scholarly journals Genome annotation of Poly(lactic acid) degradingPseudomonas aeruginosaandSphingobacterium sp.

2019 ◽  
Author(s):  
Sadia Mehmood Satti ◽  
Aamer Ali Shah ◽  
Rafael Auras ◽  
Terence L. Marsh
Keyword(s):  
Lactic Acid ◽  
Genome Annotation ◽  
Environmental Pollutants ◽  
Poly Lactic Acid ◽  
Protein Coding ◽  
Genetic Elements ◽  
Protein Coding Genes ◽  
Catabolic Genes ◽  
Insight Into ◽  
Gaining Insight

AbstractPseudomonas aeruginosaandSphinogobacterium sp. are well known for their ability to decontaminate many environmental pollutants like PAHs, dyes, pesticides and plastics. The present study reports the annotation of genomes fromP. aeruginosaandSphinogobacterium sp. that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA, at mesophillic temperatures (~30°C). Draft genomes of both the strains were assembled from Illumina reads, annotated and viewed with an aim of gaining insight into the genetic elements involved in degradation of PLA. The draft-assembled genome of strainSphinogobacteriumstrain S2 was 5,604,691 bp in length with 435 contigs (maximum length of 434,971 bp) and an average G+C content of 43.5%. The assembled genome ofP. aeruginosastrain S3 was 6,631,638 bp long with 303 contigs (maximum contig length of 659,181 bp) and an average G+C content 66.17 %. A total of 5,385 (60% with annotation) and 6,437 (80% with annotation) protein-coding genes were predicted for strains S2 and S3 respectively. Catabolic genes for biodegradation of xenobiotic and aromatic compounds were identified on both draft genomes. Both strains were found to have the genes attributable to the establishment and regulation of biofilm, with more extensive annotation for this in S3. The genome ofP. aeruginosaS3 had the complete cascade of genes involved in the transport and utilization of lactate whileSphinogobacterium strainS2 lacked lactate permease, consistent with its inability to grow on lactate. As a whole, our results reveal and predict the genetic elements providing both strains with the ability to degrade PLA at mesophilic temperature.

scholarly journals Genome Annotation of Poly(lactic acid) Degrading Pseudomonas aeruginosa, Sphingobacterium sp. and Geobacillus sp.

2021 ◽  
Vol 22 (14) ◽  
pp. 7385
Author(s):  
Sadia Mehmood Satti ◽  
Edgar Castro-Aguirre ◽  
Aamer Ali Shah ◽  
Terence L. Marsh ◽  
Rafael Auras
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Lactic Acid ◽  
Draft Genome ◽  
Environmental Pollutants ◽  
Poly Lactic Acid ◽  
Thermostable Enzymes ◽  
Protein Coding ◽  
Genetic Elements ◽  
Catabolic Genes ◽  
Insight Into

Pseudomonas aeruginosa and Sphingobacterium sp. are well known for their ability to decontaminate many environmental pollutants while Geobacillus sp. have been exploited for their thermostable enzymes. This study reports the annotation of genomes of P. aeruginosa S3, Sphingobacterium S2 and Geobacillus EC-3 that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA. Draft genomes of the strains were assembled from Illumina reads, annotated and viewed with the aim of gaining insight into the genetic elements involved in degradation of PLA. The draft genome of Sphinogobacterium strain S2 (435 contigs) was estimated at 5,604,691 bp and the draft genome of P. aeruginosa strain S3 (303 contigs) was estimated at 6,631,638 bp. The draft genome of the thermophile Geobacillus strain EC-3 (111 contigs) was estimated at 3,397,712 bp. A total of 5385 (60% with annotation), 6437 (80% with annotation) and 3790 (74% with annotation) protein-coding genes were predicted for strains S2, S3 and EC-3, respectively. Catabolic genes for the biodegradation of xenobiotics, aromatic compounds and lactic acid as well as the genes attributable to the establishment and regulation of biofilm were identified in all three draft genomes. Our results reveal essential genetic elements that facilitate PLA metabolism at mesophilic and thermophilic temperatures in these three isolates.

scholarly journals Complete Genome Sequence of Streptomyces Phage Sentinel

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Andrew Talcott ◽  
Russell Moreland ◽  
Jolene Ramsey ◽  
James Clark ◽  
Isla Hernandez ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Genome Annotation ◽  
Complete Genome ◽  
Protein Coding ◽  
Protein Coding Genes

ABSTRACT The Streptomyces genus produces over two-thirds of clinically useful, natural antibiotics. Here, we describe the isolation and genome annotation of siphophage Sentinel, which utilizes Streptomyces sp. strain Mg1 as a host. It has a 50,272-bp genome and 83 protein-coding genes and shows similarity to other Streptomyces phages in the Arequatrovirus genus.

scholarly journals Evidence for adaptive introgression of exons across a hybrid swarm in deer

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Margaret L. Haines ◽  
Gordon Luikart ◽  
Stephen J. Amish ◽  
Seth Smith ◽  
Emily K. Latch
Keyword(s):  
Mule Deer ◽  
Secondary Contact ◽  
Mountain Range ◽  
Reproductive Barriers ◽  
Hybrid Swarm ◽  
Evolutionary Trajectory ◽  
Protein Coding ◽  
Adaptive Introgression ◽  
Protein Coding Genes ◽  
Insight Into

Abstract Background Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes. Results We observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat. Conclusions Our data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa.

scholarly journals The Gene Rearrangement, Loss, Transfer, and Deep Intronic Variation in Mitochondrial Genomes of Conidiobolus

2021 ◽  
Vol 12 ◽  
Author(s):  
Yong Nie ◽  
Heng Zhao ◽  
Zimin Wang ◽  
Zhengyu Zhou ◽  
Xiaoyong Liu ◽  
...  
Keyword(s):  
Gene Rearrangement ◽  
Core Protein ◽  
Gc Content ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
Protein Coding ◽  
Circular Dna ◽  
Protein Coding Genes ◽  
Main Factors ◽  
Insight Into

The genus Conidiobolus s.s. was newly delimited from Conidiobolus s.l. In order to gain insight into its mitochondrial genetic background, this study sequenced six mitochondrial genomes of the genus Conidiobolus s.s. These mitogenomes were all composed of circular DNA molecules, ranging from 29,253 to 48,417 bp in size and from 26.61 to 27.90% in GC content. The order and direction for 14 core protein-coding genes (PCGs) were identical, except for the atp8 gene lost in Conidiobolus chlamydosporus, Conidiobolus polyspermus, and Conidiobolus polytocus, and rearranged in the other Conidiobolus s.s. species. Besides, the atp8 gene split the cox1 gene in Conidiobolus taihushanensis. Phylogenomic analysis based on the 14 core PCGs confirmed that all Conidiobolus s.s. species formed a monophyly in the Entomophthoromycotina lineage. The number and length of introns were the main factors contributing to mitogenomic size, and deep variations and potential transfer were detected in introns. In addition, gene transfer occurred between the mitochondrial and nuclear genomes. This study promoted the understanding of the evolution and phylogeny of the Conidiobolus s.s. genus.

Abstract 055: Locating Genetic Determinants Of Translational Significance Using The Rat Genome

Hypertension ◽  
2014 ◽  
Vol 64 (suppl_1) ◽  
Author(s):  
Ying Nie ◽  
Sivarajan Kumaraswamy ◽  
Xi Cheng ◽  
Harshal Waghulde ◽  
Blair Mel ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Human Chromosome ◽  
Chromosome 9 ◽  
Genome Wide Association Studies ◽  
Chromosome 2 ◽  
Protein Coding ◽  
Positional Candidate ◽  
Genetic Elements ◽  
Protein Coding Genes ◽  
Rat Genome

Genome-wide association studies (GWAS) have detected associations of genetic elements on human chromosome 2 with hypertension but lack the ability to discern whether these associations are/are not causal factors for hypertension. Using rat genetic models of hypertension, we have identified that factors linked to the inheritance of hypertension map to rat chromosome 9, which is homologous to human chromosome 2. Here we report that by applying high resolution mapping approaches, we have prioritized two regions on rat chromosome 9, one spanning < 788kb and a second region spanning < 81.8kb, as genomic segments containing novel inherited genetic elements controlling blood pressure. The <788kb region contains 3 protein coding genes, Trmp8 , Spp2 and Arl4c , which are also associated with human hypertension. Of these, there was only one nonsynonymous polymorphism within the gene Spp2 between the Dahl S and S.SHR strains used to map this locus. The expression of Spp2 was significantly higher in the S.SHR rat compared with S. We therefore prioritize Spp2 as a positional candidate for the <788kb region. The <81.8kb region contains no known/predicted protein-coding genes. We hypothesized that polymorphisms within gene regulatory elements underlie the <81.8kb locus. By combining the locations of the relevant polymorphisms with promoters predicted by the Proscan promoter prediction software, 5 regions were prioritized for further analysis. Alleles from the normotensive R rat from 1 out of these 5 regions had a 5.14 fold higher luciferase activity compared with that of the hypertensive S rat alleles (p<0.05). This region maps from chr9:80880396 to chr9:80882643 (Rnor5.0) on the rat genome. The downstream target for this promoter activity is unknown. Interestingly, within 110,419bp downstream of this region, there is a predicted long non-coding RNA in the mouse (AK079660) and in humans ( DIRC4) . By RT-PCR using rat kidney, we detected a novel rat transcript that is potentially a rat homologue of the mouse and human predictions. Collectively, these data point to conserved syntenic regions in rats and humans that contain novel promoter sequence variants and variants within the conserved gene, Spp2 , as potential quantitative trait nucleotides for blood pressure regulation.

scholarly journals Draft Genome Sequence of the Immunobiotic Strain Lactobacillus jensenii TL2937

2017 ◽  
Vol 5 (9) ◽  
Author(s):  
Julio Villena ◽  
Yuki Masumizu ◽  
Hikaru Iida ◽  
Wakako Ikeda-Ohtsubo ◽  
Leonardo Albarracin ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Lactobacillus Jensenii ◽  
Immunomodulatory Properties ◽  
Genome Information ◽  
Insight Into ◽  
Gaining Insight

ABSTRACT The genome of the immunomodulatory strain Lactobacillus jensenii TL2937 is described here. The draft genome has a total length of 1,678,416 bp, a G+C content of 34.3%, and 1,470 predicted protein-coding sequences. The genome information will be useful for gaining insight into the immunomodulatory properties of the TL2937 strain in the porcine host.

scholarly journals Whole-Genome Sequence of Lactobacillus sakei LT-13 Isolated from Moto Starter of Sake

2017 ◽  
Vol 5 (31) ◽  
Author(s):  
Shiro Kato ◽  
Tadao Oikawa
Keyword(s):  
Lactic Acid ◽  
Genome Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Lactobacillus Sakei ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Content Type ◽  
Putative Protein ◽  
Protein Coding Genes

ABSTRACT Lactobacillus sakei strain LT-13 is a lactic acid bacterium isolated from moto starter of Japanese sake. This genome analysis revealed that the genome is composed of a circular chromosome and one plasmid, which contain 1,938 and 8 putative protein-coding genes, respectively.

scholarly journals Complete Genome Sequence of Gelria sp. Strain Kuro-4, a Thermophilic Anaerobe Isolated from a Thermophilic Anaerobic Digestion Reactor Treating Poly( L -Lactic Acid)

2021 ◽  
Vol 10 (33) ◽  
Author(s):  
Takeshi Yamada ◽  
Masako Hamada ◽  
Misaki Kurobe ◽  
Takashi Narihiro ◽  
Hideto Tsuji ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Anaerobic Digestion ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Thermophilic Anaerobic Digestion ◽  
Circular Genome

Strain Kuro-4 was isolated as a novel member of the genus Gelria from a thermophilic anaerobic digestion reactor treating poly( l -lactic acid). Here, we report a 2,880,462-bp complete circular genome sequence of Kuro-4, with a G+C content of 61.9%. The chromosome harbors 2,831 protein-coding genes and 62 RNA-coding genes.

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