Article
Biology
Jing Li, Jilin Zhang, Jing Liu, Yang Zhou, Cheng Cai, Luohao Xu, Xuelei Dai, Shaohong Feng, Chunxue Guo, Jinpeng Rao, Kai Wei, Erich D. Jarvis, Yu Jiang, Zhengkui Zhou, Guojie Zhang, Qi Zhou
Summary: Utilizing long-read sequencing and multiplatform scaffolding techniques, we resolved the genome assembly issues in ducks and found extensive overlap in chromosome features between ducks and chickens. The duck W chromosome shares similarities with the human Y chromosome in terms of chromosome structure and suppression of homologous recombination.
Article
Multidisciplinary Sciences
Yang Zhou, Linda Shearwin-Whyatt, Jing Li, Zhenzhen Song, Takashi Hayakawa, David Stevens, Jane C. Fenelon, Emma Peel, Yuanyuan Cheng, Filip Pajpach, Natasha Bradley, Hikoyu Suzuki, Masato Nikaido, Joana Damas, Tasman Daish, Tahlia Perry, Zexian Zhu, Yuncong Geng, Arang Rhie, Ying Sims, Jonathan Wood, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Qiye Li, Huanming Yang, Jian Wang, Stephen D. Johnston, Adam M. Phillippy, Kerstin Howe, Erich D. Jarvis, Oliver A. Ryder, Henrik Kaessmann, Peter Donnelly, Jonas Korlach, Harris A. Lewin, Jennifer Graves, Katherine Belov, Marilyn B. Renfree, Frank Grutzner, Qi Zhou, Guojie Zhang
Summary: The study of egg-laying mammals' genomes offers insights into mammalian evolution, highlighting ancestral and lineage-specific genomic changes in monotremes and mammals. Unique chromosome complex in monotremes may have originated from ancestral chromosome configuration, and differences in specific genes underlie ecological adaptations of monotremes compared to therians.
Article
Multidisciplinary Sciences
Zhen Huang, Luohao Xu, Cheng Cai, Yitao Zhou, Jing Liu, Zaoxu Xu, Zexian Zhu, Wen Kang, Wan Cen, Surui Pei, Duo Chen, Chenggang Shi, Xiaotong Wu, Yongji Huang, Chaohua Xu, Yanan Yan, Ying Yang, Ting Xue, Wenjin He, Xuefeng Hu, Yanding Zhang, Youqiang Chen, Changwei Bi, Chunpeng He, Lingzhan Xue, Shijun Xiao, Zhicao Yue, Yu Jiang, Jr-Kai Yu, Erich D. Jarvis, Guang Li, Gang Lin, Qiujin Zhang, Qi Zhou
Summary: By studying the chromosomal genomes of three amphioxus species, we have gained insight into the evolution of these genomes and the sex-determining regions. These findings are important for understanding the origin and evolution of vertebrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Rafael Kretschmer, Marcelo Santos de Souza, Ivanete de Oliveira Furo, Michael N. Romanov, Ricardo Jose Gunski, Analia del Valle Garnero, Thales Renato Ochotorena de Freitas, Edivaldo Herculano Correa de Oliveira, Rebecca E. O'Connor, Darren K. Griffin
Summary: Interchromosomal rearrangements involving microchromosomes are rare in birds, predominantly found in certain orders. Our study on microchromosomes in different bird orders revealed conservation of ancestral microchromosomal syntenies in some species, while others showed chromosome reorganization.
Article
Biochemistry & Molecular Biology
Sarah Bailey, Joseph Guhlin, Dinindu S. S. Senanayake, Phoebe Scherer, Patricia Brekke, John G. G. Ewen, Anna W. W. Santure, Annabel Whibley
Summary: By assembling the genome of a threatened passerine bird endemic to New Zealand, high-quality reference genomes were generated to assess the evolutionary potential of the species. The assembled genomes were of high quality and provided valuable information about the DNA methylation patterns and sex-specific evolutionary processes. These reference genomes will help in evaluating the adaptive potential and conservation management of this threatened species.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemical Research Methods
Xiaobin Zheng, Joseph R. Tran, Yixian Zheng
Summary: By using the CscoreTool-M method based on probabilistic modeling, multiple 3D genome sub-compartments can be inferred from Hi-C data. This method is more accurate in identifying sub-compartments corresponding to both active and repressed chromatin, and it can quantify the heterogeneity in sub-compartment localization within cell populations. It can also identify sub-compartments related to specific cell cycle stages and gene functions.
Article
Genetics & Heredity
Nicolas Lichilin, Walter Salzburger, Astrid Boehne
Summary: Research shows that the sex determination system can vary between populations of the same fish species. A study on Astatotilapia burtoni, a fish species found in Lake Tanganyika, revealed that there are different sex determination systems in natural populations compared to laboratory strains. The analysis of the species' genomes did not detect differentiated sex chromosomes, suggesting that the sex determination system in A. burtoni is more flexible and may involve non-genetic or poorly differentiated sex chromosomes.
G3-GENES GENOMES GENETICS
(2023)
Article
Plant Sciences
Aretuza Sousa, Veit Schubert, Susanne S. Renner
Summary: The study identified different types of sex chromosomes in liverworts, investigated their recombination environments using molecular cytogenetics and super-resolution microscopy, and found that the heteromorphic sex chromosomes in Frullania dilatata are distinct from autosomes and each other. The similarity between the U chromosomes suggests they may have originated from a non-disjunction event.
Article
Evolutionary Biology
Corentin Dechaud, Sho Miyake, Anabel Martinez-Bengochea, Manfred Schartl, Jean-Nicolas Volff, Magali Naville
Summary: This study using transcriptomic data from male and female gonads of Japanese medaka reveals the correlation between sexually biased genes and TEs. The findings show that more TE copies are overexpressed in testis than in ovaries and sex-biased genes and TEs tend to form clusters with the same expression bias in the genome.
GENOME BIOLOGY AND EVOLUTION
(2021)
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)
Article
Biochemistry & Molecular Biology
Miguel Baltazar-Soares, Patrik Karell, Dominic Wright, Jan-Ake Nilsson, Jon E. Brommer
Summary: This study collected pairwise genome-mitogenome data of the order Strigiformes and identified nuclear insertions of mitochondrial origin (NUMTs) by comparing mitochondrial genomes with nuclear genome assemblies. The results showed that the size of NUMTs negatively correlated with their sequence similarity to the original mtDNA region. Comparative genomics analysis revealed variable phylogenetic patterns of these insertions, suggesting that some insertions might pre-date speciation events within Strigiformes.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Cell Biology
Yasutaka Kakui, Christopher Barrington, Yoshiharu Kusano, Rahul Thadani, Todd Fallesen, Toru Hirota, Frank Uhlmann
Summary: Mitotic chromosomes in different organisms have various dimensions, which may be related to chromatin contacts, thickness, and species-specific organizing principles.
Article
Biology
Mariannah Pravatti Barcellos de Oliveira, Rafael Kretschmer, Geize Aparecida Deon, Gustavo Akira Toma, Tariq Ezaz, Caio Augusto Gomes Goes, Fabio Porto-Foresti, Thomas Liehr, Ricardo Utsunomia, Marcelo de Bello Cioffi
Summary: In this study, the dynamics of satellite DNAs (SatDNAs) accumulation and elimination during W chromosome differentiation in Triportheus fish were investigated. The majority of repetitive sequences were eliminated as speciation occurred in five additional Triportheus species. While the W chromosomes continued to degenerate, the Z chromosomes in some species began to accumulate TauSatDNAs. Species-specific SatDNAs were likely amplified in the heterochromatic regions of both Z and W chromosomes in each species. Thus, the W chromosomes of various Triportheus species underwent significant evolutionary changes within a short period of time (15-25 Myr) after divergence.
Article
Biochemistry & Molecular Biology
Alexander Kostmann, Barbora Augstenova, Daniel Frynta, Lukas Kratochvil, Michail Rovatsos
Summary: Lizards of the Scincoidea clade, including cordylids, gerrhosaurids, skinks, and xantusiids, exhibit almost worldwide distribution and significant ecological and morphological diversity. Despite limited variability in cytogenetic traits, different species show conservation in diploid chromosome numbers but significant variation in chromosome morphology and the presence of interstitial telomeric sequences. Sex chromosomes, identified as XX/XY, are only found in Tiliqua scincoides within this clade, indicating a generally poor stage of differentiation in sex chromosomes among these lizards.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Ecology
Gustavo A. Bravo, C. Jonathan Schmitt, Scott V. Edwards
Summary: The increased capacity of DNA sequencing has led to the availability of over 500 avian reference genomes, contributing to advancements in phylogenomics and comparative, functional, and population genomics. Community-based initiatives like the Bird 10,000 Genomes Project play a crucial role in promoting international collaboration in avian comparative genomics.
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 52, 2021
(2021)
Review
Biochemistry & Molecular Biology
Cesar Martins, Maryam Jehangir
Summary: B chromosomes (Bs) in cichlid fishes have been extensively studied using classical cytogenetics and high-scale DNA, RNA, and epigenetics analysis. They are found only in females in some species and contain genes, relics of genes, transposable elements, and sequences transcribing for significant biological functions. The genic content of B chromosomes in cichlids is related to cell cycle and chromosome structure, influencing sex rates and potentially affecting transcription and epigenetic modifications of the entire genome.
Article
Biotechnology & Applied Microbiology
Jordana Inacio Nascimento-Oliveira, Bruno Evaristo Almeida Fantinatti, Ivan Rodrigo Wolf, Adauto Lima Cardoso, Erica Ramos, Nathalie Rieder, Rogerio de Oliveira, Cesar Martins
Summary: This study is the first to report the connection of B chromosomes and miRNAs in a vertebrate species. The B chromosome impacts the miRNAs expression in several tissues and these miRNAs target several mRNAs involved with important biological processes. The differentially expressed miRNA targets in samples carrying the B chromosome are related to nuclear matrix organization and response to stimulus.
Review
Fisheries
Syed Farhan Ahmad, Maryam Jehangir, Kornsorn Srikulnath, Cesar Martins
Summary: The rapid transformation of fish genomics and the availability of high-quality datasets provide important roadmaps for research, highlighting fish genomes as vital resources for genomic studies.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2022)
Article
Genetics & Heredity
Matheus Azambuja, Viviane Nogaroto, Orlando Moreira-Filho, Cesar Martins, Michelle Orane Schemberger, Marcelo Ricardo Vicari
Summary: By analyzing the U snRNA genes in Apareiodon sp., this study identified nine snRNA multigene families and recognized functional/defective copies. In addition, in situ localization of snDNAs revealed their involvement in chromosomal location changes and dispersion. The findings suggest that defective copies trigger chromosome differentiation and diversification events in Parodontidae.
Article
Genetics & Heredity
Cassiane Furlan Lopes, Alice Lemos Costa, Jaqueline Fernanda Dionisio, Andres Delgado Canedo, Renata da Rosa, Analia Del Valle Garnero, Jose Ricardo Inacio Ribeiro, Ricardo Jose Gunski
Summary: This study evaluated the chromosomal composition, DNA content, and distribution of rDNA clusters in three species of electric-light bugs (Belostoma angustum, Belostoma sanctulum, and Belostoma nessimiani), revealing significant differences among them. Additionally, a comparative analysis showed that genome size represents the DNA content of a common ancestor, with the genomes of different species evolving through gene duplication and heterochromatinization events.
Article
Biochemistry & Molecular Biology
Bruno Rafael Ribeiro de Almeida, Renata Coelho Rodrigues Noronha, Adauto Lima Cardoso, Cesar Martins, Jonas Gama Martins, Rudi Emerson de Lima Procopio, Cleusa Yoshiko Nagamachi, Julio Cesar Pieczarka
Summary: This study investigates meiotic associations and failures in multiple species of Tityus scorpions, as well as the expression of genes in the recombination process. The results show the importance of gamma H2AX and holocentric chromosomes in maintaining the quadrivalent and normal meiotic cycle.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Adauto Lima Cardoso, Natalia Bortholazzi Venturelli, Irene da Cruz, Fabio Malta de Sa Patroni, Diogo de Moraes, Rogerio Antonio de Oliveira, Ricardo Benavente, Cesar Martins
Summary: In this study, the meiotic behavior and transmission rates of the B chromosome in A. latifasciata were investigated. The B chromosome was found to have self-pairing behavior in the meiotic structure, indicating that isochromosome formation may be a step in the evolution of the B chromosome. Additionally, copies of cell cycle genes were identified in the B chromosome and were found to be transcribed in the encephalon, muscle, and gonads of the host, potentially providing beneficial effects and contributing to the maintenance of the B chromosome.
MOLECULAR GENETICS AND GENOMICS
(2022)
Article
Genetics & Heredity
Renata C. R. Noronha, Bruno R. R. Almeida, Monique C. S. Chagas, Flavia S. Tavares, Adauto L. Cardoso, Carlos E. M. C. Bastos, Natalia K. N. Silva, Alex G. C. M. Klautau, Fabia O. Luna, Fernanda L. N. Attademo, Danielle S. Lima, Luiz A. Sabioni, Maria I. C. Sampaio, Jairo Moura Oliveira, Luis Adriano Santos do Nascimento, Cesar Martins, Marcelo R. Vicari, Cleusa Y. Nagamachi, Julio C. Pieczarka
Summary: Significant efforts have been made to preserve manatees, with a recent study identifying a hybrid zone between Trichechus inunguis and Trichechus manatus manatus. Karyotype analysis revealed differences among manatee hybrids, suggesting they may represent different generations formed through crossing or F1 generations with karyotype variations resulting from different mechanisms.
Article
Agriculture, Dairy & Animal Science
Thays Duarte de Oliveira, Natasha Avila Bertocchi, Rafael Kretschmer, Edivaldo H. C. de Oliveira, Marcelo de Bello Cioffi, Thomas Liehr, Thales R. O. de Freitas
Summary: In this study, molecular cytogenetic analysis was used to investigate the genomic elements involved in the population variation observed in the Neotropical underground rodents of the genus Ctenomys. The results suggest that there is a correlation between repetitive genomic content and localization of evolutionary breakpoint regions, highlighting their direct impact on promoting chromosomal rearrangements.
Article
Biology
Jordana Inacio Nascimento Oliveira, Adauto Lima Cardoso, Ivan Rodrigo Wolf, Rogerio Antonio de Oliveira, Cesar Martins
Summary: This study characterized PIWI-interacting RNA (piRNA) clusters and pathways responsible for silencing the mobilization of transposable elements (TEs) in the gonads of the cichlid fish Astatotilapia latifasciata carrying the B chromosome. The study predicted and annotated piRNA clusters in the A. latifasciata genome for the first time and observed biased expression related to sex and the presence of the B chromosome. The study also identified three piRNA clusters in the B chromosome, with two of them exclusively expressed in gonads of samples with the B chromosome. The study suggests that the B chromosome has its own genomic guardians to prevent uncontrolled TE mobilization.
Article
Biochemistry & Molecular Biology
Anelise Fernandes e Silva, Thays Duarte de Oliveira, Natasha Avila Bertocchi, Vera Lucia da Silva Valente, Edison Zefa, Marindia Depra
Summary: This study investigated the chromosome set and phylogenetic relationships of four Neotropical species, revealing variations in diploid number and sex-chromosome systems. The research suggests the occurrence of descending dysploidy events during the evolution of the group.
GENETICS AND MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Natasha Avila Bertocchi, Thays Duarte de Oliveira, Marindia Depra, Beatriz Goni, Vera Lucia S. Valente
Summary: Transposable elements are an important part of the genome that can influence organisms through various mechanisms. In this study, we compared and evaluated the presence, structure, and copy number of three hAT superfamily transposons in different strains of Drosophila willistoni species. We found that these transposons were widely distributed in the species, but with some variations among strains. These differences could reflect the genomic and chromosomal plasticity of D. willistoni in adapting to different environments.
GENETICS AND MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ivanete de Oliveira Furo, Rafael Kretschmer, Patricia C. M. O'Brien, Jorge Claudio da Costa Pereira, Ricardo Jose Gunski, Analia Del Valle Garnero, Rebecca E. O'Connor, Darren Karl Griffin, Malcolm A. Ferguson-Smith, Edivaldo Herculano Correa de Oliveira
Summary: The study analyzed the karyotype of Gallinula melanops using classical and molecular cytogenetics, revealing chromosome rearrangements similar to those found in the Fulica clade, including fissions of chromosomes 4 and 5 and fusions between GGA4/GGA5 segments. This confirms the placement of G. melanops in the Gallinula genus despite suggestions to include it in the Porphyriops genus.
GENETICS AND MOLECULAR BIOLOGY
(2021)
