@article{MTMT:34817462, title = {Improved reference quality genome sequence of the plastic-degrading greater wax moth, Galleria mellonella}, url = {https://m2.mtmt.hu/api/publication/34817462}, author = {Young, Reginald and Ahmed, Khandaker Asif and Court, Leon and Castro-Vargas, Cynthia and Marcora, Anna and Boctor, Joseph and Paull, Cate and Wijffels, Gene and Rane, Rahul and Edwards, Owain and Walsh, Tom and Pandey, Gunjan}, doi = {10.1093/g3journal/jkae070}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, unique-id = {34817462}, issn = {2160-1836}, abstract = {Galleria mellonella is a pest of honeybees in many countries because its larvae feed on beeswax. However, G. mellonella larvae can also eat various plastics, including polyethylene, polystyrene, and polypropylene, and therefore, the species is garnering increasing interest as a tool for plastic biodegradation research. This paper presents an improved genome (99.3% completed lepidoptera_odb10 BUSCO; genome mode) for G. mellonella. This 472 Mb genome is in 221 contigs with an N50 of 6.4 Mb and contains 13,604 protein-coding genes. Genes that code for known and putative polyethylene-degrading enzymes and their similarity to proteins found in other Lepidoptera are highlighted. An analysis of secretory proteins more likely to be involved in the plastic catabolic process has also been carried out.}, keywords = {bioremediation; polyethylene; genome assembly; secretory proteins; Plastic degradation}, year = {2024}, eissn = {2160-1836}, orcid-numbers = {Young, Reginald/0009-0005-5163-7567; Wijffels, Gene/0000-0001-5552-4416; Rane, Rahul/0000-0003-4616-6244; Pandey, Gunjan/0000-0002-3514-4624} } @article{MTMT:34789182, title = {The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi}, url = {https://m2.mtmt.hu/api/publication/34789182}, author = {Balamurugan, Charu and Steenwyk, Jacob and Goldman, Gustavo and Rokas, Antonis}, doi = {10.1093/g3journal/jkae063}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, unique-id = {34789182}, issn = {2160-1836}, abstract = {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.}, keywords = {RESISTANCE; SEQUENCE; DELETION; INFERENCE; Virulence; PROFILES; CONTRIBUTES; evolutionary biology; ASPERGILLUS-FUMIGATUS; Comparative genomics; secondary metabolism; plant pathogen; duplication and loss; secondary metabolic gene clusters}, year = {2024}, eissn = {2160-1836}, orcid-numbers = {Goldman, Gustavo/0000-0002-2986-350X; Rokas, Antonis/0000-0002-7248-6551} } @article{MTMT:34748320, title = {Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae}, url = {https://m2.mtmt.hu/api/publication/34748320}, author = {Armstrong, Ellie E. and Bissell, Ky L. and Fatima, H. Sophia and Heikkinen, Maya A. and Jessup, Anika and Junaid, Maryam O. and Lee, Dong H. and Lieb, Emily C. and Liem, Josef T. and Martin, Estelle M. and Moreno, Mauricio and Otgonbayar, Khuslen and Romans, Betsy W. and Royar, Kim and Adler, Mary Beth and Needle, David B. and Harkess, Alex and Kelley, Joanna L. and Mooney, Jazlyn A. and Mychajliw, Alexis M.}, doi = {10.1093/g3journal/jkae034}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, unique-id = {34748320}, issn = {2160-1836}, abstract = {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.}, keywords = {GENE; EVOLUTION; ECOLOGY; ALIGNMENT; dog; Carnivora; Canidae; SIMPLE SEQUENCE REPEATS; Prdm9; Gray fox; GREY FOX}, year = {2024}, eissn = {2160-1836}, orcid-numbers = {Armstrong, Ellie E./0000-0001-7107-6318} } @article{MTMT:34642791, title = {Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906.}, url = {https://m2.mtmt.hu/api/publication/34642791}, author = {Christinaki, Anastasia C and Myridakis, Antonis I and Kouvelis, Vassili N}, doi = {10.1093/g3journal/jkae006}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, unique-id = {34642791}, issn = {2160-1836}, abstract = {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.}, keywords = {GENOME; secondary metabolism; Horizontal gene transfer (HGT); fungicolous fungi; biosynthetic gene cluster (BGC); Cladobotryum mycophilum}, year = {2024}, eissn = {2160-1836} } @article{MTMT:34638935, title = {Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements}, url = {https://m2.mtmt.hu/api/publication/34638935}, author = {Silver, Brianna D. and Willett, Courtney G. and Maher, Kelsey A. and Wang, Dongxue and Deal, Roger B.}, doi = {10.1093/g3journal/jkae016}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, unique-id = {34638935}, issn = {2160-1836}, keywords = {PROMOTER; TRANSCRIPTION; ENHANCER; rna polymerase; histone modification; Cis-regulatory element}, year = {2024}, eissn = {2160-1836} } @article{MTMT:34638906, title = {Knockdown of Kmt2d leads to growth impairment by activating the Akt/β-catenin signaling pathway}, url = {https://m2.mtmt.hu/api/publication/34638906}, author = {Shangguan, Huakun and Huang, Xiaozhen and Lin, Jinduan and Chen, Ruimin and Bannasch, D.}, doi = {10.1093/g3journal/jkad298}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, unique-id = {34638906}, issn = {2160-1836}, keywords = {GROWTH; chondrocyte; KMT2D; AKT/beta-catenin}, year = {2024}, eissn = {2160-1836} } @article{MTMT:34623042, title = {The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss}, url = {https://m2.mtmt.hu/api/publication/34623042}, author = {Benson, Christopher W. and Sheltra, Matthew R. and Huff, David R.}, doi = {10.1093/g3journal/jkad238}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, volume = {14}, unique-id = {34623042}, issn = {2160-1836}, keywords = {Extended phenotype; smut fungi; Host manipulation; fungal pathogen; Tilletia; Bouteloua dactyloides; adaptive locus; Salmacisia buchloeana; OK1}, year = {2024}, eissn = {2160-1836} } @article{MTMT:34597975, title = {The chromosome-scale genome and the genetic resistance machinery against insect herbivores of the Mexican toloache, Datura stramonium}, url = {https://m2.mtmt.hu/api/publication/34597975}, author = {De-la-Cruz, Ivan M. and Oyama, Ken and Nunez-Farfan, Juan}, doi = {10.1093/g3journal/jkad288}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, volume = {14}, unique-id = {34597975}, issn = {2160-1836}, abstract = {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.}, keywords = {SOLANACEAE; Herbivory; Plant resistance; Plant Genetics and Genomics; genomics of plant defense; quantitative trait loci (QTLs) of plant resistance}, year = {2024}, eissn = {2160-1836}, orcid-numbers = {Nunez-Farfan, Juan/0000-0001-5829-8338} } @article{MTMT:34597459, title = {Transvection between nonallelic genomic positions in Drosophila}, url = {https://m2.mtmt.hu/api/publication/34597459}, author = {Blum, Jacob A. and Wells, Michelle and Huxley-Reicher, Zina and Johnson, Justine E. and Bateman, Jack R.}, doi = {10.1093/g3journal/jkad255}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, volume = {14}, unique-id = {34597459}, issn = {2160-1836}, abstract = {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.}, keywords = {PROMOTER; Chromatin; transvection; position effects; LONG-RANGE ENHANCER; somatic homolog pairing}, year = {2024}, eissn = {2160-1836} } @article{MTMT:34592456, title = {Heritable epigenetic variation facilitates long-term maintenance of epigenetic and genetic variation}, url = {https://m2.mtmt.hu/api/publication/34592456}, author = {Webster, Amy K. and Phillips, Patrick C. and Kronholm, I}, doi = {10.1093/g3journal/jkad287}, journal-iso = {G3-GENES GENOM GENET}, journal = {G3-GENES GENOMES GENETICS}, volume = {14}, unique-id = {34592456}, issn = {2160-1836}, abstract = {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.}, keywords = {Genetic Variation; theory; population genetics; epigenetics; epigenetic inheritance; EPIGENETIC VARIATION}, year = {2024}, eissn = {2160-1836} }