scholarly journals 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

2017 ◽  
Vol 35 (7) ◽  
pp. 676-683 ◽  
Author(s):  
Supratim Mukherjee ◽  
Rekha Seshadri ◽  
Neha J Varghese ◽  
Emiley A Eloe-Fadrosh ◽  
Jan P Meier-Kolthoff ◽  
...  
Keyword(s):  
Chemical Structure ◽  
Phylogenetic Diversity ◽  
Scientific Discovery ◽  
Valuable Resource ◽  
Sequence Coverage ◽  
Functional Interpretation ◽  
Type Strains ◽  
Reference Genomes ◽  
Genomic Encyclopedia ◽  
Novel Protein

Abstract We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

scholarly journals A comparative genomics multitool for scientific discovery and conservation

Nature ◽  
2020 ◽  
Vol 587 (7833) ◽  
pp. 240-245 ◽  
Author(s):  
Keyword(s):  
Phylogenetic Diversity ◽  
Scientific Discovery ◽  
Genome Alignment ◽  
Evolutionary Selection ◽  
Risk Of Extinction ◽  
Biological Discovery ◽  
Whole Genome Alignment ◽  
Genome Assemblies ◽  
Reference Genomes ◽  
Conservation Of Biodiversity

AbstractThe Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

The Chemical Structure Association Trust

2016 ◽  
Vol 38 (2) ◽  
Author(s):  
Bonnie Lawlor
Keyword(s):  
Chemical Structure ◽  
Scientific Discovery ◽  
Research Work ◽  
50Th Anniversary ◽  
The United States ◽  
Chemical Information ◽  
Structure Information ◽  
Chemical Structures ◽  
Grant Program ◽  
Structure Association

AbstractThe Chemical Structure Association Trust (CSA Trust) is an internationally-recognized, registered charity that promotes and supports the advancement of scientific discovery through the application of computer technologies in the management and analysis of chemical structure information. In support of its Charter, the Trust provides grants specifically to nurture young scientists, ages thirty-five or younger, who have demonstrated excellence in research related to the storage, retrieval, and analysis of chemical structures, reactions, and compounds. Since its inception in 1988, almost one hundred students and researchers worldwide have benefited from travel bursaries and the CSA Trust Grant Program to further their education and research work, but the organization has a rich history that predates the formalization of its charity status. Its roots were planted half a century ago in 1965, when the Chemical Notation Association (CNA) was formed in the United States. It has been an interesting journey from the CNA to the CSA Trust and I have been blessed to have been a part of it almost from the beginning, along with other members of the American Chemical Society’s Division of Chemical Information. In honor of the organization’s 50th Anniversary, I’d like to give a brief overview of its past and its present activities.

scholarly journals Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

2013 ◽  
Vol 9 (3) ◽  
pp. 1278-1284 ◽  
Author(s):  
Nikos C. Kyrpides ◽  
Tanja Woyke ◽  
Jonathan A. Eisen ◽  
George Garrity ◽  
Timothy G. Lilburn ◽  
...  
Keyword(s):  
Phase I ◽  
Microbial Genomes ◽  
The One ◽  
Type Strains ◽  
Genomic Encyclopedia

scholarly journals Phylogenetic diversity of bacteria in rock salt of the Verkhnekamskoe deposit (Perm Krai)

2021 ◽  
pp. 256-262
Author(s):  
Anna A. Pyankova ◽  
◽  
Yulia A. Beloglazova ◽  
Ekaterina S. Korsakova ◽  
Boris A. Bachurin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Rock Salt ◽  
Phylogenetic Diversity ◽  
Molecular Genetic ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sample Depth ◽  
Perm Krai ◽  
Total Dna ◽  
Type Strains

New data on the phylogenetic diversity of bacteria in the salt of the Verkhnekamskoe deposit (Perm Krai) have been obtained using molecular genetic methods. Analysis of the 16S rRNA genes of total DNA from the rock salt sample (depth intervals of 239.7-239 m) evinces the presence of bacteria belonging to the classes: Actinobacteria (closely related to the genera Rhodococcus, Demequina), Gammaproteobacteria (the genera Pseudomonas, Serratia, Shigella), Betaproteobacteria (the genus Ralstonia) and Alphaproteobacteria (the genus Phyllobacterium). In addition, we identified two phylotypes of the Alphaproteobacteria (clone 66BA (GenBank MH410136) and clone 12BA (GenBank MH410128) that show lower similarity in 16S rRNA genes (98.46%) with the closest type strains of the genus Mesorhizobium (M. alhagi CCNWXJ12-2T) and the genus Chelativorans (C. multitrophicus DSM9103T). The identified phylotypes may represent new taxonomic units.

scholarly journals Diversity of Carotenoid Synthesis Gene Clusters from Environmental Enterobacteriaceae Strains

2005 ◽  
Vol 71 (12) ◽  
pp. 8141-8146 ◽  
Author(s):  
Natalia Sedkova ◽  
Luan Tao ◽  
Pierre E. Rouvière ◽  
Qiong Cheng
Keyword(s):  
Escherichia Coli ◽  
Gene Cluster ◽  
Environmental Samples ◽  
Phylogenetic Diversity ◽  
Gene Clusters ◽  
Type Ii ◽  
Carotenoid Synthesis ◽  
Derivatives Of ◽  
Type Strains ◽  
Biochemical Diversity

ABSTRACT Eight Enterobacteriaceae strains that produce zeaxanthin and derivatives of this compound were isolated from a variety of environmental samples. Phylogenetic analysis showed that these strains grouped with different clusters of Erwinia type strains. Four strains representing the phylogenetic diversity were chosen for further characterization, which revealed their genetic diversity as well as their biochemical diversity. The carotenoid synthesis gene clusters cloned from the four strains had three different gene organizations. Two of the gene clusters, those from strains DC416 and DC260, had the classical organization crtEXYIBZ; the gene cluster from DC413 had the rare organization crtE-idi-XYIBZ; and the gene cluster from DC404 had the unique organization crtE-idi-YIBZ. Besides the diversity in genetic organization, these genes also exhibited considerable sequence diversity. On average, they exhibited 60 to 70% identity with each other, as well as with the corresponding genes of the Pantoea type strains. The four different clusters were individually expressed in Escherichia coli, and the two idi-containing clusters gave more than fivefold-higher carotenoid titers than the two clusters lacking idi. Expression of the crtEYIB genes with and without idi confirmed the effect of increasing carotenoid titer by the type II idi gene linked with the carotenoid synthesis gene clusters.

scholarly journals Neuromaps: structural and functional interpretation of brain maps

2022 ◽  
Author(s):  
Ross D Markello ◽  
Justine Y Hansen ◽  
Zhen-Qi Liu ◽  
Vincent Bazinet ◽  
Golia Shafiei ◽  
...  
Keyword(s):  
Open Access ◽  
Human Brain ◽  
Software Package ◽  
Scientific Discovery ◽  
Enrichment Analysis ◽  
Coordinate Systems ◽  
Functional Interpretation ◽  
Biological Ontologies ◽  
Brain Maps ◽  
Brain Structure And Function

Imaging technologies are increasingly used to generate high-resolution reference maps of brain structure and function. Modern scientific discovery relies on making comparisons between new maps (e.g. task activations, group structural differences) and these reference maps. Although recent data sharing initiatives have increased the accessibility of such brain maps, data are often shared in disparate coordinate systems (or ``spaces''), precluding systematic and accurate comparisons among them. Here we introduce the neuromaps toolbox, an open-access software package for accessing, transforming, and analyzing structural and functional brain annotations. We implement two registration frameworks to generate high-quality transformations between four standard coordinate systems commonly used in neuroimaging research. The initial release of the toolbox features >40 curated reference maps and biological ontologies of the human brain, including maps of gene expression, neurotransmitter receptors, metabolism, neurophysiological oscillations, developmental and evolutionary expansion, functional hierarchy, individual functional variability, and cognitive specialization. Robust quantitative assessment of map-to-map similarity is enabled via a suite of spatial autocorrelation-preserving null models. By combining open-access data with transparent functionality for standardizing and comparing brain maps, the neuromaps software package provides a systematic workflow for comprehensive structural and functional annotation enrichment analysis of the human brain.

scholarly journals The Diversity of Cyanobacterial Toxins on Structural Characterization, Distribution and Identification: A Systematic Review

Toxins ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 530 ◽  
Author(s):  
Xingde Du ◽  
Haohao Liu ◽  
Le Yuan ◽  
Yueqin Wang ◽  
Ya Ma ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Cyclic Peptides ◽  
Chemical Structure ◽  
Developed Countries ◽  
Valuable Resource ◽  
Comprehensive Review ◽  
Widespread Distribution ◽  
Detection And Identification ◽  
Detection Technology ◽  
Identification Techniques

The widespread distribution of cyanobacteria in the aquatic environment is increasing the risk of water pollution caused by cyanotoxins, which poses a serious threat to human health. However, the structural characterization, distribution and identification techniques of cyanotoxins have not been comprehensively reviewed in previous studies. This paper aims to elaborate the existing information systematically on the diversity of cyanotoxins to identify valuable research avenues. According to the chemical structure, cyanotoxins are mainly classified into cyclic peptides, alkaloids, lipopeptides, nonprotein amino acids and lipoglycans. In terms of global distribution, the amount of cyanotoxins are unbalanced in different areas. The diversity of cyanotoxins is more obviously found in many developed countries than that in undeveloped countries. Moreover, the threat of cyanotoxins has promoted the development of identification and detection technology. Many emerging methods have been developed to detect cyanotoxins in the environment. This communication provides a comprehensive review of the diversity of cyanotoxins, and the detection and identification technology was discussed. This detailed information will be a valuable resource for identifying the various types of cyanotoxins which threaten the environment of different areas. The ability to accurately identify specific cyanotoxins is an obvious and essential aspect of cyanobacterial research.

scholarly journals Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

PLoS Biology ◽  
2014 ◽  
Vol 12 (8) ◽  
pp. e1001920 ◽  
Author(s):  
Nikos C. Kyrpides ◽  
Philip Hugenholtz ◽  
Jonathan A. Eisen ◽  
Tanja Woyke ◽  
Markus Göker ◽  
...  
Keyword(s):  
Type Strains ◽  
Genomic Encyclopedia
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