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Genome assembly, analysis, and mining of Kocuria flava NIO_001. A thiopeptide antibiotic synthesizing bacterium isolated from marine sponge.

IF 2.3 3区生物学

Genome Pub Date : 2025-03-13 DOI: 10.1139/gen-2024-0162

Kartik Juyal, Heena Ulhas Devkar, Aabha Deshpande, Narsinh L Thakur

{"title":"Genome assembly, analysis, and mining of Kocuria flava NIO_001. A thiopeptide antibiotic synthesizing bacterium isolated from marine sponge.","authors":"Kartik Juyal, Heena Ulhas Devkar, Aabha Deshpande, Narsinh L Thakur","doi":"10.1139/gen-2024-0162","DOIUrl":"https://doi.org/10.1139/gen-2024-0162","url":null,"abstract":"Genome mining has been a key strategy for finding Biosynthetic Gene Clusters (BGCs) coding for secondary metabolites in the recent past. Actinomycetia is among the important bacterial classes found in marine habitats, renowned for producing high-value secondary metabolites. Kocuria is one such gram-positive bacteria that has been reported to produce the potent antibacterial molecule kocurin/PM181104. The objective of this study was to confirm the production of kocurin/PM181104 followed by sequencing, assembly, and mining of the genome of Kocuria flava NIO_001. AntiSMASH analysis predicted the biosynthetic gene clusters involved in the production of kocurin along with eight promising secondary metabolite-producing BGCs including Non-alpha poly-amino acids like e-Polylysin (NAPAA), ribosomally synthesised and post-translationally modified peptide like (RiPP-like), Non-ribosomal peptide synthetase like (NRPS-like), NRPS-independent IucA/IucC-like siderophores (NI-siderophore), Type III polyketide synthase (T3PKS), ε-Poly-L-lysine (NAPAA), terpene, and betalactone. KEGG pathway analysis showed the presence of biosynthetic pathways involved in terpenoid backbone synthesis and the presence of certain hemolysin-like proteins. The present investigation is highly valuable for designing experiments to over-produce this potent antibiotic molecule by using a reverse engineering approach.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Pathway to Increase Standards and Competency of eDNA Surveys (PISCeS) 2023 Conference - Towards standardization and data management in the field of eDNA.

IF 2.3 3区生物学

Genome Pub Date : 2025-03-13 DOI: 10.1139/gen-2024-0158

Morgan Ruth Hurlburt Humphrey, Tzitziki Loeza-Quintana, Kate Gerarda Lindsay, Margaret Docker, Caren Helbing, Robert H Hanner

引用次数: 0

Evolutionary Speed of Proteins in the Genus Staphylococcus: A Focus on Proteins Involved in Natural Competence.

IF 2.3 3区生物学

Genome Pub Date : 2025-03-13 DOI: 10.1139/gen-2024-0134

Antony T Vincent

引用次数: 0

Museum insights for conservation: Unraveling the Extinction Factors in the Jambato Harlequin Frog, Atelopus ignescens .

IF 2.3 3区生物学

Genome Pub Date : 2025-03-06 DOI: 10.1139/gen-2024-0032

Mónica A A Guerra, Chengchen Gao, Samuel Crickenberger, Michelle Vélez, Luis A Coloma, Silu Wang

{"title":"Museum insights for conservation: Unraveling the Extinction Factors in the Jambato Harlequin Frog, Atelopus ignescens .","authors":"Mónica A A Guerra, Chengchen Gao, Samuel Crickenberger, Michelle Vélez, Luis A Coloma, Silu Wang","doi":"10.1139/gen-2024-0032","DOIUrl":"https://doi.org/10.1139/gen-2024-0032","url":null,"abstract":"Natural history museums harbor invaluable resources for conserving endangered species by providing insights into the mechanism of historical population declines. We conducted data synthesis to better understand the extinction factors of the iconic Jambato Harlequin frog, Atelopus ignescens, which was widespread in the Ecuadorian Andes before 1985 but vanished in 1988. We synthesized historical data from natural history museums, the Global Biodiversity Information Facility (GBIF), and mtDNA sequences to examine whether Batrachochytrium dendrobatidis (Bd) fungus infection, climate change, and/or their interaction contributed to the rapid population decline. We found excessive rare alleles reflected in the negative Tajima's D estimated from the mtDNA samples from 1984, indicating a selective sweep or population bottleneck. Sex and geography showed stronger effects on adult body sizes than Bd epizootic timing. The body sizes of adult males formed a geographic cline. Species distribution modeling based on temperature and precipitation accurately predicted the occupancy of A. ignescens in 1960-69, which further projected a rapid decline in species distribution between 1970-2020. This investigation revealed strong climate effect and weak epizootics effect on A. ignescens extinction, and inspires future museum genomic studies to dissect the potential climatic maladaptation behind dramatic historical extinctions.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape.

IF 2.3 3区生物学

Genome Pub Date : 2025-02-11 DOI: 10.1139/gen-2024-0166

Leonardo Tresoldi Gonçalves, Pedro Henrique Pezzi, Flávia Regina Girardi Montagner, Wellington Vasconcelos de Souza, Elaine Françoso, Maríndia Deprá

{"title":"The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape.","authors":"Leonardo Tresoldi Gonçalves, Pedro Henrique Pezzi, Flávia Regina Girardi Montagner, Wellington Vasconcelos de Souza, Elaine Françoso, Maríndia Deprá","doi":"10.1139/gen-2024-0166","DOIUrl":"https://doi.org/10.1139/gen-2024-0166","url":null,"abstract":"We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (Bombus bellicosus). This is an endemic species in southern South America facing local extinction due to habitat loss and climate change. During the COVID-19 social distancing in Brazil, we launched a citizen science initiative via social media to locate remaining bellicose bumblebee populations, leading to the collection of a specimen for genome sequencing. Analysis of the novel genome revealed lower genetic diversity in the bellicose bumblebee compared to a widespread related species (B. pascuorum). However, the absence of extensive runs of homozygosity indicated a lack of recent inbreeding, offering a promising perspective for the conservation of this species. Furthermore, demographic history analysis indicates population expansion during past glacial periods, in contrast to Palearctic bumblebees which suffered a stark decline during glaciations. Our findings provide invaluable information for the conservation of this species and for further studies about its biology and evolution, particularly under a scenario of rapid environmental change.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The repetitive DNA landscape in the 'brizantha' agamic complex of Urochloa P. Beauv.

IF 2.3 3区生物学

Genome Pub Date : 2025-01-31 DOI: 10.1139/gen-2024-0096

Caio Túlio Rodrigues Corrêa, Magdalena Vaio, Sanzio Carvalho Lima Barrios, Cacilda Borges do Valle, Giovana Augusta Torres, Vania Helena Techio

{"title":"The repetitive DNA landscape in the 'brizantha' agamic complex of Urochloa P. Beauv.","authors":"Caio Túlio Rodrigues Corrêa, Magdalena Vaio, Sanzio Carvalho Lima Barrios, Cacilda Borges do Valle, Giovana Augusta Torres, Vania Helena Techio","doi":"10.1139/gen-2024-0096","DOIUrl":"https://doi.org/10.1139/gen-2024-0096","url":null,"abstract":"Urochloa P. Beauv. (formerly classified as Brachiaria (Trin.) Griseb.) is a genus of African perennial grasses that is extensively cultivated in tropical countries for cattle nutrition. Three of the most economically relevant species, Urochloa brizantha, U. decumbens, and U. ruziziensis, form the 'brizantha' agamic complex, which includes allopolyploid series with distinct subgenomes. Investigating the composition and organization of repetitive DNA, a major component of grass genomes, can provide insights into their genomic relationships and evolutionary history. This study aimed to characterize the repetitive DNA landscape of selected Urochloa species belonging to the 'brizantha' agamic complex; identify and compare major repeat classes across species and evaluate their potential as cytogenetic markers on mitotic chromosomes using fluorescent in situ hybridization (FISH). Clustering analysis revealed that repetitive DNA constitutes 56-65% of the genomes, with Ty3/Gypsy retrotransposons, particularly the Athila and Retand lineages, representing the most abundant repeat class. U. decumbens exhibited the highest proportion of Ty3/Gypsy retrotransposons, while U. ruziziensis had the highest satellite DNA content. The chromosomal location of representative satellites (UroSat-1a, UroSat-2a, and UroSat-3) was determined in all three species via FISH. UroSat-1a was detected in all centromeres, while UroSat-2a and UroSat-3 signals varied in number and position. Our findings validate the use of satDNA as cytogenetic markers in the Urochloa 'brizantha' agamic complex and revealed genomic relationships among different species and ploidy levels.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Peroxisome inter-organelle cooperation in Drosophila. 果蝇的过氧物酶体细胞器间合作

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0082

Andy Y Cheng, Andrew J Simmonds

{"title":"Peroxisome inter-organelle cooperation in Drosophila.","authors":"Andy Y Cheng, Andrew J Simmonds","doi":"10.1139/gen-2024-0082","DOIUrl":"10.1139/gen-2024-0082","url":null,"abstract":"Many cellular functions are compartmentalized within the optimized environments of organelles. However, processing or storage of metabolites from the same pathway can occur in multiple organelles. Thus, spatially separated organelles need to cooperate functionally. Coordination between organelles in different specialized cells is also needed, with shared metabolites passed via circulation. Peroxisomes are membrane-bounded organelles responsible for cellular redox and lipid metabolism in eukaryotic cells. Peroxisomes coordinate with other organelles including mitochondria, endoplasmic reticulum, lysosomes, and lipid droplets. This functional coordination requires, or is at least enhanced by, direct contact between peroxisomes and other organelles. Peroxisome dysfunction in humans leads to multiorgan effects including neurological, metabolic, developmental, and age-related diseases. Thus, increased understanding of peroxisome coordination with other organelles, especially cells in various organs is essential. Drosophila melanogaster (fruit fly) has emerged recently as an effective animal model for understanding peroxisomes. Here we review current knowledge of pathways regulating coordination between peroxisomes with other organelles in flies, speculating about analogous roles for conserved Drosophila genes encoding proteins with known organelle coordinating roles in other species.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A quick guide to the calcium-dependent protein kinase family in Brassica napus. 油菜钙依赖性蛋白激酶家族快速指南。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-11-05 DOI: 10.1139/gen-2024-0053

Virginia Natali Miguel, Jacqueline Monaghan

引用次数: 0

A phylogenetic perspective of chromosome evolution in Formicidae. 从系统进化的角度看姬蜂科的染色体进化。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-12-16 DOI: 10.1139/gen-2024-0124

Danon Clemes Cardoso, Maykon Passos Cristiano

{"title":"A phylogenetic perspective of chromosome evolution in Formicidae.","authors":"Danon Clemes Cardoso, Maykon Passos Cristiano","doi":"10.1139/gen-2024-0124","DOIUrl":"10.1139/gen-2024-0124","url":null,"abstract":"Chromosomes, as carriers of genes, are the fundamental units of heredity, with the eukaryotic genome divided into multiple chromosomes. Each species typically has a consistent number of chromosomes within its lineage. Ants, however, display remarkable diversity in chromosome numbers, and previous studies have shown that this variation may correlate with ant diversity. As ants evolved, various karyotypes emerged, primarily through chromosomal fissions, leading to an increase in chromosome number and a decrease in chromosome size. In this study, we investigate chromosome evolution in ants from a phylogenetic perspective using ancestral reconstruction. Our analysis indicates that the most recent common ancestor of ants had an ancestral haploid chromosome number of 11, likely composed of biarmed chromosomes. The bimodal distribution of karyotypes and the trend toward increased chromosome numbers align with previous assumptions. However, both dysploidy and ploidy changes have been indicated as likely mechanisms of chromosome number evolution. Descending dysploidy occurs consistently throughout the phylogeny, while changes in ploidy are believed to occur occasionally within the subfamilies during genus diversification. We propose, based on our results and previous evidence (e.g., genome size in ants), that both fusions and fissions contribute equally to karyotype changes in Formicidae. Additionally, changes in ploidy should not be fully ignored, as they can occur across specific lineages.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-10"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142835349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The filamins of Drosophila.

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0159

Tiara Mulder, Jennifer Johnson, Nicanor González-Morales

引用次数: 0