TY - JOUR AU - Balamurugan, Charu AU - Steenwyk, Jacob AU - Goldman, Gustavo AU - Rokas, Antonis TI - The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET PY - 2024 PG - 8 SN - 2160-1836 DO - 10.1093/g3journal/jkae063 UR - https://m2.mtmt.hu/api/publication/34789182 ID - 34789182 N1 - Funding Agency and Grant Number: Arnold and Mabel Beckman Foundation; Vanderbilt Data Science Institute; Beckman Scholars Program; Advanced Computing Center for research and Education at Vanderbilt University in Nashville, TN Funding text: We thank members of the Rokas Laboratory at Vanderbilt University for support and feedback on this work. We also thank the Vanderbilt Data Science Institute and the Beckman Scholars Program for their undergraduate enrichment opportunities. This work was performed in part using resources contained within the Advanced Computing Center for research and Education at Vanderbilt University in Nashville, TN. AB - Fungi biosynthesize diverse secondary metabolites, small organic bioactive molecules with key roles in fungal ecology. Fungal secondary metabolites are often encoded by physically clustered genes known as biosynthetic gene clusters (BGCs). Fungi in the genus Penicillium produce a cadre of secondary metabolites, some of which are useful (e.g. the antibiotic penicillin and the cholesterol-lowering drug mevastatin) and others harmful (e.g. the mycotoxin patulin and the immunosuppressant gliotoxin) to human affairs. Fungal genomes often also encode resistance genes that confer protection against toxic secondary metabolites. Some Penicillium species, such as Penicillium decumbens, are known to produce gliotoxin, a secondary metabolite with known immunosuppressant activity. To investigate the evolutionary conservation of homologs of the gliotoxin BGC and of genes involved in gliotoxin resistance in Penicillium, we analyzed 35 Penicillium genomes from 23 species. Homologous, lesser fragmented gliotoxin BGCs were found in 12 genomes, mostly fragmented remnants of the gliotoxin BGC were found in 21 genomes, whereas the remaining 2 Penicillium genomes lacked the gliotoxin BGC altogether. In contrast, broad conservation of homologs of resistance genes that reside outside the BGC across Penicillium genomes was observed. Evolutionary rate analysis revealed that BGCs with higher numbers of genes evolve slower than BGCs with few genes, suggestive of constraint and potential functional significance or more recent decay. Gene tree-species tree reconciliation analyses suggested that the history of homologs in the gliotoxin BGC across the genus Penicillium likely involved multiple duplications, losses, and horizontal gene transfers. Our analyses suggest that genes encoded in BGCs can have complex evolutionary histories and be retained in genomes long after the loss of secondary metabolite biosynthesis. LA - English DB - MTMT ER - TY - JOUR AU - Armstrong, Ellie E. AU - Bissell, Ky L. AU - Fatima, H. Sophia AU - Heikkinen, Maya A. AU - Jessup, Anika AU - Junaid, Maryam O. AU - Lee, Dong H. AU - Lieb, Emily C. AU - Liem, Josef T. AU - Martin, Estelle M. AU - Moreno, Mauricio AU - Otgonbayar, Khuslen AU - Romans, Betsy W. AU - Royar, Kim AU - Adler, Mary Beth AU - Needle, David B. AU - Harkess, Alex AU - Kelley, Joanna L. AU - Mooney, Jazlyn A. AU - Mychajliw, Alexis M. TI - Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET PY - 2024 PG - 11 SN - 2160-1836 DO - 10.1093/g3journal/jkae034 UR - https://m2.mtmt.hu/api/publication/34748320 ID - 34748320 N1 - Funding Agency and Grant Number: Revive and Restore; Cantata Bio; Dovetail Genomics as part of an "AG4" program; Washington Research Foundation Postdoctoral Fellowship Funding text: The support for this project was provided by Revive and Restore, Cantata Bio, and Dovetail Genomics as part of an "AG4" program award to EEA, JLK, and AMM. EEA was supported by a Washington Research Foundation Postdoctoral Fellowship. AB - Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases, respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern United States and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago. LA - English DB - MTMT ER - TY - JOUR AU - Christinaki, Anastasia C AU - Myridakis, Antonis I AU - Kouvelis, Vassili N TI - Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906. JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET PY - 2024 PG - 21 SN - 2160-1836 DO - 10.1093/g3journal/jkae006 UR - https://m2.mtmt.hu/api/publication/34642791 ID - 34642791 AB - Mycophilic or fungicolous fungi can be found wherever fungi exist since they are able to colonize other fungi, which occupy a diverse range of habitats. Some fungicolous species cause important diseases on basidiomycetes and thus, they are the main reason for the destruction of mushroom cultivations. Nonetheless, despite their ecological significance, their genomic data remain limited. Cladobotrum mycophilum is one of the most aggressive species of the genus, destroying the economically important Agaricus bisporus cultivations. The 40.7 Mb whole genome of the Greek isolate ATHUM6906 is assembled in 16 fragments, including the mitochondrial genome and two small circular mitochondrial plasmids, in this study. This genome includes a comprehensive set of 12,282 protein coding, 56 rRNA, and 273 tRNA genes. Transposable elements, CAZymes and pathogenicity related genes were also examined. The genome of C. mycophilum contained a diverse arsenal of genes involved in secondary metabolism, forming 106 Biosynthetic Gene Clusters, which renders this genome as one of the most BGC abundant among fungicolous species. Comparative analyses were performed for genomes of species of the family Hypocreaceae. Some BGCs identified in C. mycophilum genome exhibited similarities to clusters found in family Hypocreaceae, suggesting vertical heritage. In contrast, certain BGCs showed a scattered distribution among Hypocreaceae species or were solely found in Cladobotryum genomes. This work provides evidence of extensive BGC losses, Horizontal Gene Transfer events and formation of novel BGCs during evolution, potentially driven by neutral or even positive selection pressures. These events may increase Cladobotryum fitness under various environmental conditions and potentially during host-fungus interaction. LA - English DB - MTMT ER - TY - JOUR AU - Silver, Brianna D. AU - Willett, Courtney G. AU - Maher, Kelsey A. AU - Wang, Dongxue AU - Deal, Roger B. TI - Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET PY - 2024 PG - 11 SN - 2160-1836 DO - 10.1093/g3journal/jkae016 UR - https://m2.mtmt.hu/api/publication/34638935 ID - 34638935 LA - English DB - MTMT ER - TY - JOUR AU - Shangguan, Huakun AU - Huang, Xiaozhen AU - Lin, Jinduan AU - Chen, Ruimin AU - Bannasch, D. TI - Knockdown of Kmt2d leads to growth impairment by activating the Akt/β-catenin signaling pathway JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET PY - 2024 PG - 11 SN - 2160-1836 DO - 10.1093/g3journal/jkad298 UR - https://m2.mtmt.hu/api/publication/34638906 ID - 34638906 LA - English DB - MTMT ER - TY - JOUR AU - Benson, Christopher W. AU - Sheltra, Matthew R. AU - Huff, David R. TI - The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET VL - 14 PY - 2024 IS - 2 PG - 14 SN - 2160-1836 DO - 10.1093/g3journal/jkad238 UR - https://m2.mtmt.hu/api/publication/34623042 ID - 34623042 LA - English DB - MTMT ER - TY - JOUR AU - De-la-Cruz, Ivan M. AU - Oyama, Ken AU - Nunez-Farfan, Juan TI - The chromosome-scale genome and the genetic resistance machinery against insect herbivores of the Mexican toloache, Datura stramonium JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET VL - 14 PY - 2024 IS - 2 PG - 15 SN - 2160-1836 DO - 10.1093/g3journal/jkad288 UR - https://m2.mtmt.hu/api/publication/34597975 ID - 34597975 AB - Plant resistance refers to the heritable ability of plants to reduce damage caused by natural enemies, such as herbivores and pathogens, either through constitutive or induced traits like chemical compounds or trichomes. However, the genetic architecture-the number and genome location of genes that affect plant defense and the magnitude of their effects-of plant resistance to arthropod herbivores in natural populations remains poorly understood. In this study, we aimed to unveil the genetic architecture of plant resistance to insect herbivores in the annual herb Datura stramonium (Solanaceae) through quantitative trait loci mapping. We achieved this by assembling the species' genome and constructing a linkage map using an F2 progeny transplanted into natural habitats. Furthermore, we conducted differential gene expression analysis between undamaged and damaged plants caused by the primary folivore, Lema daturaphila larvae. Our genome assembly resulted in 6,109 scaffolds distributed across 12 haploid chromosomes. A single quantitative trait loci region on chromosome 3 was associated with plant resistance, spanning 0 to 5.17 cM. The explained variance by the quantitative trait loci was 8.44%. Our findings imply that the resistance mechanisms of D. stramonium are shaped by the complex interplay of multiple genes with minor effects. Protein-protein interaction networks involving genes within the quantitative trait loci region and overexpressed genes uncovered the key role of receptor-like cytoplasmic kinases in signaling and regulating tropane alkaloids and terpenoids, which serve as powerful chemical defenses against D. stramonium herbivores. The data generated in our study constitute important resources for delving into the evolution and ecology of secondary compounds mediating plant-insect interactions. LA - English DB - MTMT ER - TY - JOUR AU - Blum, Jacob A. AU - Wells, Michelle AU - Huxley-Reicher, Zina AU - Johnson, Justine E. AU - Bateman, Jack R. TI - Transvection between nonallelic genomic positions in Drosophila JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET VL - 14 PY - 2024 IS - 2 PG - 10 SN - 2160-1836 DO - 10.1093/g3journal/jkad255 UR - https://m2.mtmt.hu/api/publication/34597459 ID - 34597459 AB - In Drosophila, pairing of maternal and paternal homologous chromosomes can permit trans-interactions between enhancers on one homolog and promoters on another, an example of transvection. Although trans-interactions have been observed at many loci in the Drosophila genome and in other organisms, the parameters that govern enhancer action in trans remain poorly understood. Using a transgenic reporter system, we asked whether enhancers and promoters at nonallelic, but nearby, genomic positions can communication in trans. Using one transgenic insertion carrying the synthetic enhancer GMR and another nearby insertion carrying the hsp70 promoter driving a fluorescent reporter, we show that transgenes separated by 2.6 kb of linear distance can support enhancer action in trans at the 53F8 locus. Furthermore, transvection between the nonallelic insertions can be augmented by a small deletion flanking one insert, likely via changes to the paired configuration of the homologs. Subsequent analyses of other insertions in 53F8 that carry different transgenic sequences demonstrate that the capacity to support transvection between nonallelic sites varies greatly, suggesting that factors beyond the linear distance between insertion sites play an important role. Finally, analysis of transvection between nearby nonallelic sites at other genomic locations shows evidence of position effects, where one locus supported GMR action in trans over a linear distance of over 10 kb, whereas another locus showed no evidence of transvection over a span <200 bp. Overall, our data demonstrate that transvection between nonallelic sites represents a complex interplay between genomic context, interallelic distance, and promoter identity. LA - English DB - MTMT ER - TY - JOUR AU - Webster, Amy K. AU - Phillips, Patrick C. AU - Kronholm, I TI - Heritable epigenetic variation facilitates long-term maintenance of epigenetic and genetic variation JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET VL - 14 PY - 2024 IS - 2 PG - 15 SN - 2160-1836 DO - 10.1093/g3journal/jkad287 UR - https://m2.mtmt.hu/api/publication/34592456 ID - 34592456 N1 - Export Date: 22 February 2024 Correspondence Address: Webster, A.K.; Institute of Ecology and Evolution, United States; email: awebst10@uoregon.edu AB - How genetic and phenotypic variation are maintained has long been one of the fundamental questions in population and quantitative genetics. A variety of factors have been implicated to explain the maintenance of genetic variation in some contexts (e.g. balancing selection), but the potential role of epigenetic regulation to influence population dynamics has been understudied. It is well recognized that epigenetic regulation, including histone methylation, small RNA expression, and DNA methylation, helps to define differences between cell types and facilitate phenotypic plasticity. In recent years, empirical studies have shown the potential for epigenetic regulation to also be heritable for at least a few generations without selection, raising the possibility that differences in epigenetic regulation can act alongside genetic variation to shape evolutionary trajectories. Heritable differences in epigenetic regulation that arise spontaneously are termed "epimutations." Epimutations differ from genetic mutations in 2 key ways-they occur at a higher rate and the loci at which they occur often revert back to their original state within a few generations. Here, we present an extension of the standard population genetic model with selection to incorporate epigenetic variation arising via epimutation. Our model assumes a diploid, sexually reproducing population with random mating. In addition to spontaneous genetic mutation, we included parameters for spontaneous epimutation and back-epimutation, allowing for 4 potential epialleles at a single locus (2 genetic alleles, each with 2 epigenetic states), each of which affect fitness. We then analyzed the conditions under which stable epialleles were maintained. Our results show that highly reversible epialleles can be maintained in long-term equilibrium under neutral conditions in a manner that depends on the epimutation and back-epimutation rates, which we term epimutation-back-epimutation equilibrium. On the other hand, epialleles that compensate for deleterious mutations cause deviations from the expectations of mutation-selection balance by a simple factor that depends on the epimutation and back-epimutation rates. We also numerically analyze several sets of fitness parameters for which large deviations from mutation-selection balance occur. Together, these results demonstrate that transient epigenetic regulation may be an important factor in the maintenance of both epigenetic and genetic variation in populations. LA - English DB - MTMT ER - TY - JOUR AU - Bai, X. AU - Golden, A. TI - Transmembrane protein 120A (TMEM-120A/TACAN) coordinates with PIEZO channel during Caenorhabditis elegans reproductive regulation JF - G3-GENES GENOMES GENETICS J2 - G3-GENES GENOM GENET VL - 14 PY - 2024 IS - 1 SN - 2160-1836 DO - 10.1093/g3journal/jkad251 UR - https://m2.mtmt.hu/api/publication/34552774 ID - 34552774 N1 - Department of Biology, University of Florida, Gainesville, FL 32610, United States Genetics Institute, University of Florida, Gainesville, FL 32610, United States National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States Export Date: 1 February 2024 Correspondence Address: Bai, X.; Department of Biology, Cancer & Genetics Research Complex, 2033 Mowry Road, United States; email: baixiaofei@ufl.edu Chemicals/CAS: Caenorhabditis elegans Proteins; Membrane Proteins Funding details: National Institutes of Health, NIH Funding details: National Institute of General Medical Sciences, NIGMS, 1K99 GM145224-01, K99/R00 Funding details: National Institute of Diabetes and Digestive and Kidney Diseases, NIDDK Funding details: Office of Research Infrastructure Programs, ORIP, NIH, P40OD010440 Funding text 1: This work was, in part, supported by the Intramural Research Program of the National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases (XB and AG) and an National Institutes of Health, National Institute of General Medical Sciences Pathway to Independence Award (K99/R00), 1K99 GM145224-01, National Institute of General Medical Sciences (XB), and 4R00GM145224-02 National Institute of General Medical Sciences (XB). Funding text 2: We thank the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40OD010440), for providing strains for this study. We thank Dr. Erin Cram for the critical feedback and comments on the manuscript. We are grateful to all members of the Baltimore Worm Club for providing feedback and suggestions for our project. This work is dedicated to Dr. Andy Golden, who greatly supported this study. AB - Membrane protein TMEM120A (also known as TACAN) was presumed to be both a mechanically activated molecule and a lipid-modifying enzyme. TMEM120A has been identified as a negative regulator of the essential excitatory mechanosensitive protein PIEZO2. However, the extent to which TMEM120A mediates PIEZO2's activity during physiological processes remains largely unknown. In this study, we used the Caenorhabditis elegans reproductive tract to explore the functional contribution of tmem-120, the sole TMEM120A/B ortholog, and its genetic interaction with pezo-1 in vivo. tmem-120 was expressed throughout the C. elegans development, particularly in the germline, embryos, and spermatheca. A tmem-120 mutant with a full-length deletion (tmem-120Δ) displayed deformed germline, maternal sterility, and a reduced brood size. In vivo live imaging revealed that pinched zygotes were frequently observed in the uterus of tmem-120Δ mutant animals, suggesting damage during spermathecal contraction. We then employed the auxin-inducible degradation system to degrade TMEM-120 protein in all somatic tissues or the germline, both of which resulted in reduced brood sizes. These findings suggested that multiple inputs of tmem-120 from different tissues regulate reproduction. Lastly, the loss of tmem-120 alleviated the brood size reduction and defective sperm navigation behavior in the pezo-1Δ mutant. Overall, our findings reveal a role for tmem-120 in regulating reproductive physiology in C. elegans, and suggest an epistatic interaction between pezo-1 and tmem-120 when governing proper reproduction. © The Author(s) 2023. LA - English DB - MTMT ER -