Article
Biochemistry & Molecular Biology
Ethan R. Tolman, Christopher D. Beatty, Jonas Bush, Manpreet K. Kohli, Paul B. Frandsen, J. Stephen Gosnell, Jessica L. Ware
Summary: Using genome assemblies of damselfly and dragonfly species, the study found that the autosomes of Odonata have maintained chromosomal orthology despite millions of years of separation. Various factors, such as repeat dynamics, GC content, and chromosome position, influence the density of syntenic blocks across chromosomes, but there is no consistent pattern between species. Additionally, the micro-chromosomes in Odonata are descended from a common ancestor, and, in one species, the micro-chromosome was lost through fusion with autosomes.
Article
Multidisciplinary Sciences
Joana Damas, Marco Corbo, Jaebum Kim, Jason Turner-Maier, Marta Farre, Denis M. Larkin, Oliver A. Ryder, Cynthia Steiner, Marlys L. Houck, Shaune Hall, Lily Shiue, Stephen Thomas, Thomas Swale, Mark Daly, Jonas Korlach, Marcela Uliano-Silva, Camila J. Mazzoni, Bruce W. Birren, Diane P. Genereux, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K. Karlsson, Martin T. Nweeia, Rebecca N. Johnson, Harris A. Tewin
Summary: Decrypting the rearrangements that drive mammalian chromosome evolution is crucial for understanding speciation, adaptation, and disease susceptibility. By computationally reconstructing ancestral karyotypes and syntenic relationships, the study reveals the chromosome structure and evolutionary history of the mammalian ancestors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Thomas C. Mathers, Roland H. M. Wouters, Sam T. Mugford, David Swarbreck, Cock van Oosterhout, Saskia A. Hogenhout
Summary: Chromosome rearrangements in aphids have led to a significant reorganization over the past 30 million years, resulting in the inability to determine chromosome homology between Aphidini and Macrosiphini tribes. Despite rapid sequence evolution, low gene expression, and high transposable element load, gene content of the aphid sex (X) chromosome remained unchanged. Blood-feeding hemipterans, despite being more diverged, have conserved synteny, suggesting that rapid evolution of genome structure may be a unique characteristic of aphids.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Heling Jiang, Xiaoni Zhang, Luhong Leng, Desheng Gong, Xiaohui Zhang, Junyang Liu, Dan Peng, Zhiqiang Wu, Yingxue Yang
Summary: In this study, the haplotype-resolved genome of D. caryophyllus 'Aili' was assembled for the first time at the chromosome level. The lengths of the two assembled haplotypes were determined, and structural variations between the haplotypes were identified. Phylogenetic analysis revealed the species differentiation time between carnation and gypsophila to be approximately 54.43 million years ago. This assembled and annotated genome will facilitate molecular biology studies and contribute to genome-level evolutionary research.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Yunjie Pan, Gangqi Fang, Zhibo Wang, Yanghui Cao, Yongjian Liu, Guiyun Li, Xiaojing Liu, Qiang Xiao, Shuai Zhan
Summary: This study fully sequenced and de novo assembled the reference genome of the tea geometrid Ectropis grisescens, providing insight into its genome structure and characteristics, and focusing on gene families related to host plant adaptation and camouflage.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biotechnology & Applied Microbiology
Qian Xiong, Yuxin Hu, Wenqi Lv, Qinghua Wang, Guoxiang Liu, Zhengyu Hu
Summary: The study identified five chloroplast genomes of Oedogonium species, revealing their structural conservation but variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses suggested that both Oedocladium and Oedogonium are polyphyletic groups. The identification of a positively selected gene in certain species indicates adaptive evolution in terrestrial Oedogoniales taxa.
Article
Multidisciplinary Sciences
Zhen Huang, Zaoxu Xu, Hao Bai, Yongji Huang, Na Kang, Xiaoting Ding, Jing Liu, Haoran Luo, Chentao Yang, Wanjun Chen, Qixin Guo, Lingzhan Xue, Xueping Zhang, Li Xu, Meiling Chen, Honggao Fu, Youling Chen, Zhicao Yue, Tatsuo Fukagawa, Shanlin Liu, Guobin Chang, Luohao Xu
Summary: Microchromosomes are prevalent in nonmammalian vertebrates, but some are missing in bird genome assemblies. This study presents a new chicken reference genome, including all autosomes and sex chromosomes, and provides detailed characterization of small microchromosomes (dot chromosomes) with unique sequence and epigenetic features, shedding insights into the structure and evolution of chromosomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Xianxin Zhao, Hongxing Xu, Kang He, Zhenmin Shi, Xi Chen, Xinhai Ye, Yang Mei, Yajun Yang, Meizhen Li, Libin Gao, Le Xu, Huamei Xiao, Ying Liu, Zhongxian Lu, Fei Li
Summary: The genome of the rice leaffolder was sequenced and assembled successfully, providing a high-quality resource for further research in insect migration, chromosome evolution, and pest control. The genome assembly revealed insights into repeat sequences, expanded gene families associated with hormone biosynthesis, and high chromosomal synteny with other lepidopteran insects. Specifically, the identification of a near-intact W chromosome with enriched metabolic pathways is a significant finding with potential implications for understanding the species.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Xin Long, Deborah Charlesworth, Jianfei Qi, Ruiqiong Wu, Meiling Chen, Zongji Wang, Luohao Xu, Honggao Fu, Xueping Zhang, Xinxin Chen, Libin He, Leyun Zheng, Zhen Huang, Qi Zhou
Summary: Unlike birds and mammals, many teleosts have homomorphic sex chromosomes, and turnovers are common in these chromosomes. This study focused on two seahorse species to investigate the evolution of new sex-determining regions and the accumulation of evolutionary changes in newly sex-linked regions. The analysis revealed that both seahorse species have XY sex chromosome systems with non-homologous sex chromosome pairs, suggesting a turnover event. The Y-linked regions were found to occupy a significant proportion of the sex chromosome and exhibited occasional recombination, indicating that they did not evolve through recombination suppression.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Yuanning Li, Hongyue Liu, Jacob L. Steenwyk, Abigail L. LaBella, Marie-Claire Harrison, Marizeth Groenewald, Xiaofan Zhou, Xing-Xing Shen, Tao Zhao, Chris Todd Hittinger, Antonis Rokas
Summary: Examining the changes in order and arrangement of homologous genes is crucial for understanding genome evolution in eukaryotes. This study analyzed 120 high quality genomes of budding yeast species to investigate the evolution of genome organization and compared it with animals and plants. The decay of macrosynteny and microsynteny was strongly associated with evolutionary divergence in the budding yeast major clades. However, the microsynteny of many genes, especially in metabolic clusters, was deeply conserved within major clades and across subphylum. Comparing genomes with similar divergence times, budding yeasts showed lower conservation in macrosynteny compared to animals and filamentous fungi, but higher conservation than angiosperms. In contrast, they exhibited similar levels of microsynteny conservation with mammals, while angiosperms had very low conservation.
Article
Biochemistry & Molecular Biology
Matthew A. Conte, Frances E. Clark, Reade B. Roberts, Luohao Xu, Wenjing Tao, Qi Zhou, Deshou Wang, Thomas D. Kocher
Summary: This study investigates the evolution of a giant sex chromosome in cichlid fish, finding that it consists of three distinct regions and contains unprecedented amounts of endogenous retroviral elements, immunoglobulin genes, and long non-coding RNAs. Comparative analysis across 69 teleost genomes supports the hypothesis that the giant sex chromosome originated from the fusion of a B chromosome.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Zeynal Akparov, Sabina Hajiyeva, Mehraj Abbasov, Sukhjiwan Kaur, Aladdin Hamwieh, Alsamman M. Alsamman, Elchin Hajiyev, Sevda Babayeva, Vusala Izzatullayeva, Ziyafat Mustafayeva, Sabina Mehdiyeva, Orkhan Mustafayev, Ilham Shahmuradov, Peter Kosarev, Victor Solovyev, Asaf Salamov, Abdulqader Jighly
Summary: This study investigates chromosome evolution in pomegranate and identifies two major chromosome evolution events. Additionally, it reveals a unique admixture between soft- and hard-seeded pomegranate cultivars that can be used to enhance diversity and adaptability in pomegranate varieties worldwide.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Yongxin Sun, Xiangfeng Liu, Xi Xie, Yongan Bai, Shuo Wang, Weiming Teng, Dacheng Li, Hualin Li, Zuoan Yu, Ming Zhang, Zunchun Zhou, Xu Liu, Hongtao Nie, Shaojun Du, Xiaodong Li, Qi Li, Qingzhi Wang
Summary: Mactra veneriformis is an economically important bivalve mollusk in China. In this study, a high-quality chromosome-level genome assembly of M. veneriformis was reported. The assembled genome provides valuable resources for investigating molecular mechanisms and will aid in genetic improvement and disease treatment. Additionally, the study sheds light on the early genomic evolution of Bivalvia.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Yun-Xia Luan, Yingying Cui, Wan-Jun Chen, Jian-Feng Jin, Ai-Min Liu, Cheng-Wang Huang, Mikhail Potapov, Yun Bu, Shuai Zhan, Feng Zhang, Sheng Li
Summary: This study obtained high-quality genomes of two strains of Folsomia candida and conducted comparative genomic analyses. The results showed differences in genome structure, chromosome size, and gene numbers between the parthenogenetic and sexual strains. The high similarity between genomes of the parthenogenetic strains suggested that they are conspecific. Strain-specific genes and gene families were found to be related to environmental adaptation.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Genetics & Heredity
Fengqi Zang, Yan Ma, Xiaolong Tu, Ping Huang, Qichao Wu, Zhimin Li, Tao Liu, Furong Lin, Surui Pei, Dekui Zang, Xuemei Zhang, Yongqi Zheng, Yunyan Yu
Summary: Rosa rugosa, an important shrub with economic, ecological, and pharmaceutical value, had its genome sequenced using PacBio and Hi-C technologies. The assembled genome had a size of 407.1 Mb, with 98% of the sequences anchored to seven pseudochromosomes. Phylogenetic and synteny analysis revealed the evolutionary history and gene conservation between R. rugosa and other closely related species. The genome provides valuable resources for molecular-assisted breeding and horticultural genomics research.
Article
Cell & Tissue Engineering
Thi Minh Xuan Nguyen, Marketa Vegrichtova, Tereza Tlapakova, Magdalena Krulova, Vladimir Krylov
STEM CELLS INTERNATIONAL
(2019)
Article
Biochemistry & Molecular Biology
Eyal Seroussi, Martin Knytl, Frederique Pitel, Daniel Elleder, Vladimir Krylov, Sophie Leroux, Mireille Morisson, Sara Yosefi, Shoval Miyara, Saibaba Ganesan, Mark Ruzal, Leif Andersson, Miriam Friedman-Einat
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Reproductive Biology
Ales Petelak, Vladimir Krylov
Correction
Cell & Tissue Engineering
Thi Minh Xuan Nguyen, Marketa Vegrichtova, Tereza Tlapakova, Magdalena Krulova, Vladimir Krylov
STEM CELLS INTERNATIONAL
(2019)
Article
Chemistry, Multidisciplinary
Blanka Stiburkova, Jana Bohata, Iveta Minarikova, Andrea Mancikova, Jiri Vavra, Vladimir Krylov, Zdenek Dolezel
APPLIED SCIENCES-BASEL
(2019)
Article
Biology
Thi Minh Xuan Nguyen, Marketa Vegrichtova, Tereza Tlapakova, Magdalena Krulova, Vladimir Krylov
Article
Medicine, Research & Experimental
Marketa Vegrichtova, Michaela Hajkova, Bianka Porubska, Daniel Vasek, Vladimir Krylov, Tereza Tlapakova, Magdalena Krulova
Summary: This study demonstrated the ability of Sertoli cells to migrate and modulate the immune response in a phylogenetically distant host. It was found that Sertoli cells induce the expression of molecules associated with immunosuppression, such as IL-10 and PD-1 ligands.
XENOTRANSPLANTATION
(2022)
Article
Genetics & Heredity
Martin Knytl, Nicola R. Fornaini, Barbora Bergelov, Vaclav Gvozdik, Halina Cernohorska, Svatava Kubickova, Eric B. Fokam, Ben J. Evans, Vladimir Krylov
Summary: In this study, cytogenetic and molecular FISH techniques were used to investigate the chromosome morphology and rearrangements in an allotetraploid species of the sister subgenus Silurana. The results showed that the subgenomes of this species have distinctive characteristics, with one subgenome being more conserved and resembling a closely related diploid species, while the other subgenome evolves more rapidly and exhibits pronounced changes in chromosome structure.
Article
Ecology
Nicola R. Fornaini, Barbora Bergelova, Vaclav Gvozdik, Halina Cernohorska, Vladimir Krylov, Svatava Kubickova, Eric B. Fokam, Gabriel Badjedjea, Ben J. Evans, Martin Knytl
Summary: Using fluorescence in situ hybridization and genomic data, we mapped repetitive elements in six species of African clawed frogs and found that polyploidization and divergence play important roles in the evolution of repetitive elements. We also observed conserved loci number and position in one of the subgenus species, while the number of signals varied in other species derived from different polyploidization events.
EUROPEAN JOURNAL OF WILDLIFE RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Barbara Elsnicova, Daniela Hornikova, Veronika Tibenska, David Kolar, Tereza Tlapakova, Benjamin Schmid, Markus Mallek, Britta Eggers, Ursula Schloetzer-Schrehardt, Viktoriya Peeva, Carolin Berwanger, Bettina Eberhard, Hacer Durmus, Dorothea Schultheis, Christian Holtzhausen, Karin Schork, Katrin Marcus, Jens Jordan, Thomas Luecke, Peter F. M. van der Ven, Rolf Schroeder, Christoph S. Clemen, Jitka M. Zurmanova
Summary: Desmin mutations cause cardiomyopathies and negatively impact mitochondria. The deficiency of desmin results in impaired oxidative phosphorylation and fatty and amino acid metabolism in cardiac mitochondria. Increased glucose utilization and upregulation of fetal creatine kinase are compensatory mechanisms to maintain myocardial energy supply.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell & Tissue Engineering
Bianka Porubska, Daniel Vasek, Veronika Somova, Michaela Hajkova, Michaela Hlaviznova, Tereza Tlapakova, Vladimir Holan, Magdalena Krulova
Summary: Sertoli cells (SCs) have been shown to undergo osteogenic, chondrogenic, and adipogenic differentiation successfully, with anti-inflammatory and protective effects. Compared to MSCs, SCs more effectively induce M2 macrophage polarization and regulate inflammatory polarization. Additionally, SCs have demonstrated the ability to transfer mitochondria to immune cells.
STEM CELL REVIEWS AND REPORTS
(2021)
Article
Ecology
Cintia P. Targueta, Vladimir Krylov, Tobias E. Nondilo, Jucivaldo Lima, Luciana B. Lourenco
Summary: In some vertebrate groups like fishes, amphibians, and lizards, interruptions in sex chromosome differentiation are believed to be caused by frequent sex chromosome turnover and occasional recombination between sex chromosomes. The Amazonian frogs of the genus Engystomops have shown evidence of the loss of sex chromosome heteromorphism, with highly divergent karyotypes and unique X and Y chromosome evolution. The phylogenetic data suggest that sex chromosome heteromorphism may have appeared early in the evolution of Engystomops species in the Amazon, but has been lost in some unnamed candidate species.
