Review
Cell Biology
Kornsorn Srikulnath, Syed Farhan Ahmad, Worapong Singchat, Thitipong Panthum
Summary: Vertebrates, with over 70,000 living species, play a significant role in biology and research, especially in the study of karyotype evolution. The mysterious presence of microchromosomes in many vertebrate karyotypes raises questions about their evolutionary origins and unique genome structure characteristics. Recent studies have shed light on the high gene densities, low heterochromatin levels, and high recombination rates of microchromosomes, expanding our understanding of karyotype evolution dynamics.
Article
Genetics & Heredity
Areli Ruiz-Mena, Pablo Mora, Eugenia E. Montiel, Teresa Palomeque, Pedro Lorite
Summary: The ant species T. ibericum from the Iberian Peninsula may form supercolonies, potentially invasive and pest species. The complete mitogenome of T. ibericum was analyzed, revealing gene rearrangements unique to Tapinoma species and potentially phylogenetically informative. Phylogenetic analysis supported the monophyletic nature of the genus Tapinoma within the Dolichoderinae subfamily.
Editorial Material
Biochemistry & Molecular Biology
Filip Husnik
Summary: A recent study identifies host-derived cell-division proteins that are directed to the cell envelope of a bacterial endosymbiont in unicellular eukaryotes, highlighting their role in symbiotic cell division.
Article
Multidisciplinary Sciences
Kyung-Ah Kim, Kyeong-Sik Cheon
Summary: This study aimed to assemble and annotate the chloroplast genome of Adenophora racemosa, an endemic species in Korea, and compare it with genomes of related species. The analysis revealed differences in gene order and nucleotide diversity between A. racemosa and other congeners.
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
Biotechnology & Applied Microbiology
Abdullah, Claudia L. Henriquez, Furrukh Mehmood, Amir Hayat, Abdul Sammad, Shahid Waseem, Mohammad Tahir Waheed, Peter J. Matthews, Thomas B. Croat, Peter Poczai, Ibrar Ahmed
Summary: The study elucidated the molecular evolution in cp genomes of species in the Dracunculus clade, revealing high similarity in gene content and genetic characteristics across different genera. It also identified suitable polymorphic loci for phylogenetic inference, broadening our understanding of the chloroplast genome evolution in aroids.
Article
Biochemistry & Molecular Biology
Noah Hensen, Lucas Bonometti, Ivar Westerberg, Ioana Onut Brannstrom, Sonia Guillou, Sandrine Cros-Aarteil, Sara Calhoun, Sajeet Haridas, Alan Kuo, Stephen Mondo, Jasmyn Pangilinan, Robert Riley, Kurt Labutti, Bill Andreopoulos, Anna Lipzen, Cindy Chen, Mi Yan, Chris Daum, Vivian Ng, Alicia Clum, Andrei Steindorff, Robin A. Ohm, Francis Martin, Philippe Silar, Donald O. Natvig, Christophe Lalanne, Valerie Gautier, Sandra Lorena Ament-Velasquezi, Asa Kruys, Miriam I. Hutchinson, Amy Jo Powell, Kerrie Barry, Andrew N. Miller, Igor Grigoriev, Robert Debuchy, Pierre Gladieux, Markus Hiltunen Thoren, Hanna Johannesson
Summary: This study analyzed the genomes of 99 Sordariales species, including 52 newly sequenced genomes, to understand their taxonomy and genome evolution. The results revealed the variations in genomic traits among different families within the order and provided a comprehensive framework for studying genome evolution in this important group of fungi.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Plant Sciences
Dong-Mei Li, Jie Li, Dai-Rong Wang, Ye-Chun Xu, Gen-Fa Zhu
Summary: This study sequenced, assembled, and analyzed ten complete chloroplast genomes of Zingiberoideae plants, providing valuable resources for understanding molecular evolutionary dynamics in the Zingiberaceae family. Divergent hotspots identified in the genomes can be used for developing molecular markers for phylogenetic inference and species identification.
Article
Plant Sciences
Radka Vozarova, Wencai Wang, Jana Lunerova, Fengqing Shao, Jaume Pellicer, Ilia J. Leitch, Andrew R. Leitch, Ales Kovarik
Summary: This study analyzed the abundance and homogeneity of telomeric repeats in a wide range of plant species and found a positive correlation between repeat abundance and intragenomic sequence heterogeneity. The research revealed unique patterns of telomeric repeat diversity in different plant taxa.
Article
Multidisciplinary Sciences
Fushun Wang, Ruolan Zhang, Xiaohua Sun, Junhao Wang, Hongquan Liu, Kang Zhang, Chunyang Wang
Summary: A novel automatic karyotype analysis method EntroCR based on information entropy is proposed in this study, which utilizes whole-genome protein sequences to construct combined figures for automatically classifying chromosome images and identifying chromosome rearrangement patterns. Validation experiments show consistent results with previous studies.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Xiao-Feng Zhang, Jacob B. Landis, Hong-Xin Wang, Zhi-Xin Zhu, Hua-Feng Wang
Summary: This study comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed species differentiation time using whole chloroplast genomes. The results showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and Onagraceae + Lythraceae as sister groups. Molecular dating suggests that the Myrtales crown originated during the Albian age of the Lower Cretaceous.
Article
Biochemistry & Molecular Biology
Hoseong Choi, Yeonhwa Jo, Soo Yeon Choi, Sang-Min Kim, Yu Mi Choi, Jin-Sung Hong, Bong Choon Lee, Won Kyong Cho
Summary: Using RNA sequencing, we obtained 7 SMV genomes from soybean germplasms and conducted a comprehensive evolutionary and phylogenetic study of 143 SMV genomes from various plant species and countries. The study revealed the existence of nine clades of SMV isolates/strains and identified 76 recombinant events and 141 recombinants in total. The study also found that recombination and plant host adaptation are important factors driving the genetic diversity of the SMV genome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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
Jun-Tong Chen, Magnus Liden, Xian-Han Huang, Liang Zhang, Xin-Jian Zhang, Tian-Hui Kuang, Jacob B. Landis, Dong Wang, Tao Deng, Hang Sun
Summary: A systematic study of Corydalis with 530 species revealed three subgenera, 25 sections, and one series as monophyletic, and proposed a new classification with four subgenera, 39 sections, including 16 consistent with previous classification, 16 recircumscribed, one reinstated, and six newly established sections.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Plant Sciences
Qiong Wu, Wei Tong, Huijuan Zhao, Ruoheng Ge, Ruopei Li, Jin Huang, Fangdong Li, Yanli Wang, Ali Inayat Mallano, Weiwei Deng, Wenjie Wang, Xiaochun Wan, Zhengzhu Zhang, Enhua Xia
Summary: Camellia plants have a great diversity and possess immense economic, ornamental, and cultural values. Through sequencing the transcriptomes of 116 Camellia plants, we have constructed a pan-transcriptome and resolved the phylogeny of the genus Camellia. We found that Camellia plants shared a recent whole genome duplication event and had large expansions of transcription factor families associated with stress resistance and secondary metabolism. Additionally, secondary metabolites related to tea quality were heavily accumulated in Camellia plants from section Thea.
Article
Genetics & Heredity
Mikhail A. Moldovan, Svetlana A. Petrova, Mikhail S. Gelfand
FUNGAL GENETICS AND BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Pavel V. Mazin, Elena Shagimardanova, Olga Kozlova, Alexander Cherkasov, Roman Sutormin, Vita V. Stepanova, Alexey Stupnikov, Maria Logacheva, Aleksey Penin, Yoichiro Sogame, Richard Cornette, Shoko Tokumoto, Yugo Miyata, Takahiro Kikawada, Mikhail S. Gelfand, Oleg Gusev
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Evolutionary Biology
Pavel V. Shelyakin, Olga O. Bochkareva, Anna A. Karan, Mikhail S. Gelfand
BMC EVOLUTIONARY BIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Olga M. Sigalova, Andrei Chaplin, Olga O. Bochkareva, Pavel Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, Mikhail S. Gelfand
Article
Microbiology
Zaira Seferbekova, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, Olga O. Bochkareva
Summary: Shigella exhibits high rates of intragenomic rearrangements compared to E. coli, with a decreased rate of homologous recombination. The accumulation of ISs influences many aspects of genome evolution and plays an important role in the evolution of intracellular pathogens. Comparative genomics based on synteny block composition highlights the significance of non-coding regions in the evolution of genomic islands.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemical Research Methods
Aleksandra A. Galitsyna, Mikhail S. Gelfand
Summary: Genome-wide assays for chromatin interactions in single cells have advanced in the past decade, but specialized processing is still needed for sparse interactome data recovery. These methods have highlighted directions for future development in this rapidly moving field.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Artem Stetsenko, Pavlo Stehantsev, Natalia O. Dranenko, Mikhail S. Gelfand, Albert Guskov
Summary: The study reports the functional and structural analysis of a membrane protein CmaX from a pathogenic Pseudomonas aeruginosa bacterium, which has a signature motif deviating from the canonical one. Despite the difference in composition, CmaX shows no changes in substrate selectivity or transport, suggesting that deviations from the canonical motif can easily alter during evolution.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemical Research Methods
Alexey Zabelkin, Yulia Yakovleva, Olga Bochkareva, Nikita Alexeev
Summary: The study defines "parallel rearrangements" and presents a formalization of the problem of parallel rearrangements calling. An algorithmic solution called PaReBrick is implemented for identifying parallel rearrangements in bacterial populations, demonstrating efficiency and accuracy in detecting genome rearrangements responsible for pathogenicity and adaptation.
Article
Biology
Natalia Zakharevich, Mikhail S. Nikitin, Alexey S. Kovtun, Vsevolod O. Malov, Olga Averina, Valery N. Danilenko, Irena I. Artamonova
Summary: The study found differences in the CRISPR-Cas systems of the gut microbiomes of children with ASD compared to the control group, but these differences did not lead to the systems participating in interspecies competition.
Article
Multidisciplinary Sciences
Alexandra M. Ozerova, Mikhail S. Gelfand
Summary: Holometabolous insects show significant changes in gene expression during metamorphosis, resembling the embryonic stage rather than the larval stage. The transition from pupa to imago shows similar gene expression patterns as the transition from embryo to larva. Genes associated with metabolism and development undergo changes in expression levels during the larval stage and revert to an embryonic-like state during metamorphosis.
SCIENTIFIC REPORTS
(2022)
Article
Gastroenterology & Hepatology
Maximilian Baumgartner, Rebecca Zirnbauer, Sabine Schlager, Daniel Mertens, Nikolaus Gasche, Barbara Sladek, Craig Herbold, Olga Bochkareva, Vera Emelianenko, Harald Vogelsang, Michaela Lang, Anton Klotz, Birgit Moik, Athanasios Makristathis, David Berry, Stefanie Dabsch, Vineeta Khare, Christoph Gasche
Summary: With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has been rising over the past two decades. This study found that the emerging pathogen atypical enteropathogenic E. coli (aEPEC) is associated with disease activity in ulcerative colitis (UC) patients, and it may disrupt immune-microbiota homeostasis.
Article
Multidisciplinary Sciences
Ivan N. Semenkov, Pavel Shelyakin, Daria D. Nikolaeva, Maria N. Tutukina, Anna Sharapova, Sergey A. Lednev, Yuliya Sarana, Mikhail S. Gelfand, Pavel P. Krechetov, Tatiana Koroleva
Summary: This article presents original data on the impact of jet-fuel spillage on topsoil properties. The data set includes information on kerosene concentration over time, as well as physicochemical and biological properties of the soil. Additionally, sequencing data on microbial communities are provided.
Article
Biochemistry & Molecular Biology
Almira Chervova, Bulat Fatykhov, Alexander Koblov, Evgeny Shvarov, Julia Preobrazhenskaya, Dmitry Vinogradov, Gennady V. Ponomarev, Mikhail S. Gelfand, Marat D. Kazanov
Summary: The mechanisms of APOBEC mutagenesis in human cancers remain poorly understood, with evidence suggesting the importance of replication and the underexplored role of transcription. Gene expression and whole genome sequencing data from five types of human cancers with significant APOBEC activity were analyzed to estimate the involvement of transcription, compare its impact with that of replication, and explore the relative effects on APOBEC mutagenesis. Active APOBEC mutagenesis was found to correlate with gene expression, with an increase in APOBEC-induced mutations in early-replicating regions, and a higher APOBEC mutation density positively correlated with gene expression levels.