mola, Iva Vrbova, Daniela S. Tosto, Magda Zrzava, Frantisek Marec
Summary: This study reveals the evolution of sex chromosome systems in dragonflies through the analysis of two species. It is found that the sex chromosome systems are formed through chromosome rearrangements. Sex in dragonflies is determined by X chromosomes, and the variations in sex chromosome systems are the result of different chromosome rearrangements.
Article
Biochemistry & Molecular Biology
Boudjema Imarazene, Kang Du, Severine Beille, Elodie Jouanno, Romain Feron, Qiaowei Pan, Jorge Torres-Paz, Celine Lopez-Roques, Adrien Castinel, Lisa Gil, Claire Kuchly, Cecile Donnadieu, Hugues Parrinello, Laurent Journot, Cedric Cabau, Margot Zahm, Christophe Klopp, Tomas Pavlica, Ahmed Al-Rikabi, Thomas Liehr, Sergey A. Simanovsky, Joerg Bohlen, Alexandr Sember, Julie Perez, Frederic Veyrunes, Thomas D. Mueller, John H. Postlethwait, Manfred Schartl, Amaury Herpin, Sylvie Retaux, Yann Guiguen
Summary: Sex chromosomes are typically derived from classical type-A chromosomes, with few alternative models proposed. B chromosomes (Bs) are supernumerary and dispensable chromosomes found in many species, considered as selfish genetic elements. Although Bs may play a role in sex determination, the characterization of putative B master sex-determining genes has not yet been provided.
Article
Biochemistry & Molecular Biology
Christophe Dufresnes, Alan Brelsford, Felix Baier, Nicolas Perrin
Summary: Sex chromosomes do not necessarily stop recombining, heterochiasmy does not necessarily constrain heterogamety, and the role of sex-antagonistic genes in the evolution of sex chromosomes may have been overemphasized.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Cell Biology
Ikuo Miura, Foyez Shams, Si-Min Lin, Marcelo de Bello Cioffi, Thomas Liehr, Ahmed Al-Rikabi, Chiao Kuwana, Kornsorn Srikulnath, Yuya Higaki, Tariq Ezaz
Summary: Translocations between sex chromosomes and autosomes can generate multiple sex chromosome systems. In a Taiwanese brown frog, a unique multiple sex chromosome system was discovered, involving three different chromosome pairs with translocations occurring among potential sex-determining chromosomes, including orthologs of sex-determining genes in various vertebrates. This rare case suggests sex-specific, nonrandom translocations, shedding light on the evolutionary significance of multiple sex chromosome systems.
Article
Biochemistry & Molecular Biology
Jun Ping, Yun Xia, Jianghong Ran, Xiaomao Zeng
Summary: In contrast to birds and mammals, cold-blooded vertebrates often have homomorphic sex chromosomes. This study on the torrent frog genus Amolops revealed that the homomorphy of sex chromosomes in these frogs is a result of turnover and X-Y recombination. Furthermore, the sex chromosomes in Amolops show heterogeneous evolution, with both homologous and non-homologous chromosomes involved. The turnover rate of non-homologous sex chromosomes is low in these torrent frogs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Cassia Fernanda Yano, Alexandr Sember, Rafael Kretschmer, Luiz Antonio Carlos Bertollo, Tariq Ezaz, Terumi Hatanaka, Thomas Liehr, Petr Rab, Ahmed Al-Rikabi, Patrik Ferreira Viana, Eliana Feldberg, Ezequiel Aguiar de Oliveira, Gustavo Akira Toma, Marcelo de Bello Cioffi
Summary: Teleost fishes demonstrate a wide array of sex determination and differentiation mechanisms, with some systems showing high genetic differentiation and evolutionary stability. This study characterized the ZZ/ZW sex chromosome system in Triportheidae and Gasteropelecidae fishes, revealing potential mechanisms driving sex chromosome differentiation. The discovery of homeologous ZW sex chromosomes between these lineages suggests their ancient origin and provides an opportunity to examine unique evolutionary forces shaping sex chromosome evolution in fishes and vertebrates.
CHROMOSOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Wenlu Yang, Deyan Wang, Yiling Li, Zhiyang Zhang, Shaofei Tong, Mengmeng Li, Xu Zhang, Lei Zhang, Liwen Ren, Xinzhi Ma, Ran Zhou, Brian J. Sanderson, Ken Keefover-Ring, Tongming Yin, Lawrence B. Smart, Jianquan Liu, Stephen P. DiFazio, Matthew Olson, Tao Ma
Summary: The study revealed that the Populus species P. euphratica and P. alba have XY and ZW sex determination systems, respectively, driven by repeated translocations of a Helitron-like transposon. This translocation may have captured sequences orthologous to a type-A cytokinin response regulator gene. This gene is hypothesized to be a master regulator of sex determination for the entire family, providing insights into the diversification of sex chromosomes in flowering plants.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Beth Osia, Thamer Alsulaiman, Tyler Jackson, Juraj Kramara, Suely Oliveira, Anna Malkova
Summary: There are substantial differences in frequency and complexity of MMB-TI events between normal and cancer cells, with MMB-TIs readily accumulating in several cancer types, particularly in breast and lung cancers. In normal human fibroblast cells, MMB-TIs only appear as germline variants and do not accumulate as de novo somatic mutations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Izolda Pasakinskiene
Summary: Festuca and Lolium grass species show trait complementarities in hybrid variety production, but they also exhibit antagonisms and rearrangements at the genome level. A rare case of an unstable hybrid was discovered, with the donor plant showing pronounced variability in its clonal parts. The study identified diploid plants with a reduced chromosome number derived from F. pratensis, which plays a significant role in recombinant chromosomes. The finding highlights the plasticity of plant genomes and the ability of F. pratensis to restructure itself from a chaotic chromosomal cocktail.
Review
Cell Biology
Syed Farhan Ahmad, Worapong Singchat, Thitipong Panthum, Kornsorn Srikulnath
Summary: Snakes have unique biological features and evolutionary characteristics, making them fascinating model systems for studying genomic evolution and the relationship between variation at the genomic level and phenotypic-level evolution. Snake genomes, similar to other eukaryotic genomes, are composed of a large proportion of repetitive DNA, including transposable elements and satellite repeats. The significance of repetitive DNA in snake genomes, particularly its structural and functional roles, remains unclear. The study highlights the diversity and composition of repetitive DNA in snake genomes, presenting snakes as an emerging and important model system for understanding the impact of repetitive DNA under sex and microchromosome evolution. Certain repetitive elements in snakes are found to be transcriptionally active and show highly dynamic lineage-specific patterns as repeat sequences, suggesting that they may trigger genomic mechanisms contributing to adaptive evolution in snakes. New approaches are reviewed for studying the expression of repetitive elements in complex genomes, such as snakes, to further explore the role of genomic repeats in shaping snake evolution.
Article
Biochemistry & Molecular Biology
Jason M. Sardell, Matthew P. Josephson, Anne C. Dalziel, Catherine L. Peichel, Mark Kirkpatrick
Summary: By comparing closely related species with homologous sex chromosomes, researchers have found that the sex chromosomes of the blackspotted stickleback experienced independent and more extensive recombination suppression, greater X-Y differentiation, and a much higher rate of Y degeneration than the other two species. This could be due to the smaller effective population size in the blackspotted stickleback. Additionally, a recent fusion between the ancestral blackspotted stickleback Y chromosome and Chromosome 12 may have been favored by the very small size of the recombining region on the ancestral sex chromosome.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Biochemistry & Molecular Biology
Ingo Schubert
Summary: DNA double-strand breaks (DSBs) are interruptions in genetic information caused by various environmental and endogenous factors, posing risks of cell lethality and deleterious mutation if mis-repaired. Evolutionary achievements in DSB processing help maintain stable inheritance and drive adaptation by generating new genetic diversity. Targeted DSBs are crucial in genome editing for research, breeding, and therapy purposes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Kohei Nagao, Yoshiki Tanaka, Rei Kajitani, Atsushi Toyoda, Takehiko Itoh, Souichirou Kubota, Yuji Goto
Summary: A study found that in Japanese hagfish, approximately 21% of the genomic DNA in germ cells consists of 16 chromosomes that are eliminated from somatic cells. The researchers identified 16 eliminated repetitive DNA families, with 6 sequences specifically localized on the eliminated chromosomes, supporting the hypothesis that the eight pairs of E-chromosomes are derived from an ancestral chromosomes pair. Through NGS analysis, the researchers also predicted over 100 repetitive and eliminated sequences. They discovered four novel eliminated repetitive DNA sequences and confirmed the chromosomal localization of all eliminated repeats using FISH.
Article
Biochemistry & Molecular Biology
Rafael Kretschmer, Caio Augusto Gomes Goes, Luiz Antonio Carlos Bertollo, Tariq Ezaz, Fabio Porto-Foresti, Gustavo Akira Toma, Ricardo Utsunomia, Marcelo de Bello Cioffi
Summary: This study investigated the composition and role of satellite DNA (satDNA) in the evolution of sex chromosomes in Triportheus species. The results revealed differences in satDNA accumulation on the Z chromosome among different species and different homogenization rates between the Z and W chromosomes. The most abundant satDNA family was found to be localized in the centromeres and potentially played a role in centromere evolution.
Article
Biochemistry & Molecular Biology
Manolo F. Perez, Isabel A. S. Bonatelli, Monique Romeiro-Brito, Fernando F. Franco, Nigel P. Taylor, Daniela C. Zappi, Evandro M. Moraes
Summary: Determining species boundaries in evolutionary biology is challenging due to cryptic diversity and gene flow, with new methods like CNNs showing promising accuracy in distinguishing complex evolutionary histories.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Developmental Biology
Rodrigo Petry Correa de Sousa, Carolina Pinheiro Vasconcelos, Nayara Furtado do Rosario, Aldemir Branco De Oliveira-Filho, Edivaldo Herculano Correa de Oliveira, Marcelo de Bello Cioffi, Marcelo Vallinoto, Glaucia Caroline Silva-Oliveira
Summary: By analyzing the karyotype and distribution of repetitive DNA in two Elopiformes species, the study found that microsatellite sequences are primarily associated with heterochromatin and may contribute to chromosome structure, while transposable elements have different distributions in the two species, indicating potential interspecific differences in their function. Comparative genome mapping provides new insights into the structure and organization of repetitive sequences in the Elopiformes genome.
Article
Biology
Fernando H. S. de Souza, Francisco de M. C. Sassi, Pedro H. N. Ferreira, Luiz A. C. Bertollo, Tariq Ezaz, Thomas Liehr, Manolo F. Perez, Marcelo B. Cioffi
Summary: This study investigated the relationship between the evolution of multiple sex chromosomes together with allopatry and genetic diversity and speciation in the fish species Erythrinus erythrinus. The presence of multiple sex chromosomes was hypothesized to contribute to genetic differentiation and potentially accelerate speciation. The results showed high genetic differentiation among populations, with long-distance allopatry as the main agent of genetic divergence.
Article
Multidisciplinary Sciences
Philipp Kirschner, Manolo F. Perez, Eliska Zaveska, Isabel Sanmartin, Laurent Marquer, Birgit C. Schlick-Steiner, Nadir Alvarez, Florian M. Steiner, Peter Schoenswetter
Summary: Quaternary climatic oscillations had a significant impact on European biogeography, particularly on the Eurasian steppe biome. Through the analysis of plant and insect species, consistent demographic responses of expansion during cold stages and contraction during warm stages were observed. Climate was identified as a driving force underlying genetic variance patterns at the biome level.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Pedro H. N. Ferreira, Fernando H. S. Souza, Renata L. de Moraes, Manolo F. Perez, Francisco de M. C. Sassi, Patrik F. Viana, Eliana Feldberg, Tariq Ezaz, Thomas Liehr, Luiz A. C. Bertollo, Marcelo de B. Cioffi
Summary: Allopatry is considered to be a main contributor to Neotropical biodiversity. In this study, the genetic divergence of five Pyrrhulina species was assessed using population genomics, and the results were combined with cytogenetic data. The findings indicate that molecular genetic diversity is consistent with chromosomal features, and species located in the same geographical region have a closer relationship.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Geize Aparecida Deon, Larissa Glugoski, Francisco de Menezes Cavalcante Sassi, Terumi Hatanaka, Viviane Nogaroto, Luiz Antonio Carlos Bertollo, Thomas Liehr, Ahmed Al-Rikabi, Orlando Moreira-Filho, Marcelo de Bello Cioffi, Marcelo Ricardo Vicari
Summary: This study investigates the differentiation processes and evolutionary history of the rare XX/XY1Y2 sex chromosome system in Harttia species. By using whole chromosome painting probes, the study reveals the existence of homeologous chromosome blocks and the impact of Robertsonian fusions and fissions on sex chromosome origins. The data also support the presence of unstable genomic sites promoting chromosomal differentiation and remodeling within the genus Harttia.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Jana Stundlova, Monika Hospodarska, Karolina Luksikova, Anna Volenikova, Tomas Pavlica, Marie Altmanova, Annekatrin Richter, Martin Reichard, Martina Dalikova, Sarka Pelikanova, Anatolie Marta, Sergey A. Simanovsky, Matyas Hirman, Marek Jankasek, Tomas Dvorak, Joerg Bohlen, Petr Rab, Christoph Englert, Petr Nguyen, Alexandr Sember
Summary: This study investigated the evolution of sex chromosomes in two sister species of African annual killifishes and found that both species shared homomorphic sex chromosomes that evolved prior to their divergence. The study also revealed differences in repetitive DNA sequences between the sex chromosomes, which may result from high turnover of repeat sequences and may not closely relate to the divergence inferred from earlier SNP analyses.
CHROMOSOME RESEARCH
(2022)
Article
Plant Sciences
Monique Romeiro-Brito, Gulzar Khan, Manolo F. Perez, Daniela C. Zappi, Nigel P. Taylor, Gerardus Olsthoorn, Fernando F. Franco, Evandro M. Moraes
Summary: This study reveals the rapid diversification pattern of Pilosocereus species in neotropical drylands and highlights the need for taxonomic rearrangements in the genus. The results indicate that the genus started spreading from the caatinga habitat during the late Pleistocene and experienced an increased diversification rate during the Calabrian age.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Biology
Anna Volenikova, Petr Nguyen, Peter Davey, Hana Sehadova, Barbara Kludkiewicz, Petr Koutecky, James R. Walters, Peter Roessingh, Irena Provaznikova, Michal Sery, Martina Zurovcova, Miluse Hradilova, Lenka Rouhova, Michal Zurovec
Summary: This study fills an important gap in our understanding of the structure, evolution, and function of silk genes. It provides genomic resources for future studies of the chemical ecology of Yponomeuta species.
COMMUNICATIONS BIOLOGY
(2022)
Article
Evolutionary Biology
Martina Dalikova, Irena Provaznikova, Jan Provaznik, Patrick Grof-Tisza, Adam Pepi, Petr Nguyen
Summary: This study investigates the peculiar organization of rDNA in Lepidoptera and suggests that satellite arrays facilitate the homology-mediated spread of rDNA through the integration of extrachromosomal rDNA circles or ectopic recombination.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Camille Cornet, Pablo Mora, Hannah Augustijnen, Petr Nguyen, Marcial Escudero, Kay Lucek
Summary: Repetitive elements can cause large-scale chromosomal rearrangements, potentially promoting reproductive isolation and speciation. The role of repetitive elements in holocentric organisms and their association with karyotype changes in Erebia butterflies and Carex sedges were investigated at both micro- and macro-evolutionary scales. The results suggest that repetitive elements are associated with population differentiation and chromosomal rearrangements in holocentric clades, playing a role in adaptation and species diversification.
Article
Biochemistry & Molecular Biology
Geize Aparecida Deon, Larissa Glugoski, Terumi Hatanaka, Francisco de Menezes Cavalcante Sassi, Viviane Nogaroto, Luiz Antonio Carlos Bertollo, Thomas Liehr, Ahmed Al-Rikabi, Orlando Moreira Filho, Marcelo de Bello Cioffi, Marcelo Ricardo Vicari
Summary: This study investigates the chromosomal rearrangements in the Neotropical armored catfish genus Harttia using powerful tools such as comparative whole chromosome painting. The results reveal the importance of translocation events in the karyotype evolution of Harttia species, as well as the independent origin of two types of multiple sex chromosomes.
GENETICS AND MOLECULAR BIOLOGY
(2022)
