Article
Biochemistry & Molecular Biology
Szymon Turek, Wojciech Plader, Yoshikazu Hoshi, Agnieszka Skarzynska, Magdalena Pawelkowicz
Summary: This study provides a more comprehensive understanding of the cucumber genome line B10v3 by reordering and comparing its contigs, identifying protein-coding genes and repetitive fragments, and comparing its functional proteins with other genomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Hyun-Hee Lee, Jungwook Park, Hyejung Jung, Young-Su Seo
Summary: Burkholderia gladioli demonstrates high adaptability and versatility in various ecological niches, with niche-associated genomes playing important roles in competition with hosts, degradation of compounds, and DNA repair. The conservation of rhizomide biosynthetic gene cluster is observed in all strains, with a higher concentration in human isolates. Additionally, absence of CRISPR/Cas system in plant and human pathogenic strains, but presence in those living in nature, suggests a potential inverse relationship with virulence.
Article
Biochemistry & Molecular Biology
Alexander Mackintosh, Roger Vila, Dominik R. Laetsch, Alex Hayward, Simon H. Martin, Konrad Lohse
Summary: Chromosome rearrangements play a role in promoting reproductive isolation between fritillary butterflies. This study investigates the speciation of Brenthis daphne and Brenthis ino and identifies nine chromosome fissions and fusions. The results show that these rearrangements have reduced gene flow and directly contribute to reproductive isolation.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemical Research Methods
Qihua Liang, Stefano Lonardi
Summary: PGV is a reference-agnostic representation of a species' pan-genome based on consensus ordering, enabling intuitive, effective, and interactive visualization of complex structural genomic variations. The PGV software can be easily installed via conda or downloaded from the website, with a companion browser available for testing using example bed tracks from the GitHub page.
BMC BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Dongzhu Jiang, Xiaodong Cai, Min Gong, Maoqin Xia, Haitao Xing, Shanshan Dong, Shuming Tian, Jialin Li, Junyao Lin, Yiqing Liu, Hong-Lei Li
Summary: This study conducted comparative genomics and phylogenetic analysis on the Zingiber genus. The results showed that the chloroplast genomes of Zingiber species have typical structures and conservative characteristics. Positive selection was identified in certain genes. The study also provided the complete chloroplast genome sequences of Zingiber species, which can be used for future research on molecular evolutionary dynamics and population variation.
Article
Biochemical Research Methods
Andre Rodrigues Oliveira, Geraldine Jean, Guillaume Fertin, Klairton Lima Brito, Ulisses Dias, Zanoni Dias
Summary: Genome rearrangements are events that affect large stretches of genomes during evolution. Considering intergenic regions can enhance distance estimation. Approximation algorithms have been developed for transposition distance and signed reversal and transposition distance.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Ecology
Anna Michalik, Eugen Bauer, Teresa Szklarzewicz, Martin Kaltenpoth
Summary: In this study, the symbionts of scale insects from the Eriococcidae family were functionally characterized using microscopic and genomic approaches. These symbionts, Burkholderia bacteria, were found to have highly reduced genomes and a low GC content. They retained biosynthetic pathways for essential amino acids and multiple cofactors. The results suggest that the symbiosis between Burkholderia and eriococcids is relatively young but functionally convergent.
Article
Evolutionary Biology
Nitish Malhotra, Aswin Sai Narain Seshasayee
Summary: Bacterial genome organization is influenced by chromosomal replication and the presence of long identical DNA repeats. The positioning of long DNA repeats in the genome is under selection, as it affects bacterial fitness and growth rate. A study found that the distribution of long DNA repeats differs between fast- and slow-growing bacteria, suggesting that their positioning is a major constraint in maintaining the genome organization and minimizing disruption.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Nikolai V. Ravin, Tatyana S. Rudenko, Dmitry D. Smolyakov, Alexey V. Beletsky, Andrey L. Rakitin, Nikita D. Markov, Alexey Fomenkov, Luo Sun, Richard J. Roberts, Andrey A. Novikov, Olga V. Karnachuk, Margarita Y. Grabovich
Summary: Two strains of filamentous, colorless sulfur bacteria were isolated from a coal mine and the White Sea, while a metagenome-assembled genome was obtained from a sulfidic spring in Russia. Phylogenetic analysis showed that all genomes belonged to the genus Thiothrix, with three proposed new species identified. The core genome of Thiothrix includes genes for metabolism, respiration, and sulfur oxidation pathways.
FRONTIERS IN MICROBIOLOGY
(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
Biochemical Research Methods
Tang Li, Yanbin Yin
Summary: The pan-genome analysis of metagenome-assembled genomes (MAGs) can be affected by issues such as fragmentation, incompleteness, and contamination. In this study, the researchers conducted a critical assessment of pan-genomics by comparing the results of complete bacterial genomes and simulated MAGs. The findings show that incompleteness leads to significant loss of core genes, while contamination mainly affects accessory genomes. Lowering the core gene threshold and using gene prediction algorithms that consider fragmented genes can alleviate the loss, but to a limited extent. The study concludes that new pan-genome analysis tools specifically for MAGs are needed.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Microbiology
Louis Berrios
Summary: The study analyzed the genomes of selected Burkholderia strains from humans and plants, revealing host-specific metabolic pathway potentials and convergent features related to pathogenic overlap between hosts.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sha Cao, Gerrit Brandis, Douglas L. Huseby, Diarmaid Hughes
Summary: Analysis of bacterial genomes reveals that the linear order of genes on the chromosome is often not conserved among different species. Through experimental research on Salmonella, this study provides the first evidence supporting the SNAP hypothesis, which suggests that positive selection during niche adaptation can drive rearrangements in chromosomal gene order. The findings show that the gene order on the Salmonella chromosome changed significantly and irreversibly after adaptation to a new environment.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Chaofang Zhong, Chaoyun Chen, Lusheng Wang, Kang Ning
Summary: Advances in sequencing technology have enabled in-depth profiling of microbial communities through pan-genome and metagenome analysis. The combination of pan-genome and metagenome approaches is seen as a promising method for tracking microbial sources and deciphering population-level evolution. Advanced analytical techniques, including big-data based artificial intelligence, are expected to further enhance our understanding of microbial community patterns.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
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
Biochemistry & Molecular Biology
Pavel V. Mazin, Xi Jiang, Ning Fu, Dingding Han, Meng Guo, Mikhail S. Gelfand, Philipp Khaitovich
Article
Multidisciplinary Sciences
Anna Kaznadzey, Pavel Shelyakin, Evgeniya Belousova, Aleksandra Eremina, Uliana Shvyreva, Darya Bykova, Vera Emelianenko, Anastasiya Korosteleva, Maria Tutukina, Mikhail S. Gelfand
SCIENTIFIC REPORTS
(2018)
Article
Microbiology
Sofya K. Garushyants, Alexandra Y. Beliavskaia, Dmitry B. Malko, Maria D. Logacheva, Maria S. Rautian, Mikhail S. Gelfand
FRONTIERS IN MICROBIOLOGY
(2018)
Article
Microbiology
Mikhail A. Moldovan, Mikhail S. Gelfand
FRONTIERS IN MICROBIOLOGY
(2018)
Article
Biochemical Research Methods
Evgeny E. Akkuratov, Mikhail S. Gelfand, Ekaterina E. Khrameeva
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Olga O. Bochkareva, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky, Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, Mikhail S. Gelfand
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
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
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
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.