Article
Microbiology
Jose Luis Maturana, Juan P. Cardenas
Summary: Blautia, a genus established in 2008, is a relatively abundant taxonomic group in the microbiome of human and other mammalian gastrointestinal tracts. Despite the increasing knowledge about Blautia, its diversity is still poorly understood. Pangenome analysis of 225 Blautia genomes revealed 33 potential species, 17 of which were previously undescribed.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Ecology
Nathanael D. Herrera, Kayce C. Bell, Colin M. Callahan, Erin Nordquist, Brice A. J. Sarver, Jack Sullivan, John R. Demboski, Jeffrey M. Good
Summary: Discovery of cryptic species within western chipmunks using genomic data highlights the presence of a new species and two subspecies, with evidence of hybridization with other species.
Article
Biochemistry & Molecular Biology
Maria Recuerda, Juan Carlos Illera, Guillermo Blanco, Rafael Zardoya, Borja Mila
Summary: This study used phylogenomics and genetic diversity patterns to infer the colonization sequence and timing of mainland common chaffinches to Macaronesia, and assessed whether colonization of different archipelagos led to a species-level radiation. Results revealed a rapid radiation of common chaffinches across Macaronesia, driven by sequential colonization of different archipelagos, resulting in genetically distinct, independent evolutionary lineages.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biology
Jessica R. Glass, Richard C. Harrington, Peter F. Cowman, Brant C. Faircloth, Thomas J. Near
Summary: Inferring patterns of speciation in marine organisms is challenging due to the lack of species-level phylogenies and information on species' distributions, as well as conflicting relationships between species' dispersal, range size, and co-occurrence. However, a recent study on Carangoidei fish species found that there is widespread sympatry among sister species pairs, regardless of node age, and most species pairs coexist across large portions of their ranges.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
Xuewen Wang, Shiyu Chen, Xiao Ma, Anna E. J. Yssel, Srinivasa R. Chaluvadi, Matthew S. Johnson, Prakash Gangashetty, Falalou Hamidou, Moussa D. Sanogo, Arthur Zwaenepoel, Jason Wallace, Yves Van de Peer, Jeffrey L. Bennetzen, Allen Van Deynze
Summary: White fonio, a vital crop in West Africa, was found to have a highly diverse genome with potential for future improvement. Genomic analysis revealed genetic diversity largely partitioned across a north-south gradient coinciding with distinct grassland domains. This information should empower future research into further domestication and improvement of fonio.
Article
Plant Sciences
Chung-Shien Wu, Chung-I. Chen, Shu-Miaw Chaw
Summary: Convolvulaceae is a large family of plants with economic value. However, the phylogenetic relationships within this family and the complexity of plastid genomes are still not well understood. In this study, we analyzed 78 plastomes from different genera within Convolvulaceae and found various plastomic rearrangements, including inversions, duplications, and loss of genes and introns. Our findings also shed light on the uncertain positions of the genera Cuscuta and Erycibe and provide a rare example of gene transfer from mitochondria to plastids in angiosperms.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Minjie Li, Zeyu Zheng, Juncheng Liu, Yongzhi Yang, Guangpeng Ren, Dafu Ru, Shangzhe Zhang, Xin Du, Tao Ma, Richard Milne, Jianquan Liu
Summary: The study found that the alpine tetraploid Allium tetraploideum evolved from at least two closely related diploid species, with at least one extinct diploid species involved in its ancestry. It appears that A. tetraploideum arose via homoploid hybrid speciation from two extinct allotetraploid parents, which further derived from the aforementioned diploids, showcasing the complex origins of some polyploid species involving both homoploid hybrid speciation and extinct ancestors.
Article
Microbiology
Aleksandar Stanojkovic, Svatopluk Skoupy, Pavel Skaloud, Petr Dvorak
Summary: The sympatric occurrence of closely related lineages displaying conserved morphological and ecological traits is characteristic of free-living microbes. Gene flow, recombination, selection, and mutations govern the genetic variability between these cryptic lineages and drive their differentiation. However, insufficient population-level sampling has hindered the study of intra-species genetic diversity and speciation in cyanobacteria. In this study, using phylogenomics and a population genomic approach, the authors investigated the extent of local genomic diversity and the mechanisms underlying sympatric speciation in Laspinema thermale. They found two cryptic lineages of Laspinema with high genetic diversity. Recombination occurred more frequently within the lineages, suggesting a barrier to gene flow that maintains divergence. Genomic regions associated with possible adaptations to different environmental conditions were found, indicating the influence of both genomic and ecological processes on Laspinema species diversification.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Plant Sciences
James W. Clark
Summary: Plant evolution has led to increased complexity through major innovations in vegetative and reproductive traits. Genome evolution has played a crucial role, with instances of gene and whole-genome duplication, horizontal gene transfer, and gene loss shaping plant diversity. The coevolution of plant genomes and phenotypes at a macroevolutionary scale has been observed during periods of dynamic genome evolution. While the role of gene duplication has been extensively studied, the association between gene loss and plant phenotypic diversity deserves more attention, especially considering reductive evolution in multiple plant lineages.
Article
Biochemistry & Molecular Biology
Deyan Ge, Zhixin Wen, Anderson Feijo, Andrey Lissovsky, Wei Zhang, Jilong Cheng, Chaochao Yan, Huishang She, Dezhi Zhang, Yalin Cheng, Liang Lu, Xinlai Wu, Danping Mu, Yubo Zhang, Lin Xia, Yanhua Qu, Alfried P. Vogler, Qisen Yang
Summary: Climate-sensitive pikas in the Qinghai-Tibetan Plateau and its vicinity have experienced population reduction due to climate changes and human disturbance, while the plateau pika remains common. By sequencing the whole genomes of six closely related species, we found evidence of ancient introgression, lineage replacement, and bidirectional introgression. The strongest gene flow occurred from the dominant plateau pika to ecologically distinct species in peripheral areas. Our findings highlight the differences in hybridization consequences and the unique role of the Qinghai-Tibetan Plateau in conserving evolutionary processes.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Qinpeng Liu, Yingqi Liu, Qiaoqiao Liu, Li Tian, Hu Li, Fan Song, Wanzhi Cai
Summary: The recently reorganized classification of Mantodea has made progress in resolving homoplasy problems, although some relationships among higher taxa remain uncertain. In this study, newly sequenced mitogenomes and nuclear gene sequences were used to compare the structure of mantodean mitogenomes and perform phylogenomic studies. The results reveal conserved mitogenome organizations with some gene rearrangements. The phylogenetic analysis shows compositional heterogeneity and lineage-specific evolutionary rates among mantodean mitogenomes, and the use of a heterogeneous mixture model produces better-fit topologies. The results confirm the monophyly of several superfamilial groups and provide insights into the phylogeny of Mantodea.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Letter
Evolutionary Biology
Leeban H. H. Yusuf, Venera Tyukmaeva, Anneli Hoikkala, Michael G. G. Ritchie
Summary: Gene flow plays a crucial role in speciation and evolution. In the virilis group of Drosophila, species show mixed genomes and conflicting phylogenetic relationships. Some genes are associated with adaptation and isolation. These findings enhance our understanding of gene flow and phylogenetics.
Article
Biochemistry & Molecular Biology
Chao Zhang, Siavash Mirarab
Summary: This paper introduces a threshold-free weighting scheme for quartet-based species tree inference, which improves the utility of summary methods and reduces incongruence with gene concatenation.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Attila Matis, Tamas Malkocs, Thomas Kuhn, Levente Laczko, Ivan Moysiyenko, Anna Szabo, Alexandru S. Badarau, Gabor Sramko
Summary: This study used morphometric and phylogenomic analyses and found an overlooked species of Salvia. The new species differs from closely related taxa in floral structure, habitat preference, and distribution.
Review
Biochemistry & Molecular Biology
Qiuyue Chen, Weiya Li, Lubin Tan, Feng Tian
Summary: This study provides a comprehensive summary of the domestication processes of maize and rice, highlighting their genetic solutions and distinct regulatory and evolutionary mechanisms. It discusses how knowledge from past domestication processes can be used with emerging technologies to improve modern crop breeding and domesticate new crops to meet increasing human demands.
Article
Microbiology
Man-Man Wang, Marizeth Groenewald, Feng Wu, Yun-Tong Guo, Qi-Ming Wang, Teun Boekhout
Summary: The six synonyms of Saccharomycodes ludwigii were investigated for by phenotypic properties, while the sequence diversity of rRNA and protein coding genes has not yet been determined. A multi-locus sequence analysis (MLSA) approach was used to analyze nine strains, including the type strains of synonyms of S. ludwigii, which revealed that they are conspecific. Additionally, a new species of Saccharomycodes, S. pseudoludwigii sp. nov., was proposed.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yuanning Li, Jacob L. Steenwyk, Ying Chang, Yan Wang, Timothy Y. James, Jason E. Stajich, Joseph W. Spatafora, Marizeth Groenewald, Casey W. Dunn, Chris Todd Hittinger, Xing-Xing Shen, Antonis Rokas
Summary: Phylogenomic studies using genome-scale data have greatly improved understanding of the tree of life, and a robust phylogenomic framework of the fungal kingdom has been established through analysis of gene matrices. Historically poorly resolved relationships were supported, along with evidence of polytomies, and discrepancies between current taxonomic circumscription and evolutionary divergence levels were identified. This study offers directions for future fungal phylogenetic and taxonomic research.
Article
Microbiology
Neza Cadez, Denes Dlauchy, Miha Tome, Gabor Peter
Summary: Taphrinomycotina, the smallest subphylum of Ascomycota, consists of distantly related early diverging lineages, supported by phylogenomic analyses. A novel budding species, Novakomyces olei, was isolated from extra virgin olive oil, with genetic analysis placing it next to Schizosaccharomyces species. Functional analysis revealed gene biases towards biosynthesis of organic molecules and regulation of mRNA, showing discordance between phenotype and genotype in Taphrinomycotina species.
Article
Ecology
Ana Moya-Beltran, Simon Beard, Camila Rojas-Villalobos, Francisco Issotta, Yasna Gallardo, Ricardo Ulloa, Alejandra Giaveno, Mauro Degli Esposti, D. Barrie Johnson, Raquel Quatrini
Summary: Researchers conducted a systematic analysis of the genus Acidithiobacillus, defining 19 Acidithiobacillia lineages at different taxonomic levels. This study provides the most comprehensive classification and pangenomic analysis of this deep-branching class of Proteobacteria to date, shedding light on the evolutionary history and molecular evolution of relevant aerobic respiratory proteins.
Article
Food Science & Technology
Laura Perez-Traves, Rosa de Llanos, Allen Flockhart, Lydia Garcia-Domingo, Marizeth Groenewald, Roberto Perez-Torrado, Amparo Querol
Summary: The number of human infections associated with yeast species involved in food processing is increasing, with some strains posing a potential risk for human health.
Article
Microbiology
Yao-Yao Li, Man-Man Wang, Marizeth Groenewald, Ai-Hua Li, Yun-Tong Guo, Feng Wu, Bing-Qian Zhang, Eiji Tanaka, Qi-Ming Wang, Feng-Yan Bai, Dominik Begerow
Summary: In the past 20 years, a total of 244 ustilaginomycetous yeast or yeast-like strains have been isolated from various sources, including 203 strains representing known species and 41 strains representing novel species. Sequence analyses of rDNA genes and protein genes led to the proposal of new taxonomic units and species.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Ricardo Franco-Duarte, Neza Cadez, Teresa Rito, Joao Drumonde-Neves, Yazmid Reyes Dominguez, Celia Pais, Maria Joao Sousa, Pedro Soares
Summary: In this study, the genomes of Clavispora santaluciae strains were sequenced, assembled, and compared for the first time. The analysis revealed specific differences between strains, reflecting their isolation in different ecological niches and their adaptation to the environmental features of their respective locations.
Article
Microbiology
Lucija Slemc, Jernej Jakse, Alessandro Filisetti, Damir Baranasic, Antonio Rodriguez-Garcia, Francesco Del Carratore, Stefano Maria Marino, Jurica Zucko, Antonio Starcevic, Martin Sala, Mercedes Perez-Bonilla, Marina Sanchez-Hidalgo, Ignacio Gonzalez, Fernando Reyes, Olga Genilloud, Vicki Springthorpe, Dusan Goranovic, Gregor Kosec, Gavin H. Thomas, Davide De Lucrezia, Hrvoje Petkovic, Miha Tome
Summary: Streptomyces rimosus ATCC 10970 is a challenging bacterium to assemble due to its long repeats, high GC content, and a single giant linear plasmid (GLP). In this study, a hybrid sequencing approach was used to generate a high-quality reference genome for this industrially important bacterium. The GLP of the parent strain ATCC 10970 and two semi-industrial progenitor strains were sequenced, revealing rearrangements accompanied by transposase genes. This study sheds light on the role of transposases in genome plasticity and provides valuable information on secondary metabolite biosynthetic pathways.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Varunya Sakpuntoon, Gabor Peter, Marizeth Groenewald, Denes Dlauchy, Savitree Limtong, Nantana Srisuk
Summary: The systematic position of 16 yeast strains isolated from different countries were evaluated using various analyses, leading to the discovery of a new yeast species and the reassignment of two existing species. The close relationship between certain yeast species was unexpected and required further clarification. Morphological and physiological characteristics were shared among the three yeast species. The findings contribute to a better understanding of yeast taxonomy and evolution.
Article
Biotechnology & Applied Microbiology
Estifanos Hawaz, Mesfin Tafesse, Anteneh Tesfaye, Dereje Beyene, Solomon Kiros, Gessese Kebede, Teun Boekhout, Bart Theelen, Marizeth Groenewald, Ayantu Degefe, Sissay Degu, Alene Admas, Diriba Muleta
Summary: The present study aimed to isolate, screen, and characterize wild yeasts recovered from bio-waste and co-products of Ethiopian sugar factories for bioethanol production. The results showed that strain M. caribbica MJTm3 exhibited high ethanol tolerance and fermentation potential and could be further utilized for industrial bioethanol production.
ANNALS OF MICROBIOLOGY
(2022)
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
Mycology
M. Groenewald, C. T. Hittinger, K. Bensch, D. A. Opulente, X. -X. Shen, Y. Li, C. Liu, A. L. LaBella, X. Zhou, S. Limtong, S. Jindamorakot, P. Goncalves, V. Robert, K. H. Wolfe, C. A. Rosa, T. Boekhout, N. Cadez, G. Peter, J. P. Sampaio, M. -A. Lachance, A. M. Yurkov, H. -M. Daniel, M. Takashima, K. Boundy-Mills, D. Libkind, K. Aoki, T. Sugita, A. Rokas
Summary: The subphylum Saccharomycotina is a diverse lineage within the fungal phylum Ascomycota, consisting of over 1,200 known species divided into 16 families, one order, and one class. It exhibits high genomic diversity and includes both opportunistic human pathogens and species important in biotechnological applications. However, the biotechnological potential of most yeast species remains unexplored. The current classification of Saccharomycotina as a single class and order underestimates its diversity, and an updated classification with seven classes and 12 orders is proposed based on genome content analysis and phylogenetic relationships.
STUDIES IN MYCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Dana A. Opulente, Quinn K. Langdon, Martin Jarzyna, Kelly V. Buh, Max A. B. Haase, Marizeth Groenewald, Chris Todd Hittinger
Summary: A novel budding yeast species was identified and analyzed through phylogenetic and genomic analyses, comparing its phenotypic data to other related species. The study revealed that the inability to utilize certain carbon and nitrogen sources was correlated with the absence of metabolic genes. Based on these findings, the new species was named Pichia galeolata sp. nov.
