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Ettinger CL, Ostovar T, Yacoub M, Ahrendt S, Hice RH, Federici BA, Stajich JE. Genomes and transcriptomes help unravel the complex life cycle of the blastoclad fungus, Coelomomyces lativittatus, an obligate parasite of mosquitoes and microcrustaceans. Mycologia 2023; 115:630-647. [PMID: 37494633 DOI: 10.1080/00275514.2023.2228182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023]
Abstract
Species of the phylum Blastocladiomycota, early-diverging zoosporic (flagellated) lineages of fungi, are vastly understudied. This phylum includes the genus Coelomomyces, which consists of more than 80 fungal species that are obligate parasites of arthropods. Known Coelomomyces species lack a complete asexual life cycle, instead surviving through an obligate heterecious alternation of generations life cycle. Despite their global distribution and interesting life cycle, little is known about the genomics of any Coelomomyces species. To address this, we generated three draft-level genomes and annotations for C. lativittatus representing its haploid meiospore, orange gamete, and amber gamete life stages. These draft genome assemblies ranged in size from 5002 to 5799 contigs, with a total length of 19.8-22.8 Mb and a mean of 7416 protein-coding genes. We then demonstrated the utility of these genomes by combining the draft annotations as a reference for analysis of C. lativittatus transcriptomes. We analyzed transcriptomes from across host-associated life stages, including infected larvae and excised mature sporangia from the mosquito Anopheles quadrimaculatus. We identified differentially expressed genes and enriched GO terms both across and within life stages and used these to make hypotheses about C. lativittatus biology. Generally, we found the C. lativittatus transcriptome to be a complex and dynamic expression landscape; GO terms related to metabolism and transport processes were enriched during infection and terms related to dispersal were enriched during sporulation. We further identified five high mobility group (HMG)-box genes in C. lativittatus, three belonging to clades with mating type (MAT) loci from other fungi, as well as four ortholog expansions in C. lativittatus compared with other fungi. The C. lativittatus genomes and transcriptomes reported here are a valuable resource and may be leveraged toward furthering understanding of the biology of these and other early-diverging fungal lineages.
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Affiliation(s)
- Cassandra L Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
| | - Talieh Ostovar
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
- UCR/SDSU Joint Doctoral Program in Evolutionary Biology, San Diego State University, San Diego, California 92182
| | - Mark Yacoub
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
| | - Steven Ahrendt
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
| | - Robert H Hice
- Department of Entomology, University of California, Riverside, Riverside, California 92521
| | - Brian A Federici
- Department of Entomology, University of California, Riverside, Riverside, California 92521
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521
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Kuse R, Ishii K. Flexible Attachment and Detachment of Centromeres and Telomeres to and from Chromosomes. Biomolecules 2023; 13:1016. [PMID: 37371596 DOI: 10.3390/biom13061016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
Accurate transmission of genomic information across multiple cell divisions and generations, without any losses or errors, is fundamental to all living organisms. To achieve this goal, eukaryotes devised chromosomes. Eukaryotic genomes are represented by multiple linear chromosomes in the nucleus, each carrying a centromere in the middle, a telomere at both ends, and multiple origins of replication along the chromosome arms. Although all three of these DNA elements are indispensable for chromosome function, centromeres and telomeres possess the potential to detach from the original chromosome and attach to new chromosomal positions, as evident from the events of telomere fusion, centromere inactivation, telomere healing, and neocentromere formation. These events seem to occur spontaneously in nature but have not yet been elucidated clearly, because they are relatively infrequent and sometimes detrimental. To address this issue, experimental setups have been developed using model organisms such as yeast. In this article, we review some of the key experiments that provide clues as to the extent to which these paradoxical and elusive features of chromosomally indispensable elements may become valuable in the natural context.
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Affiliation(s)
- Riku Kuse
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
| | - Kojiro Ishii
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
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Lustig AJ. Investigating the origin of subtelomeric and centromeric AT-rich elements in Aspergillus flavus. PLoS One 2023; 18:e0279148. [PMID: 36758027 PMCID: PMC9910759 DOI: 10.1371/journal.pone.0279148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
An in silico study of Aspergillus flavus genome stability uncovered significant variations in both coding and non-coding regions. The non-coding insertions uniformly consisted of AT-rich sequences that are evolutionarily maintained, albeit distributed at widely different sites in an array of A. flavus strains. A survey of ≥ 2kb AT-rich elements (AT ≥ 70%; ATEs) in non-centromeric regions uncovered two major categories of ATEs. The first category is composed of homologous insertions at ectopic, non-allelic sites that contain homology to transposable elements (TEs; Classes B, C, D, and E). Strains differed significantly in frequency, position, and TE type, but displayed a common enrichment in subtelomeric regions. The TEs were heavily mutated, with patterns consistent with the ancestral activity of repeat-induced point mutations (RIP). The second category consists of a conserved set of novel subtelomeric ATE repeats (Classes A, G, G, H, I and J) which lack discernible TEs and, unlike TEs, display a constant polarity relative to the telomere. Members of one of these classes are derivatives of a progenitor ATE that is predicted to have undergone extensive homologous recombination during evolution. A third category of ATEs consists of ~100 kb regions at each centromere. Centromeric ATEs and TE clusters within these centromeres display a high level of sequence identity between strains. These studies suggest that transposition and RIP are forces in the evolution of subtelomeric and centromeric structure and function.
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Affiliation(s)
- Arthur J. Lustig
- Department of Biochemistry and Molecular Biology, Tulane University Medical School, New Orleans, LA, United States of America
- * E-mail:
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Contreras SM, Zambrano Siri RT, Rivera EM, Cristaldi C, Kamenetzky L, Kim K, Clemente M, Ocampo J, Vanagas L, Angel SO. Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres. EPIGENOMES 2022; 6:29. [PMID: 36135316 PMCID: PMC9498087 DOI: 10.3390/epigenomes6030029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Subtelomeres (ST) are chromosome regions that separate telomeres from euchromatin and play relevant roles in various biological processes of the cell. While their functions are conserved, ST structure and genetic compositions are unique to each species. This study aims to identify and characterize the subtelomeric regions of the 13 Toxoplasma gondii chromosomes of the Me49 strain. Here, STs were defined at chromosome ends based on poor gene density. The length of STs ranges from 8.1 to 232.4 kbp, with a gene density of 0.049 genes/kbp, lower than the Me49 genome (0.15 kbp). Chromatin organization showed that H3K9me3, H2A.X, and H3.3 are highly enriched near telomeres and the 5' end of silenced genes, decaying in intensity towards euchromatin. H3K4me3 and H2A.Z/H2B.Z are shown to be enriched in the 5' end of the ST genes. Satellite DNA was detected in almost all STs, mainly the sat350 family and a novel satellite named sat240. Beyond the STs, only short dispersed fragments of sat240 and sat350 were found. Within STs, there were 12 functional annotated genes, 59 with unknown functions (Hypothetical proteins), 15 from multigene FamB, and 13 from multigene family FamC. Some genes presented low interstrain synteny associated with the presence of satellite DNA. Orthologues of FamB and FamC were also detected in Neospora caninum and Hammondia hammondi. A re-analysis of previous transcriptomic data indicated that ST gene expression is strongly linked to the adaptation to different situations such as extracellular passage (evolve and resequencing study) and changes in metabolism (lack of acetyl-CoA cofactor). In conclusion, the ST region of the T. gondii chromosomes was defined, the STs genes were determined, and it was possible to associate them with high interstrain plasticity and a role in the adaptability of T. gondii to environmental changes.
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Affiliation(s)
- Susana M. Contreras
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Romina T. Zambrano Siri
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires C1428ADN, Argentina
| | - Elías M. Rivera
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Constanza Cristaldi
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Laura Kamenetzky
- Laboratorio de Genómica y Bioinformática de Patógenos, iB3|Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Marina Clemente
- Laboratorio de Molecular Farming y Vacunas, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Josefina Ocampo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires C1428ADN, Argentina
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Sergio O. Angel
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
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