Article
Genetics & Heredity
Congcong Dong, Shang Wang, Han Zhang, Jianquan Liu, Minjie Li
Summary: Cornaceae is a representative family in Cornales, with Cornus as the only genus, consisting of around 55 species widely distributed in the Northern Hemisphere. Despite their horticultural, medicinal, and manufacturing importance, no genome sequences were available for this family. This study reported a chromosome-level genome for Cornus controversa, revealing evidence of a whole-genome duplication event unique to this species. The evolutionary features indicated that expanded and unique genes may contribute to stress response, stimulus, and defense. Furthermore, the high genomic diversification observed among living genomes highlights the role of WGD in speciation and diversification, providing insights into the evolutionary history of Cornaceae and the diversification of Asterids.
Review
Genetics & Heredity
Simone Fouche, Ursula Oggenfuss, Emilie Chanclud, Daniel Croll
Summary: Transposable elements play a major role in genome expansions through self-copying mechanisms. Plant pathogens finely control the expression of virulence factors through epigenetic regulation targeted at nearby transposable elements. However, the derepression of transposable elements during stress and infection processes may lead to long-term evolutionary conflicts and genome size expansions, posing a devil's bargain for pathogens.
TRENDS IN GENETICS
(2022)
Review
Plant Sciences
Rocio Deanna, Maria Cristina Acosta, Marisel Scaldaferro, Franco Chiarini
Summary: This review summarizes the cytogenetics knowledge of Solanaceae, discusses its current applications, and explores prospects for progress in systematic botany and plant evolution. The study provides insights into the importance of chromosomal features in understanding family evolution and emphasizes the need for continued production of this type of data. The potential applications in plant biology are outlined, and insights into the mechanisms underlying Solanaceae's diversification are provided.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biology
Zhenyue Wang, Ying Li, Pengchuan Sun, Mingjia Zhu, Dandan Wang, Zhiqiang Lu, Hongyin Hu, Renping Xu, Jin Zhang, Jianxiang Ma, Jianquan Liu, Yongzhi Yang
Summary: This study reveals the phylogenetic relationships and chromosomal evolution of Buxales based on high-quality genome analysis, and provides genomic resources for early-diverging eudicots.
Article
Genetics & Heredity
Qiulu Liang, Gyamfua Afriyie, Zizhao Chen, Zhenmin Xu, Zhongdian Dong, Yusong Guo, Zhongduo Wang
Summary: Opsin, a member of the G protein-coupled receptors superfamily, plays important roles in visual imaging and non-imaging functions in fish. Crimson snapper, a significant economic fish in the South China Sea, was found to have 32 opsin genes in its genome, with high expression levels in the retina and brain.
Article
Biochemistry & Molecular Biology
Duojia Li, Dhyey Gandhi, Tomohiro Kumon, Yukiko M. Yamashita, Amanda Larracuente
Summary: Karyotype refers to the configuration of the genomes in a set of chromosomes. Differences in karyotype between species can hinder biological processes and contribute to incompatibility. This study describes a unique karyotype of a Drosophila melanogaster strain isolated from the Seychelles archipelago, which has lost the ribosomal DNA locus on the X chromosome. The strain also carries a truncated Y chromosome that is stably maintained in the population, despite its inability to support male fertility. The study suggests that the Y chromosome has a larger negative impact on female fitness than the truncated Y chromosome. Furthermore, an independent strain lacking X rDNA quickly evolved multiple karyotypes, including new truncated Y chromosomes and X chromosome fusions containing the Y-derived rDNA fragment, eliminating females' dependence on the Y chromosome. The study proposes that rDNA loci instability may be one of the driving forces of karyotype evolution, a phenomenon also observed in humans.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Jianhua Wang, Guan-Zhu Han
Summary: In this study, a novel retrotransposon lineage called Odin retrotransposons was discovered within the genomes of sea anemones. Phylogenetic analyses showed that Odin retrotransposons were closely related to lokiretroviruses and retroviruses, providing insights into the origin and evolution of retroviruses.
Article
Biochemistry & Molecular Biology
Thomas D. Brekke, Alexander S. T. Papadopulos, Eva Julia, Oscar Fornas, Beiyuan Fu, Fengtang Yang, Roberto de la Fuente, Jesus Page, Tobias Baril, Alexander Hayward, John F. Mulley
Summary: Chromosome-scale genome assemblies using ultralong-read sequencing technologies reveal fine-scale centromere structure and large-scale variation in genome features. A new chromosome-scale genome of the Mongolian gerbil with complete centromere sequence is presented. Gerbil centromeres consist of four different repeats of various lengths in alternating arrays, spanning 1-6 Mb. The study highlights the importance of karyotypic features in genome interpretation and uncovers novel patterns in chromosome evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Hai-Nan Liu, Mao-Song Pei, Charles Ampomah-Dwamena, Guang-Qi He, Tong-Lu Wei, Qiao-Fang Shi, Yi-He Yu, Da-Long Guo
Summary: This study assessed the distribution of long terminal repeat retrotransposons (LTR-RTs) in four cucurbit species and found that they played a significant role in the diversification of cucurbit species, especially in genome size variation. The study also revealed that LTR-RTs had an impact on genes related to dietary fiber synthesis and increased our understanding of genome evolution and trait characterization in cucurbits.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Plant Sciences
Flavia Mascagni, Elena Barghini, Marilena Ceccarelli, Luciana Baldoni, Carlos Trapero, Concepcion Munoz Diez, Lucia Natali, Andrea Cavallini, Tommaso Giordani
Summary: Research has identified a unique model of genome evolution in the Olea genus, in which the expansion of tandem repeated sequences is closely tied to changes in nuclear architecture. There are significant differences in the composition of repetitive DNA among different Olea taxa, and the abundance of tandem repeat sequences is inversely correlated with that of retrotransposons.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Fei Qi, Shuang Liang, Piyi Xing, Yinguang Bao, Richard R. -C. Wang, Xingfeng Li
Summary: This study used molecular cytogenetics to investigate the karyotype composition of intermediate wheatgrass and found variability in the karyotypes of different accessions. The researchers concluded that the chromosomes of intermediate wheatgrass mainly originated from Dasypyrum breviaristatum and the genus Pseudoroegneria.
Article
Biotechnology & Applied Microbiology
Leonardo Adabo Cintra, Thaissa Boldieri de Souza, Leticia Maria Parteka, Lucas Mesquita Barreto, Luiz Filipe Protasio Pereira, Marcos Letaif Gaeta, Romain Guyot, Andre Luis Laforga Vanzela
Summary: In this study, repetitive DNA sequences were identified in the Coffea genus using genome sequencing. A specific short tandem repeat, Coffea_sat11, was found in the pericentromeres of Coffea chromosomes and showed associations with other transposable element fragments. This arrangement appears to have a strong regulatory role in the organization of chromatin around centromeres.
Article
Plant Sciences
Alberto Vangelisti, Samuel Simoni, Gabriele Usai, Flavia Mascagni, Maria Ventimiglia, Lucia Natali, Andrea Cavallini, Tommaso Giordani
Summary: This study identified and characterized the LTP multigenic family in sunflower using the reliable genome sequence, finding a total of 101 putative LTP genes. Sunflower LTPs were categorized into four clades, reflecting their genomic and structural organization. Further analysis showed the prevalence of tandem and whole genome duplication events in the origin of these genes, in line with the polyploidization events in sunflower genome evolution. The expression of LTP genes in response to external stimuli, particularly abscisic acid, auxin, and saline environment, was demonstrated, with some genes exclusively expressed in sunflower seeds.
Article
Biology
Srinjoy Sil, Sarah Keegan, Farida Ettefa, Lance T. Denes, Jef D. Boeke, Liam J. Holt
Summary: LINE-1 (L1) is the dominant retrotransposon in the human genome, accounting for 17% of the genome. The condensation of ORF1p, a RNA-binding protein encoded by L1, is critical for efficient L1 retrotransposition. By studying the assembly dynamics and material properties of ORF1p, we propose that dynamic oligomerization of ORF1p on L1 RNA drives the formation of an essential L1 ribonucleoprotein (RNP) condensate for retrotransposition.
Article
Genetics & Heredity
Renata Luiza Rosa de Moraes, Francisco de Menezes Cavalcante Sassi, Luiz Antonio Carlos Bertollo, Manoela Maria Ferreira Marinho, Patrik Ferreira Viana, Eliana Feldberg, Vanessa Cristina Sales Oliveira, Geize Aparecida Deon, Ahmed B. H. Al-Rikabi, Thomas Liehr, Marcelo de Bello Cioffi
Summary: The study combined classical and molecular cytogenetic analyses to investigate the karyotypes of five Pyrrhulina species. It found significant differences in chromosome numbers and positions among the species, while repetitive DNA content remained relatively consistent. The results suggest that karyotype differentiation in Pyrrhulina is primarily driven by structural rearrangements.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Victor Spangenberg, Marine Arakelyan, Eduard Galoyan, Irena Martirosyan, Alexandra Bogomazova, Elena Martynova, Marcelo de Bello Cioffi, Thomas Liehr, Ahmed Al-Rikabi, Fedor Osipov, Varos Petrosyan, Oxana Kolomiets
Summary: The study reported the cytogenetic characteristics and meiotic process of the diploid parthenogenetic species Darevskia unisexualis from the new population Keti in Armenia. The species was found to have 37 pairs of chromosomes, including 36 acrocentric chromosomes and a single metacentric autosomal chromosome. The study also revealed chromosome fusion occurred between two chromosomes inherited from the maternal species, providing insight into the mechanisms of meiotic recombination between homeologous chromosomes.
MOLECULAR REPRODUCTION AND DEVELOPMENT
(2021)
Article
Cell Biology
Rafael Kretschmer, Ricardo Jose Gunski, Analia del Valle Garnero, Thales Renato Ochotorena de Freitas, Gustavo Akira Toma, Marcelo de Bello Cioffi, Edivaldo Herculano Correa de Oliveira, Rebecca E. O'Connor, Darren K. Griffin
Summary: The study found extensive chromosome reorganization in the smooth-billed ani, including interchromosomal rearrangements involving macro and microchromosomes. Intrachromosomal rearrangements were also observed in some macrochromosomes, with the most notable finding being a rare event of Robertsonian translocation between microchromosome 17 and the Z chromosome.
Article
Environmental Sciences
Vanessa Cristina Sales Oliveira, Patrik Ferreira Viana, Maria Claudia Gross, Eliana Feldberg, Ronis Da Silveira, Marcelo de Bello Cioffi, Luiz Antonio Carlos Bertollo, Carlos Henrique Schneider
Summary: The Amazon aquatic ecosystems are affected by human population growth, leading to changes in water bodies and aquatic biota. The study showed that the spectacled alligator living in urban streams of Manaus city is impacted by environmental pollution, altering the genome and genetic material of the specimens.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Genetics & Heredity
Francisco de M. C. Sassi, Manolo F. Perez, Vanessa Cristina S. Oliveira, Geize A. Deon, Fernando H. S. de Souza, Pedro H. N. Ferreira, Ezequiel A. de Oliveira, Terumi Hatanaka, Thomas Liehr, Luiz A. C. Bertollo, Marcelo de B. Cioffi
Summary: The study revealed that the giant trahiras have a specific and distinct evolutionary pathway within the Hoplias genus, showing a more conservative karyotype compared to species in the H. malabaricus group. Additionally, significant changes were observed in their inner chromosomal level and genetic diversity, highlighting their different evolutionary histories.
Article
Cell Biology
Alex M. V. Ferreira, Patrik F. Viana, Jansen Zuanon, Tariq Ezaz, Marcelo B. Cioffi, Fabio H. Takagui, Eliana Feldberg
Summary: This study presents the karyotype of Panaqolus tankei for the first time, revealing significant differences compared with available data, particularly in terms of karyotype formulae, heterochromatin regions, and rDNA sites.
CYTOGENETIC AND GENOME RESEARCH
(2021)
Article
Cell Biology
Vanessa C. S. Oliveira, Marie Altmanova, Patrik F. Viana, Tariq Ezaz, Luiz A. C. Bertollo, Petr Rab, Thomas Liehr, Ahmed Al-Rikabi, Eliana Feldberg, Terumi Hatanaka, Sebastian Scholz, Alexander Meurer, Marcelo de Bello Cioffi
Summary: This study analyzed the karyotypes of eight species from the Alligatoridae family using various cytogenetic techniques. The research revealed significant differences in chromosome number and morphology between Caimaninae and Alligatorinae species, suggesting fusion/fission rearrangements. Sequence divergence among caiman genomes was also observed, with Paleosuchus exhibiting the highest level of divergence.
Article
Biology
Francisco de M. C. Sassi, Orlando Moreira-Filho, Geize A. Deon, Alexandr Sember, Luiz A. C. Bertollo, Thomas Liehr, Vanessa C. S. Oliveira, Patrik F. Viana, Eliana Feldberg, Marcelo R. Vicari, Marcelo de B. Cioffi
Summary: Fishes from the genus Harttia in the Amazon region exhibit karyotype variability, with some species possessing different chromosome numbers and showing signs of sex chromosome differentiation. This study provides new evidence supporting Harttia as a valuable model for investigating teleost karyotype and sex chromosome dynamics.
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
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
Plant Sciences
Rodrigo Xavier Soares, Clovis Coutinho da Motta Neto, Gideao Wagner Werneck Felix da Costa, Marcelo de Bello Cioffi, Luiz Antonio Carlos Bertollo, Amanda Torres Borges, Wagner Franco Molina
Summary: Carangidae is an important and widespread family of pelagic predatory fishes. Cytogenetic comparisons among representatives of different tribes help understand the process of karyotype divergence. Analysis of four species showed they have similar karyotypes, likely due to pericentric inversions.
COMPARATIVE CYTOGENETICS
(2021)
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
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
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)
Article
Zoology
Mauro Nirchio, Maria Cecilia Masache, Fabilene Gomes Paim, Marcelo de Bello Cioffi, Orlando Moreira Filho, Ramiro Barriga, Claudio Oliveira, Anna Rita Rossi
Summary: Parodontidae is a small group of Neotropical characiform fishes with three genera and 32 species. This study describes the karyotype of S. wagneri, revealing a diploid chromosome number of 2n = 54 and the presence of ZZ/ZW type sex chromosomes. The data suggest a conservative karyotype structure in Parodontidae and hint at an ancient origin of the sex chromosomes in this group of fishes.
NEOTROPICAL ICHTHYOLOGY
(2021)