Journal of Genomics最新文献

Whole-Genome sequencing and phylogenomic analyses of Alternaria japonica and A. telliensis (Section Japonicae). 日本稻交虫和日本稻交虫全基因组测序及系统基因组分析。

Journal of Genomics Pub Date : 2026-10-09 eCollection Date: 2026-01-01 DOI: 10.7150/jgen.142347

Roumaissa Barkat, Nabahat Bessadat, Justine Colou, Philippe Simoneau

{"title":"Whole-Genome sequencing and phylogenomic analyses of Alternaria japonica and A. telliensis (Section Japonicae).","authors":"Roumaissa Barkat, Nabahat Bessadat, Justine Colou, Philippe Simoneau","doi":"10.7150/jgen.142347","DOIUrl":"10.7150/jgen.142347","url":null,"abstract":"Species of Alternaria are necrotrophic fungi responsible for leaf spot diseases on a wide range of cultivated and wild plants. Species delimitation within this genus, however, often relies on morphological features and a limited set of molecular markers, which can constrain phylogenetic resolution at finer taxonomic scales. This is the case for Alternaria telliensis, a species recently described from Algeria and subsequently reported in Iran, whose relationships within section Japonicae require clarification. To provide a higher resolution framework for this species, we performed whole-genome sequencing, assembly, and BUSCO completeness assessment for type strains of A. telliensis (CBS 145643) and A. japonica (CBS 118390), using Oxford Nanopore Technologies MinION sequencing. The genome assembly of A. telliensis spans 34.4 Mbp across 132 contigs, with an N50 of 2.2 Mbp and a GC content of 50.94%. The A. japonica assembly comprises 33.5 Mbp in 196 contigs, with an N50 of 1.6 Mbp and a GC content of 51.47%. Phylogenomic analysis places A. telliensis alongside A. japonica within section Japonicae. These genomic data support the classification of A. telliensis and contribute to clarifying taxonomic relationships within the genus Alternaria.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"14 ","pages":"30-33"},"PeriodicalIF":0.0,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13654648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Draft Genome Sequence of Multidrug-Resistant Acinetobacter baumannii smu isolated from a Bloodstream Infection in Sikkim, India. 从印度锡金的一种血液感染中分离出的多药耐药鲍曼不动杆菌smu的基因组序列草图。

Journal of Genomics Pub Date : 2026-05-01 eCollection Date: 2026-01-01 DOI: 10.7150/jgen.130521

Rekha Sharma, Rohit Das, Yezey Rikzing Bhutia, Neha Pradhan, Anil Bhattarai

{"title":"Draft Genome Sequence of Multidrug-Resistant Acinetobacter baumannii smu isolated from a Bloodstream Infection in Sikkim, India.","authors":"Rekha Sharma, Rohit Das, Yezey Rikzing Bhutia, Neha Pradhan, Anil Bhattarai","doi":"10.7150/jgen.130521","DOIUrl":"10.7150/jgen.130521","url":null,"abstract":"Septicemia remains a major cause of death in intensive care units and its treatment is increasingly challenged by multidrug-resistant pathogens. This study investigated bloodstream infections in 89 ICU patients at a tertiary hospital in Sikkim where the Neonatal ICU showed the highest burden. Acinetobacter baumannii was the predominant pathogen, including 13 MDR isolates. One highly resistant isolate, A. baumannii smu was selected for whole-genome sequencing. The smu strain had a genome size of 4.0 Mbp, assembled into three contigs with 182× coverage, an N50 of 3.98 Mb, and a GC content of 39.16%. Nineteen resistance genes were identified including β-lactamases (ADC-15B, OXA-98), aminoglycoside-modifying enzymes, and multiple efflux pumps. Virulence factors included acinetobactin-mediated iron uptake, biofilm-associated genes, OmpA, and phospholipases. The genome also harbored mobile genetic elements including insertion sequences and prophages. Pangenome analysis revealed 13 distinct genes associated with stress, tolerance, stability of plasmids, and possible resistance. This study provides a comprehensive genomic characterization of an MDR A. baumannii isolate from Sikkim, revealing its extensive resistance and virulence features, and providing baseline genomic data to support improved antibiotics use and infection control in the region.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"14 ","pages":"18-29"},"PeriodicalIF":0.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13143519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Draft Genomes of Geographically Distinct Strains and Progeny of the Ectomycorrhizal Basidiomycete Laccaria bicolor. 外生菌根担子菌双色拉卡菌的地理差异菌株和后代基因组草图。

Journal of Genomics Pub Date : 2026-01-30 eCollection Date: 2026-01-01 DOI: 10.7150/jgen.130158

Francis M Martin, Emmanuelle Morin, Alan Kuo, Igor Miquel, Jessy Labbé, François Le Tacon, Laure Fauchery, Annegret Kohler, William Andreopoulos, Alex Copeland, Hui Sun, Asaf Salamov, Anna Lipzen, James Han, Kurt LaButti, Andrew Tritt, Kerry Barry, Igor V Grigoriev

{"title":"Draft Genomes of Geographically Distinct Strains and Progeny of the Ectomycorrhizal Basidiomycete Laccaria bicolor.","authors":"Francis M Martin, Emmanuelle Morin, Alan Kuo, Igor Miquel, Jessy Labbé, François Le Tacon, Laure Fauchery, Annegret Kohler, William Andreopoulos, Alex Copeland, Hui Sun, Asaf Salamov, Anna Lipzen, James Han, Kurt LaButti, Andrew Tritt, Kerry Barry, Igor V Grigoriev","doi":"10.7150/jgen.130158","DOIUrl":"10.7150/jgen.130158","url":null,"abstract":"The ectomycorrhizal fungus Laccaria bicolor is a key symbiotic mutualist in forest ecosystems, where it enhances nutrient uptake and promotes the growth of host trees. Here, we present genome assemblies of 14 geographically distinct strains and progeny of L. bicolor, providing new insights into the intraspecific genomic diversity. Pangenome analysis revealed substantial variation in assembly size (42-96 Mbp), gene content (16,084-26,800 genes), and single nucleotide polymorphism (SNP) density (0.04-12.08 SNPs/kb). This variation likely reflects genuine biological differences among strains adapted to diverse environmental conditions, although differences in assembly quality and repeat content may also play a role. These genomic resources, comprising draft genome assemblies with comprehensive annotations, will facilitate comparative studies of the genetic diversity and functional traits underlying the ecological success of this model ectomycorrhizal fungus.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"14 ","pages":"10-17"},"PeriodicalIF":0.0,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12923307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147271427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

De Novo Genome Assembly of the Myanmar Puddle Frog, Phrynoglossus myanhessei (Anura: Dicroglossidae). 缅甸水蛙，Phrynoglossus myanhessei（无尾目：双舌蛙科）基因组的重新组装。

Journal of Genomics Pub Date : 2026-01-01 DOI: 10.7150/jgen.125510

Katharina Geiß, Gunther Köhler, Axel Janke

{"title":"De Novo Genome Assembly of the Myanmar Puddle Frog, Phrynoglossus myanhessei (Anura: Dicroglossidae).","authors":"Katharina Geiß, Gunther Köhler, Axel Janke","doi":"10.7150/jgen.125510","DOIUrl":"10.7150/jgen.125510","url":null,"abstract":"The Myanmar puddle frog, Phrynoglossus myanhessei, is a recently described, small dicroglossid frog distributed across central and southern Myanmar, typically inhabiting areas adjacent to small stagnant water bodies. With that new species description, rudimentary genome data from 30-fold Illumina sequencing were published as a novel approach in taxonomy to routinely publish genome data for new holotypes. While the data allowed to assemble the entire mitochondrial genome, it was not possible to extract basic population genetic data. Therefore, we present a de novo PacBio CLR genome assembly of P. myanhessei, to aid population genomic, evolutionary and taxonomic studies. The assembled genome has a size of 2.28 Gbp, with a scaffold N50 of 44 kbp and largest scaffold being 270 kbp long. BUSCO analysis indicates a completeness score of 49%, with 26.9% complete and 22.3% fragmented BUSCOs. Approximately 43% of the genome consists of repetitive elements and about 22,500 genes could be predicted. While not an optimal assembly, the new P. myanhessei genome is a valuable resource for follow-up studies and for closing the gap in amphibian genome representation.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"14 ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12766079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145911698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Whole-Genome Shotgun Sequencing and Assembly of Anopheles gambiae G3, the Host of Malaria Parasite Plasmodium sp. 疟原虫寄主冈比亚按蚊G3的全基因组霰弹枪测序与组装。

Journal of Genomics Pub Date : 2025-10-27 eCollection Date: 2025-01-01 DOI: 10.7150/jgen.123168

Eva English, Clara Gulick, Ashley Jane, Minseo Kim, Nat Kpodonu, Aden Lee, Ramon Kodi Suzuki Lopez, Krish Patel, Achyuta Rajaram, Leyla Unver, Anne E Rankin, Shimaa M Ghazal

引用次数: 0

Identification of Splicing Variation Associated with Parental Behavior in the Burying Beetles (Nicrophorus orbicollis). 埋葬甲虫亲代行为相关剪接变异的鉴定。

Journal of Genomics Pub Date : 2025-10-20 eCollection Date: 2025-01-01 DOI: 10.7150/jgen.123113

Victoria P Blythe, Xiangjia Min, S Carmen Panaitof

{"title":"Identification of Splicing Variation Associated with Parental Behavior in the Burying Beetles (Nicrophorus orbicollis).","authors":"Victoria P Blythe, Xiangjia Min, S Carmen Panaitof","doi":"10.7150/jgen.123113","DOIUrl":"10.7150/jgen.123113","url":null,"abstract":"The molecular basis of parental behavior in burying beetles is not well understood. This study is a first attempt to evaluate the extent of alternative splicing (AS) as a source of transcriptome diversity that may facilitate flexible parenting behavior in this species. RNA-seq datasets from beetle parents exhibiting high or low care behavior and a newly available Nicrophorus orbicollis genome were used to perform AS analysis by AStalavista to comprehensively classify AS events, and specific patterns of splicing variation within and across parental groups were evaluated. Towards functional characterization, AS genes were annotated via protein family analysis. Transcriptome-wide AS profiles for each parental group were established, revealing no specific splicing patterns associated with either sex or parenting phenotype (high or low care behavior). Among simple types of AS events, intron retention was the most common (13%), while mutually exclusive exons were the least common (0.4%), with alternative acceptor (6%) and alternative donor (5%) occurring slightly more often than exon skipping (3%). Functional annotation highlighted AS genes belonging to protein families broadly linked to chemoreception, neuromodulation and JH function, all biological processes essential for the regulation of reproductive behavior and physiology. This analysis was successful in generating a large catalogue of AS events associated with parenting behavior in burying beetles. Additional analyses could expand upon this dataset to include tissue, development and species-specific splice variants, as well as functionally validate AS transcripts via RT-PCR to further clarify the role of functional AS in behavioral regulation in this species.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"13 ","pages":"49-54"},"PeriodicalIF":0.0,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12599511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145495577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Whole genome Shotgun Sequence of Anopheles stephensi, The Host of Malaria parasite, Plasmodium sp. 疟原虫宿主斯氏按蚊全基因组鸟枪序列分析。

Journal of Genomics Pub Date : 2025-09-22 eCollection Date: 2025-01-01 DOI: 10.7150/jgen.121872

Jack Farah, Junhyeok Jang, Kenza Madhi, Jessica Phan, Elizabeth Pratt, Amrita Sankrit, Nora L Sharma, Aria Suchak, Devin W Thomas, Shimaa M Ghazal

引用次数: 0

Isolation and Whole Genome Sequence Analysis of Alcaligenes and Chromobacterium Strains with Antimicrobial Activity Against ESKAPE Pathogen Relatives. 对ESKAPE病原菌具有抗菌活性的碱性菌和色杆菌的分离及全基因组序列分析。

Journal of Genomics Pub Date : 2025-06-23 eCollection Date: 2025-01-01 DOI: 10.7150/jgen.115133

Hannah W Lwin, Jonathan D Dattelbaum

{"title":"Isolation and Whole Genome Sequence Analysis of Alcaligenes and Chromobacterium Strains with Antimicrobial Activity Against ESKAPE Pathogen Relatives.","authors":"Hannah W Lwin, Jonathan D Dattelbaum","doi":"10.7150/jgen.115133","DOIUrl":"10.7150/jgen.115133","url":null,"abstract":"Discovery, development, and production of new antibiotic drugs in a form safe for human consumption have become increasingly difficult, expensive, and time-consuming, especially with an increase in antibiotic-resistant pathogens. The ESKAPE pathogens are a group of six pathogenic bacteria that can be highly virulent and are likely to, or already have, developed antibiotic resistance to many of the currently available antibiotics. New antibiotics or new activities of existing natural products are needed to combat these multi-drug resistant pathogens. Our approach was to search for soil microbes that produce antimicrobial compounds that could potentially inhibit the growth of the ESKAPE pathogens. We report one draft genome of Chromobacterium and one draft genome of Alcaligenes cultured from soil with antimicrobial activity against Staphylococcus epidermidis, a relative of ESKAPE pathogen Staphylococcus aureus. The lengths of the genomes were 5.2 and 4.0 Mbps and GC content was at 64.4% and 56.1% for Chromobacterium sp. HL1 and Alcaligenes parafaecalis HL2, respectively. Chromobacterium sp. HL1 has not been assigned to any previously known species. Phylogenetic analysis revealed that Chromobacterium sp. HL1 may be closely related to Chromobacterium fluminis and Chromobacterium alkanivorans. A. parafaecalis HL2 is likely related to Alcaligenes faecalis subsp. parafaecalis. Functional analysis revealed biosynthetic gene clusters related to betalactone, terpene, isocyanide, and T1PKS in one or both genomes analyzed. Antimicrobial properties were previously reported from the products of these gene clusters that could further aid our search for the active component of the analyzed strains.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"13 ","pages":"40-45"},"PeriodicalIF":0.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dexamethasone-Induced MerTK^+/high M2c Macrophages Exhibit a Preference for Downregulated Gene Expression Profiles. 地塞米松诱导的MerTK+/高M2c巨噬细胞表现出下调基因表达谱的偏好。

Journal of Genomics Pub Date : 2025-03-31 eCollection Date: 2025-01-01 DOI: 10.7150/jgen.108648

Zhen-Tao Lee, Farrah Putri Salmanida, Hso-Chi Chaung, Ko-Tung Chang

{"title":"Dexamethasone-Induced MerTK+/high M2c Macrophages Exhibit a Preference for Downregulated Gene Expression Profiles.","authors":"Zhen-Tao Lee, Farrah Putri Salmanida, Hso-Chi Chaung, Ko-Tung Chang","doi":"10.7150/jgen.108648","DOIUrl":"https://doi.org/10.7150/jgen.108648","url":null,"abstract":"In a prior study, adoptive cell transfer (ACT) of Dexamethasone (DEX)-induced M2c macrophages with positive expression of MerTK receptor mitigated acute allograft rejection, which was observed in the presence of apoptotic lymphocytes, while simultaneously reducing MHC-II and CD8+ T cells in the recipients. However, there has been limited exploration of the properties of adoptive M2c cells, leaving their potential for other applications unclear. In this study, we aimed to characterize the transcriptome profile of DEX-induced MerTK+/high M2c macrophages. Notably, through the analysis of differentially expressed genes (DEGs), no significant pathway could be constructed from the upregulated DEGs. Only downregulated DEGs could facilitate KEGG construction, encompassing the role of DEX-induced MerTK+/high M2c in immune tolerance. The expression of T-cell activation, pro- and anti-inflammatory cytokines modulation, leukocyte recruitment and adjustment of MHC-I/II-related proteins were entirely diminished. Nonetheless, association of these traits suggests the potential of MerTK+/high M2c macrophages for use in ACT, particularly for autoimmune conditions such as rheumatoid arthritis, inflammatory bowel disease, type-I diabetes mellitus, and AGE/RAGE signaling pathway in diabetic complications. In summary, the preference for downregulated gene expression profiles in DEX-induced MerTK+/high M2c macrophages affirms their potential for immunosuppressive adoptive cell therapy.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"13 ","pages":"24-39"},"PeriodicalIF":0.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143995149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

From Soil to Surface: Exploring the Impact of Green Infrastructure on Microbial Communities in the Built Environment. 从土壤到地表：探索绿色基础设施对建筑环境中微生物群落的影响。

Journal of Genomics Pub Date : 2025-01-18 eCollection Date: 2025-01-01 DOI: 10.7150/jgen.106245

Malin Mcgonigal, Kohei Ito

{"title":"From Soil to Surface: Exploring the Impact of Green Infrastructure on Microbial Communities in the Built Environment.","authors":"Malin Mcgonigal, Kohei Ito","doi":"10.7150/jgen.106245","DOIUrl":"10.7150/jgen.106245","url":null,"abstract":"High microbial diversity offers extensive benefits to both the environment and human health, contributing to ecosystem stability, nutrient cycling, and pathogen suppression. In built environments, factors such as building design, human activity, and cleaning protocols influence microbial communities. This study investigates the impact of landscape design on microbial diversity and function within the \"Visionary Lab\" exhibition in Tokyo, Japan, using 16S rRNA gene amplicon sequencing and shallow shotgun sequencing. Despite the limited sample size, the study suggests that the Visionary Lab samples may exhibit higher microbial diversity compared to other museum areas. Potential distinct microbial community structures may be correlated with sampling locations. However, despite this, no consistent patterns were observed in virulence factors or antimicrobial resistance genes across the samples. Metabolic function analysis showed varied profiles, suggesting diverse ecological interactions influenced that may be by the curated landscape. This suggest that the curated landscape design may have the potential to enhance microbial diversity, highlighting a possible avenue to create healthier and more sustainable built environments. However, the lack of consistent patterns in virulence factors and antimicrobial resistance genes underscores the complexity of microbial community dynamics.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"13 ","pages":"10-23"},"PeriodicalIF":0.0,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11803137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0