scholarly journals CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers

2019 ◽  
Author(s):  
Christine Pourcel ◽  
Marie Touchon ◽  
Nicolas Villeriot ◽  
Jean-Philippe Vernadet ◽  
David Couvin ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Adaptive Immunity ◽  
Complete Genome ◽  
Repeated Sequences ◽  
Whole Genome ◽  
Genome Sequences ◽  
Blast Search ◽  
Cas Genes ◽  
Genome Assemblies ◽  
Taxonomic Order

Abstract In Archaea and Bacteria, the arrays called CRISPRs for ‘clustered regularly interspaced short palindromic repeats’ and the CRISPR associated genes or cas provide adaptive immunity against viruses, plasmids and transposable elements. Short sequences called spacers, corresponding to fragments of invading DNA, are stored in-between repeated sequences. The CRISPR–Cas systems target sequences homologous to spacers leading to their degradation. To facilitate investigations of CRISPRs, we developed 12 years ago a website holding the CRISPRdb. We now propose CRISPRCasdb, a completely new version giving access to both CRISPRs and cas genes. We used CRISPRCasFinder, a program that identifies CRISPR arrays and cas genes and determine the system's type and subtype, to process public whole genome assemblies. Strains are displayed either in an alphabetic list or in taxonomic order. The database is part of the CRISPR-Cas++ website which also offers the possibility to analyse submitted sequences and to download programs. A BLAST search against lists of repeats and spacers extracted from the database is proposed. To date, 16 990 complete prokaryote genomes (16 650 bacteria from 2973 species and 340 archaea from 300 species) are included. CRISPR–Cas systems were found in 36% of Bacteria and 75% of Archaea strains. CRISPRCasdb is freely accessible at https://crisprcas.i2bc.paris-saclay.fr/.

scholarly journals Comparison of Whole-Genome Sequences from Two Colony Morphovars of Burkholderia pseudomallei

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Pei-Tan Hsueh ◽  
Yao-Shen Chen ◽  
Hsi-Hsu Lin ◽  
Pei-Ju Liu ◽  
Wen-Fan Ni ◽  
...  
Keyword(s):  
Burkholderia Pseudomallei ◽  
Repeated Sequences ◽  
Whole Genome ◽  
Genome Sequences ◽  
Single Base

The entire genomes of two isogenic morphovars (vgh16W and vgh16R) of Burkholderia pseudomallei were sequenced. A comparison of the sequences from both strains indicates that they show 99.99% identity, are composed of 22 tandem repeated sequences with <100 bp of indels, and have 199 single-base variants.

scholarly journals Complete Genome Sequences of Campylobacter hyointestinalis subsp. hyointestinalis Strain LMG 9260 and C. hyointestinalis subsp. lawsonii Strain LMG 15993

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
William G. Miller ◽  
Emma Yee ◽  
Mary H. Chapman
Keyword(s):  
Complete Genome ◽  
Whole Genome ◽  
Genome Sequences

Campylobacter hyointestinalis is isolated primarily from ruminants and swine, but is also occasionally isolated from humans. C. hyointestinalis is currently divided into two subspecies, C. hyointestinalis subsp. hyointestinalis and C. hyointestinalis subsp. lawsonii . This study describes the first closed whole-genome sequences of C. hyointestinalis subsp. hyointestinalis isolate LMG 9260 and C. hyointestinalis subsp. lawsonii isolate LMG 15993.

scholarly journals Whole-Genome Sequences of Three Plant Growth-Promoting Rhizobacteria Isolated from Solanum tuberosum L. Rhizosphere in Tanzania

2020 ◽  
Vol 9 (20) ◽  
Author(s):  
Becky N. Aloo ◽  
Ernest R. Mbega ◽  
Billy A. Makumba ◽  
Ines Friedrich ◽  
Robert Hertel ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Plant Growth ◽  
Complete Genome ◽  
Solanum Tuberosum L ◽  
Plant Growth Promoting Rhizobacteria ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Plant Growth Promoting ◽  
Growth Promoting

We present here the complete genome sequences of plant growth-promoting Klebsiella sp. strain MPUS7, Serratia sp. strain NGAS9, and Citrobacter sp. strain LUTT5, isolated from rhizosphere soils and tubers of potato (Solanum tuberosum L.) plants growing in the northern and southern highlands of Tanzania.

scholarly journals Complete Genome Sequences of Two Marine Biofilm Isolates, Leisingera sp. nov. Strains 201A and 204H, Novel Representatives of the Roseobacter Group

2020 ◽  
Vol 9 (28) ◽  
Author(s):  
Giselle S. Cavalcanti ◽  
Jessica Wasserscheid ◽  
Ken Dewar ◽  
Nicholas J. Shikuma
Keyword(s):  
New Species ◽  
Complete Genome ◽  
Genome Sequences ◽  
Marine Biofilm ◽  
Roseobacter Group ◽  
Genome Assemblies ◽  
One New Species

ABSTRACT Here, we report the complete-genome assemblies of biofilm isolates 201A and 204H. They possess six and seven plasmids, respectively, with a size ranging from 44 kb to 159 kb. Genomic comparisons place the two strains into one new species belonging to the genus Leisingera as novel representatives of the Roseobacter group.

scholarly journals Whole-Genome Sequences of Two Closely Related Bacteria, Actinomyces sp. Strain Chiba101 and Actinomyces denticolens DSM 20671T

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Yu Kanesaki ◽  
Taichiro Ishige ◽  
Yuriko Sekigawa ◽  
Tomoko Kobayashi ◽  
Yasushi Torii ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type

ABSTRACT Actinomyces sp. strain Chiba101, isolated from an arthritic leg joint of a pig raised in Japan, is a bacterium closely related to Actinomyces denticolens. Here, we deciphered the complete genome sequence of Actinomyces sp. Chiba101 and the high-quality draft genome sequence of A. denticolens DSM 20671T.

scholarly journals Whole-genome analysis reveals the complex evolutionary dynamics of Kenyan G2P[4] human rotavirus strains

2011 ◽  
Vol 92 (9) ◽  
pp. 2201-2208 ◽  
Author(s):  
Souvik Ghosh ◽  
Noriaki Adachi ◽  
Zipporah Gatheru ◽  
James Nyangao ◽  
Dai Yamamoto ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Human Rotavirus ◽  
Genotype Constellation ◽  
Common Causes

Although G2P[4] rotaviruses are common causes of acute childhood diarrhoea in Africa, to date there are no reports on whole genomic analysis of African G2P[4] strains. In this study, the nearly complete genome sequences of two Kenyan G2P[4] strains, AK26 and D205, detected in 1982 and 1989, respectively, were analysed. Strain D205 exhibited a DS-1-like genotype constellation, whilst strain AK26 appeared to be an intergenogroup reassortant with a Wa-like NSP2 genotype on the DS-1-like genotype constellation. The VP2-4, VP6-7, NSP1, NSP3 and NSP5 genes of strain AK26 and the VP2, VP4, VP7 and NSP1–5 genes of strain D205 were closely related to those of the prototype or other human G2P[4] strains. In contrast, their remaining genes were distantly related, and, except for NSP2 of AK26, appeared to originate from or share a common origin with rotavirus genes of artiodactyl (ruminant and camelid) origin. These observations highlight the complex evolutionary dynamics of African G2P[4] rotaviruses.

scholarly journals The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Ilnam Kang ◽  
Suhyun Kim ◽  
Md. Rashedul Islam ◽  
Jang-Cheon Cho
Keyword(s):  
Metabolic Pathways ◽  
Complete Genome ◽  
Whole Genome Amplification ◽  
Whole Genome ◽  
Bacterial Group ◽  
Freshwater Lakes ◽  
Genome Sequences ◽  
Genome Amplification ◽  
Axenic Cultures ◽  
Niche Diversification

Abstract The acI lineage of the phylum Actinobacteria is the most abundant bacterial group in most freshwater lakes. However, due to difficulties in laboratory cultivation, only two mixed cultures and some incomplete single-amplified or metagenome-derived genomes have been reported for the lineage. Here, we report the initial cultivation and complete genome sequences of four novel strains of the acI lineage from the tribes acI-A1, -A4, -A7, and -C1. The acI strains, initially isolated by dilution-to-extinction culturing, eventually failed to be maintained as axenic cultures. However, the first complete genomes of the acI lineage were successfully obtained from these initial cultures through whole genome amplification applied to more than hundreds of cultured acI cells. The genome sequences exhibited features of genome streamlining and showed that the strains are aerobic chemoheterotrophs sharing central metabolic pathways, with some differences among tribes that may underlie niche diversification within the acI lineage. Actinorhodopsin was found in all strains, but retinal biosynthesis was complete in only A1 and A4 tribes.

scholarly journals Eight Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. caucasica Isolated from the Common Vole (Microtus arvalis) Plague Focus in Dagestan, Russia

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Angelina A. Kislichkina ◽  
Aleksandr G. Bogun ◽  
Lidiya A. Kadnikova ◽  
Nadezhda V. Maiskaya ◽  
Viktor I. Solomentsev ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Draft Genome ◽  
Common Vole ◽  
Whole Genome ◽  
Microtus Arvalis ◽  
Genome Sequences ◽  
Content Type ◽  
The Common ◽  
Common Voles ◽  
Genome Assemblies

ABSTRACT We here report the draft genome sequences of 8 Yersinia pestis subsp. microtus bv. caucasica strains isolated from the East Caucasian (previous name, Dagestan) mountain focus (no. 39), representing the most ancient branch of the 0.PE2 phylogroup circulating in populations of common voles (Microtus arvalis).

scholarly journals Whole-Genome Assemblies for Two Yersinia pestis Strains Isolated in Mongolia

2020 ◽  
Vol 9 (41) ◽  
Author(s):  
Muzi Jin ◽  
B. Byambajav ◽  
Hongyuan Zheng ◽  
Yufei Chen ◽  
B. Natsagdorj ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Genome Assemblies

ABSTRACT Here, we report the draft genome sequences of two Yersinia pestis bv. Antiqua strains, belonging to the 3.ANT phylogroup, that were isolated in Mongolia and were circulating in marmot populations.

scholarly journals Complete Genome Sequences of Two Interactive Moderate Thermophiles,Paenibacillus napthalenovorans32O-Y andPaenibacillussp. 32O-W

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Robert R. Butler ◽  
Jia Wang ◽  
Benjamin C. Stark ◽  
Jean-François Pombert
Keyword(s):  
High Temperature ◽  
Complete Genome ◽  
Industrial Applications ◽  
Whole Genome ◽  
Genome Sequences ◽  
High Demand ◽  
Moderate Thermophiles

Microorganisms with the capability to desulfurize petroleum are in high demand with escalating restrictions currently placed on fuel purity. Thermophilic desulfurizers are particularly valuable in high-temperature industrial applications. We report the whole-genome sequences ofPaenibacillus napthalenovorans32O-Y andPaenibacillussp. 32O-W, which can and cannot, respectively, metabolize dibenzothiophene.

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