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)
Review
Plant Sciences
Shuo Wang, Yong-Qing Qian, Ru-Peng Zhao, Ling-Ling Chen, Jia-Ming Song
Summary: With the advancement of sequencing technology and reduction in sequencing costs, more and more plant genomes have been assembled, revealing extensive variations. However, a single reference genome cannot capture species diversity, leading to the development of pan-genomes. Graph-based pan-genomes have been developed to intuitively characterize structural variations, storing sequence and structural variation information in nodes and paths. This article reviews the origin and development of graph-based pan-genomes, explores their application in plant research, and highlights their potential for future plant breeding.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Sebastian G. Gornik, Victor Flores, Franziska Reinhardt, Lieselotte Erber, Dayana E. Salas-Leiva, Olga Douvropoulou, Imen Lassadi, Elin Einarsson, Mario Moerl, Anna Git, Peter F. Stadler, Arnab Pain, Ross F. Waller
Summary: This study sequenced and assembled mitochondrial genomes of four Perkinsus species and revealed a simple ancestral genome with reduced coding capacity and a tendency for rearrangement. The study identified 75 frameshifts across the four species, which are highly conserved in gene location and likely regulate protein folding. Furthermore, the mitochondrion-encoded rRNA fragments in Perkinsus spp. are incomplete, suggesting import from nuclear DNA.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Lior Glick, Itay Mayrose
Summary: The study of intraspecific genomic variation in eukaryotic species has been a focus of recent genome resequencing projects, with the use of the pan-genome concept presenting advantages over reference-based methods. However, constructing pan-genomes for eukaryotic species remains a challenging task, requiring tailored analysis pipelines and hindering research reproducibility and comparison. The software package Panoramic aims to simplify pan-genome construction for eukaryotic species by providing a user-friendly interface and efficient data processing algorithms.
MOLECULAR ECOLOGY RESOURCES
(2021)
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
Oncology
Alexander Bagaev, Nikita Kotlov, Krystle Nomie, Viktor Svekolkin, Azamat Gafurov, Olga Isaeva, Nikita Osokin, Ivan Kozlov, Felix Frenkel, Olga Gancharova, Nava Almog, Maria Tsiper, Ravshan Ataullakhanov, Nathan Fowler
Summary: Transcriptomic analysis classifies TME into subtypes correlating with immunotherapy response, providing a new approach for personalized cancer treatment.
Article
Biotechnology & Applied Microbiology
Francesco M. Carpi, Maria Magdalena Coman, Stefania Silvi, Matteo Picciolini, Maria Cristina Verdenelli, Valerio Napolioni
Summary: This study aimed to refine the taxonomy and functional characterization of Lactiplantibacillus plantarum genomes through pan-genome analysis, focusing on probiotic potential. The comprehensive genomic analysis of 127 L. plantarum strains provided new insights into the genomic content and variability, establishing a solid reference panel for future characterization of probiotic strains. The study highlighted unique features of L. plantarum strains and identified approximately 70% of probiotic marker genes belonging to the core/soft-core genome.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yingfeng Niu, Chengwen Gao, Jin Liu
Summary: Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. This study sequenced and compared the mitochondrial genomes of three Mangifera species, and found that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome was also identified.
Article
Biochemistry & Molecular Biology
Cheng-Kuo Lai, Yi-Chien Lee, Huei-Mien Ke, Min R. Lu, Wei-An Liu, Hsin-Han Lee, Yu-Ching Liu, Toyoshi Yoshiga, Taisei Kikuchi, Peichen J. Chen, Isheng Jason Tsai
Summary: In this study, the genomes of six Aphelenchoides species, including four strains of the A. besseyi species complex, were analyzed. The systematic identification of horizontal gene transfer (HGT) genes revealed that these genes were mostly acquired from bacteria, fungi, and plants. This study provides a comprehensive understanding of HGT in nematodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Connor D. Harris, Ellis L. Torrance, Kasie Raymann, Louis-Marie Bobay
Summary: The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. CoreCruncher is a robust and fast program that can construct core genomes across hundreds or thousands of genomes. Compared to other tools, CoreCruncher is more conservative and less sensitive to the presence of paralogs and xenologs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Jong Im Kim, Bok Yeon Jo, Myung Gil Park, Yeong Du Yoo, Woongghi Shin, John M. Archibald
Summary: The Raphidophyceae is an important lineage of eukaryotic organisms that play a crucial role in marine and freshwater ecosystems. By sequencing and analyzing the plastid genomes of several species, researchers have gained insights into the evolutionary history of raphidophycean plastids. The findings suggest that lateral gene transfer from diatoms has contributed to the genetic diversity and evolution of raphidophyte plastid genomes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biology
Sang-Hyuck Park, John A. Kyndt, Judith K. Brown
Summary: （English Summary:)
The resequencing of the chloroplast genome of Auxenochlorella protothecoides UTEX 25 revealed important features such as genome size, GC content, and gene organization similar to other Chlorella species. This study also identified genes related to photosynthetic efficiency, which are of interest in the biofuel field. The phylogenetic analysis showed a close relationship to Prototheca cutis and Chlorella species. Additionally, the presence of virus-like sequences suggested the possibility of horizontal gene transfer.
Article
Plant Sciences
Jianshuang Shen, Xueqin Li, Mingzhi Li, Hefeng Cheng, Xiaoling Huang, Songheng Jin
Summary: This study analyzed the organelle genome information of R. x pulchrum and its related species, revealing the characteristics of their mitochondrial and chloroplast genomes, as well as potential molecular markers. It also discovered gene rearrangement between R. x pulchrum and other species. The study showed that codon usage bias is influenced by mutation and selection, and identified homologous fragments between the chloroplast and mitochondrial genomes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ye Gao, Ina Bang, Yara Seif, Donghyuk Kim, Bernhard O. Palsson
Summary: In this study, the binding sites of the ferric uptake regulator (Fur) and the regulated genes in nine E. coli strains were identified. The results showed a small set of genes regulated by Fur that are common to all strains, but also a large number of genes regulated only in specific strains. This study reveals significant diversity in transcriptional regulation among E. coli strains.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Julie Boisard, Evelyne Duvernois-Berthet, Linda Duval, Joseph Schrevel, Laure Guillou, Amandine Labat, Sophie Le Panse, Gerard Prensier, Loic Ponger, Isabelle Florent
Summary: Our current understanding of the evolutionary history, coding, and adaptive capacities of Apicomplexa is biased towards species infecting humans, and limited information is available for early diverging apicomplexan lineages infecting invertebrates. In this study, the genome of Porospora gigantea, a marine eugregarine parasite of lobsters, was characterized. The genome analysis revealed high divergence from other known apicomplexan species and provided insights into the molecular basis of key functions such as gliding. These findings highlight the importance of studying gregarines to broaden our knowledge of apicomplexan species diversity and their molecular mechanisms.
Article
Agriculture, Dairy & Animal Science
Anisa S. Khan, Rian E. Pierneef, Narjol Gonzalez-Escalona, Meghan Maguire, Karla Georges, Woubit Abebe, Abiodun A. Adesiyun
Summary: This study conducted cross-sectional studies over 4 years to determine the phylogenies of Salmonella strains isolated from various stages of broiler production chain in Trinidad and Tobago. With the use of whole-genome sequencing, genetic relatedness and transmission of Salmonella serovars were confirmed. The results highlighted the presence of a common source of diverse serovar isolates within farms, processing plants, and retail outlets. The study also identified regional and international clustering of Salmonella serovars.
Article
Microbiology
Nyasha Mafumo, Oliver K. I. Bezuidt, Wouter le Roux, Thulani P. Makhalanyane
Summary: By studying crAssphage viruses in South African rivers, it was found that these viruses are more accurate indicators of fecal contamination in water, and crAssphage sequences can be detected in pristine rivers as well, unlike fecal coliform counts.
Review
Microbiology
Thulani P. Makhalanyane, Oliver K. I. Bezuidt, Rian E. Pierneef, Eshchar Mizrachi, Adolphe Zeze, Romain K. Fossou, Claude Ghislaine Kouadjo, Samuel Duodu, Chioma B. Chikere, Olubukola O. Babalola, Ashwil Klein, Marshall Keyster, Morne du Plessis, Nourou S. Yorou, Mohamed Hijri, Theresa Rossouw, Casper N. Kamutando, Stephanus Venter, Lucy N. Moleleki, Colin Murrell
Summary: African microbiomes have been underestimated in the past, with an overemphasis on research in the Global North. Africa possesses significant genetic diversity in its ecosystems, humans, and animals. In this Comment, we address the lack of available microbiome datasets from Africa and suggest measures to promote microbiome research in the region.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Environmental Sciences
Gilda Varliero, Pedro H. Lebre, Mark I. Stevens, Paul Czechowski, Thulani Makhalanyane, Don A. Cowan
Summary: 16S rRNA gene amplicon sequencing is commonly used to identify microbial diversity and composition. Different 16S rRNA gene amplified regions can result in differences in shared and unique taxa. However, multi-primer datasets can still be used to explore bacterial biogeographical patterns.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Microbiology
Choaro D. D. Dithugoe, Oliver K. I. Bezuidt, Emma L. L. Cavan, William P. P. Froneman, Sandy J. J. Thomalla, Thulani P. P. Makhalanyane
Summary: This study investigates the contribution of prokaryotes to the export of particulate organic matter in the Southern Ocean. The results show that bacteria and archaea in suspended and sinking particles have the ability to degrade complex organic carbon, while archaea also play a role in nitrogen metabolism. These findings highlight the importance of prokaryotes in regulating the export of particulate organic matter in the Southern Ocean.
Review
Microbiology
Gilda Varliero, Pedro H. Lebre, Beat Frey, Andrew G. Fountain, Alexandre M. Anesio, Don A. Cowan
Summary: Microbial communities and nutrient dynamics in glaciers and ice sheets are constantly changing due to hydrological conditions. Glaciers and ice sheets act as bioreactors, as microbiomes transform nutrients and impact meltwater chemistry. Global warming affects nutrient and cell export, altering proglacial systems. This review integrates current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics, highlighting their interdependence, variability, and impact on proglacial environments.
Article
Biology
Riaan F. F. Rifkin, Surendra Vikram, Jaime Alcorta, Jean-Baptiste Ramond, Don A. A. Cowan, Mattias Jakobsson, Carina M. M. Schlebusch, Marlize Lombard
Summary: By analyzing metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, about 2000 years ago, ancient DNA sequences homologous to the flea-borne typhus-like pathogen Rickettsia felis were identified, and an ancient R. felis genome was reconstructed. This provides ancient genomic evidence for the presence of Rickettsia felis in human remains from 2000 years ago, reframing previous hypotheses of R. felis as a novel or emergent pathogen in modern humans.
COMMUNICATIONS BIOLOGY
(2023)
Article
Microbiology
Molemi Evelyn Rauwane, Nokuthula Peace Mchunu, Rian Pierneef, Valery Mamogwasha Moloto, Teresa Goszczynska, Phumzile Sibisi, Khayalethu Ntushelo
Summary: This study presents a draft genome of a plant pathogenic bacterium, Pectobacterium brasiliense, isolated from potato in South Africa. The genome is 4,897,858 bp in total length and consists of 172 contigs with 4,378 genes. The GC content of the genome is 51.6%.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Yvonne Marvellous Akpudo, Oliver K. K. Bezuidt, Thulani P. P. Makhalanyane
Summary: Four archaeal metagenome-assembled genomes (MAGs) were discovered in a polar upwelling zone in the Southern Ocean. These archaea contain genes encoding enzymes involved in the degradation of PET and PHB plastics.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Editorial Material
Microbiology
Thulani P. Makhalanyane
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Itumeleng Matle, Abimbola Comfort Atanda, Rian Pierneef, Kudakwashe Magwedere, Thendo Mafuna
Summary: This study investigated the population structure, resistome, mobilome, and virulome of Enterococcus faecalis obtained from processed beef meat in South Africa. The results showed that beef meat products act as a reservoir for virulent E. faecalis strains possessing antibiotic resistance genes and virulence factors.
Article
Microbiology
Nomakorinte Gcebe, Rian Ewald Pierneef, Anita Luise Michel, Motlatso Tiny Hlokwe
Summary: This study investigated the distribution of non-tuberculous mycobacteria (NTM) and the molecular epidemiology of Mycobacterium avium complex (MAC) in South African pigs, revealing multiple subspecies. Using a typing tool, at least nine MIRU VNTR INMV types of subspecies were identified.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Yashini Naidoo, Rian E. Pierneef, Don A. Cowan, Angel Valverde
Summary: The study is important for understanding the soil resistome in deserts and its role in antibiotic resistance evolution and dissemination. The researchers characterized the bacterial communities and identified various antibiotic and metal resistance genes using targeted sequencing and shotgun metagenomics. They found a diversity of resistance elements in Namib Desert soils and suggested that horizontal gene transfer plays a crucial role in their dynamics.
INTERNATIONAL MICROBIOLOGY
(2023)
