Journal of Genomics http://www.jgenomics.com Journal of Genomics RSS feed -- Volume 9 en-us Sun, 13 Jun 2021 04:00:00 GMT Sun, 13 Jun 2021 04:00:00 GMT http://www.jgenomics.com/v09p0026.htm Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity Here, we report high-quality annotated draft genomes of eight coagulase-negative staphylococci (CoNS) isolates obtained from South Africa and Nigeria. We explored the prevalence of antibiotic resistance and virulence genes, their association with mobile genetic elements. The pan-genomic analysis highlighted the environmentally driven heterogeneity of the isolates. Isolates from Nigeria had at least one gene for cadmium resistance/tolerance, these genes were not detected in isolates from South Africa. In contrast, isolates from South Africa had a tetM gene, which was not detected among the isolates from Nigeria. The observed genomic heterogeneity correlates with anthropogenic activities in the area where the isolates were collected. Moreover, the isolates used in this study possess an open pan-genome, which could easily explain the environmentally driven heterogeneity.

]]> Tawanda Elias Maguvu, Adegboyega Oyedele Oladipo, Cornelius Carlos Bezuidenhout Journal of Genomics Ivyspring International Publisher 9 1 26 37 2021 Research Paper http://www.jgenomics.com/v09p0020.htm Draft genome sequences of three filamentous cyanobacteria isolated from brackish habitats Brackish cyanobacterial genome sequences are relatively rare. Here, we report the 5.5 Mbp, 5.8 Mbp and 6.1 Mbp draft genomes of Spirulina sp. CCY15215, Leptolyngbya sp. CCY15150 and Halomicronema sp. CCY15110 isolated from coastal microbial mats on the North Sea beach of the island of Schiermonnikoog in the Netherlands. Large scale phylogenomic analyses reveal that Spirulina sp. CCY15215 is a large cell diameter cyanobacterium, whereas Leptolyngbya sp. CCY15150 and Halomicronema sp. CCY15110 are the first reported brackish genomes belonging to the LPP clade consisting primarily of Leptolyngbya, Plectonema and Phormidium spp. Further genome mining divulges that all new draft genomes contain, ggpS and ggpP, the genes responsible for synthesising glucosylglycerol (GG), a compatible solute found in moderately salt-tolerant cyanobacteria.

]]> Joanne Sarah Boden, Michele Grego, Henk Bolhuis, Patricia Sánchez-Baracaldo Journal of Genomics Ivyspring International Publisher 9 1 20 25 2021 Research Paper http://www.jgenomics.com/v09p0010.htm The Genetic Background of Central Serous Chorioretinopathy: A Review on Central Serous Chorioretinopathy Genes Central serous chorioretinopathy is characterized by neurosensory detachment of the central retina secondary to fluid leakage through the retinal pigment epithelium. Though it has an incidence of 9,9 per 100.000 in men and 1,7 per 100.000 in women, it is the fourth most common retinal disorder. Central serous chorioretinopathy patients present with blurred vision, central scotoma, metamorphopsia, micropsia and mild color discrimination. It is usually a self-limited disorder with nearly none or minimal visual impairment but in some patients the disease persists and may cause severe visual impairment. Central serous chorioretinopathy pathophysiology is not well understood. Choroid, retinal pigment epithelium and hormonal pathways seem to play important roles in central serous chorioretinopathy pathophysiology. Also, familial cases of the disease indicate that there is a genetic background. The identification of certain disease genes could lead to the development of better diagnostic and therapeutic approaches for central serous chorioretinopathy patients.

]]> Konstantinos Giannopoulos, Maria Gazouli, Klio Chatzistefanou, Anthi Bakouli, Marilita M Moschos Journal of Genomics Ivyspring International Publisher 9 1 10 19 2021 Review http://www.jgenomics.com/v09p0006.htm Draft Genome Sequence of Enterobacter sp. AS-1, a Potential Eurytrophic Recombination Host Strain AS-1 was isolated from laboratory-scale activated sludge collected in Japan.

This strain not only grows on rich medium, including R2A medium, but also forms colonies on medium lacking organic matter other than agar (water agar), indicating it could be used as a eurytrophic recombinant host in material production processes. Here, we present a draft genome sequence of Enterobacter sp. AS-1, which consists of a total of 24 contigs containing 5,207,146 bp, with a GC content of 55.64%, and comprising 4,921 predicted coding sequences. Based on 16S rRNA gene sequence analysis, strain AS-1 was designated as Enterobacter sp. AS-1.

]]> Yuki Iwasaki, Yuya Itoiri, Sota Ihara, Hironaga Akita, Mamoru Oshiki, Zen-ichiro Kimura Journal of Genomics Ivyspring International Publisher 9 1 6 9 2021 Research Paper http://www.jgenomics.com/v09p0001.htm Isolation, draft genome sequencing and identification of Enterobacter roggenkampii CCI9 Strain CCI9, which was isolated from leaf soil collected in Japan, was capable of growth on poor-nutrient medium, at temperatures of 10°C to 45°C, at pHs of 4.5 to 10, and in the presence of 7.0% NaCl. We determined a draft genome sequence of strain CCI9, which consists of a total of 28 contigs containing 4,644,734 bp with a GC content of 56.1%. This assembly yielded 4,154 predicted coding sequences. Multilocus sequence analysis (MLSA) based on atpD, gyrB, infB, and rpoB gene sequences were performed to further identify strain CCI9. The MLSA revealed that strain CCI9 clustered tightly with Enterobacter roggenkampii EN-117T. Moreover, the average nucleotide identity value (98.6%) between genome sequences of strain CCI9 and E. roggenkampii EN-117T exceeds the cutoff value for prokaryotic subspecies delineation. Therefore, strain CCI9 was identified as E. roggenkampii CCI9. To clarify differences between E. roggenkampii EN-117T and CCI9, the coding proteins were compared against the eggNOG database.

]]> Hironaga Akita, Yuya Itoiri, Noriyo Takeda, Zen-ichiro Kimura, Hiroyuki Inoue, Akinori Matsushika Journal of Genomics Ivyspring International Publisher 9 1 1 5 2021 Research Paper