Journal of Genomics最新文献

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.

Anopheles gambiae or the African malaria mosquito is the main vector of human malaria. G3, is an Anopheles gambiae strain, that was isolated from Gambiae in 1975, We report here a 216.3 Mbp draft genome sequence and assembly for Anopheles gambiae strain G3, with almost 82 thousand scaffold, 53X coverage and a G+C content of 44.5%.

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.

Anopheles stephensi, one of the main mosquito vectors for malaria in Asia. It belongs to the same complex species of Anopheles gambiae. A genome assembly was performed on female Anopheles stephensi, the resulting genome was 201Mbp in size and consisted of 32,280 contigs with an N50 of 21,1 kb and a GC content of 45%.

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.

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.

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.

Purpose: Genetic variants encoding both low COMT and MTHFR activity are associated with idiopathic scoliosis. The combined impact of COMT and MTHFR on progression of adolescent idiopathic scoliosis (AIS) is unknown. This study investigated if COMT and MTHFR low activity variants are associated with AIS progression. Methods: Patients with AIS, at least two Cobb angle measurements in adolescence, and those with both low COMT (rs4680 AA) and low MTHFR (A1298C AC and C677T CT; A1298C AA and C677T TT) activity (Group 1) or those with intermediate or high COMT (rs4680 AG or GG) and MTHFR (A1298C AA and C677T CT; A1298C AC and C677T CC; A1298C AA and C677T CC) activity (Group 2) were included. Those with neuromuscular or syndromic scoliosis were excluded. The primary outcome was progression of scoliosis, defined as a Cobb angle increase of at least 20 degrees or spinal surgery between the time of diagnosis and skeletal maturity. The primary outcome was analyzed via a Chi-square test. Results: Seventy-two patients with AIS diagnosis and required Cobb angle measurements had both COMT and MTHFR results that met criteria for Group 1 (n=41) or Group 2 (n=31). Regarding the primary outcome, 78.0% (32/41) in Group 1 progressed versus 48.4% (15/31) of patients in Group 2 (p=0.009). Conclusion: Significantly more patients with both low COMT and low MTHFR activity variants had progression of AIS than those with intermediate or normal activity variants of COMT and MTHFR. Further understanding the role of COMT and MTHFR may inform research regarding treatment modalities.

The earthball Scleroderma, an ectomycorrhizal basidiomycete belonging to the Sclerodermataceae family, serves as a significant mutualistic tree symbiont globally. Originally, two genetically sequenced strains of this genus were obtained from fruiting bodies collected under chestnut trees (Castanea mollissima). These strains were utilized to establish in vitro ectomycorrhizal roots of chestnut seedlings. The genome sequences of these strains share characteristics with those of other ectomycorrhizal species in Boletales order, including a restricted set of genes encoding carbohydrate-active enzymes. The genome sequences presented here will aid in further exploring the factors contributing to the establishment of ectomycorrhizal symbiosis in chestnut trees.

Monilinia vacccinii-corymbosi (phylum Ascomycota, family Sclerotiniaceae) causes fruit disease 'mummy berry' on berry crops and responsible for yield losses and quality of fruits. We reported mummy berry disease of black huckleberry (Vaccinium membranaceum) first time in British Columbia, Canada. We have performed sequencing and genome assembly of M. vacccinii-corymbosi from infected fruits of huckleberry. The resulting genome was 33.8 Mbp in size and consisted of 2,437 scaffolds with an N50 of 33,816 bp. To our best knowledge, this is the first report of resource announcement of whole genome sequence of mummy berry pathogen (M. vacccinii-corymbosi) infecting black huckleberry. The genome resource will be valuable for future studies to understand the genomic structure of pathogen, and mechanisms associated with black huckleberry-M. vacccinii-corymbosi interactions.