scholarly journals Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter

2021 ◽  
Vol 9 (6) ◽  
pp. 1332
Author(s):  
Irene Artuso ◽  
Paolo Turrini ◽  
Mattia Pirolo ◽  
Gabriele Andrea Lugli ◽  
Marco Ventura ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genetic Basis ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Species Level ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Methyl Halides ◽  
Terrestrial Environments

Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all Aminobacter species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462T contains a symbiosis island implicated in nodulation and nitrogen fixation.

scholarly journals Metabolic Diversity within the Globally Abundant Marine Group IIEuryarchaeaOffers Insight into Ecological Patterns

2018 ◽  
Author(s):  
Benjamin J Tully
Keyword(s):  
Organic Matter ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Diversity ◽  
Metabolic Potential ◽  
Surface Ocean ◽  
Ecological Patterns ◽  
Reference Genomes ◽  
Insight Into

AbstractDespite their discovery over 25 years ago, the Marine Group IIEuryarchaea(MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present the comparative genomic analysis of 250 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins common in all other subclades. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.

scholarly journals Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Liangzhi Li ◽  
Zhenghua Liu ◽  
Min Zhang ◽  
Delong Meng ◽  
Xueduan Liu ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Evolutionary History ◽  
Mine Drainage ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Ecological Functions ◽  
History Of

ABSTRACT Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium. In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium. Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions. IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.

scholarly journals Eutherian comparative genomic analysis protocol

2020 ◽  
Author(s):  
Marko Premzl
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Third Party ◽  
Comparative Genomic ◽  
Data Sets ◽  
Gene Data ◽  
Sequence Errors ◽  
Analysis Protocol

Abstract The eutherian genomics momentum greatly advanced biology and medicine. Nevertheless, future revisions and updates of eutherian genomic sequence data sets were expected, due to potential genomic sequence errors and incompleteness of genomic sequences. The eutherian comparative genomic analysis protocol was established as guidance in protection against potential genomic sequence errors in public eutherian genomic sequence assemblies. The protocol revised, updated and published 12 major eutherian gene data sets, including 1853 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670, LT962964-LT963174 and LT990249-LT990597.

scholarly journals Candidate pathogenicity islands in the genome of ‘CandidatusRickettsiella isopodorum’, an intracellular bacterium infecting terrestrial isopod crustaceans

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2806 ◽  
Author(s):  
YaDong Wang ◽  
Christopher Chandler
Keyword(s):  
Genomic Island ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Photorhabdus Luminescens ◽  
Future Studies ◽  
Terrestrial Isopod ◽  
Microbe Interactions ◽  
Host Microbe Interactions

The bacterial genusRickettsiellabelongs to the order Legionellales in the Gammaproteobacteria, and consists of several described species and pathotypes, most of which are considered to be intracellular pathogens infecting arthropods. Two members of this genus,R. grylliandR. isopodorum, are known to infect terrestrial isopod crustaceans. In this study, we assembled a draft genomic sequence forR. isopodorum, and performed a comparative genomic analysis withR. grylli. We found evidence for several candidate genomic island regions inR. isopodorum, none of which appear in the previously availableR. grylligenome sequence.Furthermore, one of these genomic island candidates inR. isopodorumcontained a gene that encodes a cytotoxin partially homologous to those found inPhotorhabdus luminescensandXenorhabdus nematophilus(Enterobacteriaceae), suggesting that horizontal gene transfer may have played a role in the evolution of pathogenicity inRickettsiella. These results lay the groundwork for future studies on the mechanisms underlying pathogenesis inR. isopodorum, and this system may provide a good model for studying the evolution of host-microbe interactions in nature.

scholarly journals Eutherian comparative genomic analysis protocol

2019 ◽  
Author(s):  
Marko Premzl
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Third Party ◽  
Comparative Genomic ◽  
Data Sets ◽  
Gene Data ◽  
Sequence Errors ◽  
Analysis Protocol

Abstract The eutherian genomics momentum greatly advanced biology and medicine. Nevertheless, future revisions and updates of eutherian genomic sequence data sets were expected, due to potential genomic sequence errors and incompleteness of genomic sequences. The eutherian comparative genomic analysis protocol was established as guidance in protection against potential genomic sequence errors in public eutherian genomic sequence assemblies. The protocol revised, updated and published 11 major eutherian gene data sets, including 1504 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670 and LT962964-LT963174.

scholarly journals Eutherian comparative genomic analysis protocol

2021 ◽  
Author(s):  
Marko Premzl
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Third Party ◽  
Comparative Genomic ◽  
Data Sets ◽  
Gene Data ◽  
Sequence Errors ◽  
Analysis Protocol

Abstract The eutherian genomics momentum greatly advanced biological and medical sciences. Yet, future revisions and updates of eutherian genomic sequence data sets were expected, due to potential genomic sequence errors and incompleteness of genomic sequences. The eutherian comparative genomic analysis protocol was established as guidance in protection against potential genomic sequence errors in public eutherian genomic sequence assemblies. The protocol revised, updated and published 14 major eutherian gene data sets, including 2615 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670, LT962964-LT963174, LT990249-LT990597, LR130242-LR130508 and LR760818-LR761312.

scholarly journals Comparative genomic analysis revealed rapid differentiation in the pathogenicity-related gene repertoires betweenPyricularia oryzaeandPyricularia pennisetiisolated from aPennisetumgrass

2018 ◽  
Author(s):  
Huakun Zheng ◽  
Zhenhui Zhong ◽  
Mingyue Shi ◽  
Limei Zhang ◽  
Lianyu Lin ◽  
...  
Keyword(s):  
Genetic Study ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Blast Disease ◽  
Individual Species ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Avirulence Genes ◽  
Related Gene

AbstractBackgroundsPyriculariais a multispecies complex that could infect and cause severe blast disease on diverse hosts, including rice, wheat and many other grasses. Although the genome size of this fungal complex is small [~40 Mbp forPyricularia oryzae(syn.Magnaporthe oryzae), and ~45 Mbp forP. grisea], the genome plasticity allows the fungus to jump and adapt to new hosts. Therefore, deciphering the genome basis of individual species could facilitate the evolutionary and genetic study of this fungus. However, except for theP. oryzaesubgroup, many other species isolated from diverse hosts, such as thePennisetumgrasses, remain largely uncovered genetically.ResultsHere, we report the genome sequence of a pyriform-shaped fungal strainP. pennisetiP1609 isolated from aPennisetumgrass (JUJUNCAO) using PacBio SMRT sequencing technology. We performed a phylogenomic analysis of 28 Magnaporthales species and 5 non-Magnaporthales species and addressed P1609 into aPyriculariasubclade that is distant fromP. oryzae. Comparative genomic analysis revealed that the pathogenicity-related gene repertoires were fairly different between P1609 and theP. oryzaestrain 70-15, including the cloned avirulence genes, other putative secreted proteins, as well as some other predictedPathogen-Host Interaction(PHI) genes. Genomic sequence comparison also identified many genomic rearrangements.ConclusionTaken together, our results suggested that the genomic sequence of theP. pennisetiP1609 could be a useful resource for the genetic study of thePennisetum-infectingPyriculariaspecies.

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