Top PDF Complete genome sequence of Brachyspira murdochii type strain (56-150T)

Complete genome sequence of Brachyspira murdochii type strain (56-150T)

Complete genome sequence of Brachyspira murdochii type strain (56-150T)

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All gen- eral aspects of library construction and sequenc- ing performed can be found at the JGI website sequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 3,554 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and adjust inflated q- scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Perfor- mance Software, LLC). Possible misassemblies were corrected with Dupfinisher or transposon bombing of bridging clones [42]. A total of 300 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The error rate of the completed genome sequence is less than 1 in
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Complete genome sequence of Arcobacter nitrofigilis type strain (CIT)

Complete genome sequence of Arcobacter nitrofigilis type strain (CIT)

species do not [3]. The metabolism of A. nitrofigilis is chemoorganotrophic; organic acids and amino acids are used as carbon sources but carbohy- drates are neither oxidized nor fermented [2]. All strains of the species are halotolerant. They re- quire a minimum of 0.5% NaCl for growth and can tolerate up to 7% NaCl [28]. A. nitrofigilis is sus- ceptible to cephalothin and nalidixic acid but isre- sistant to vancomycin [3]. The G+C content of the DNA was determined by thermal denaturation to be 28.0% [3] which is slightly below the 28.4% found in the genome.

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Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T)

Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T)

Denitrovibrio acetiphilus Myhr and Torsvik 2000 is the type species of the genus Denitrovi- brio in the bacterial family Deferribacteraceae. It is of phylogenetic interest because there are only six genera described in the family Deferribacteraceae. D. acetiphilus was isolated as a representative of a population reducing nitrate to ammonia in a laboratory column simulating the conditions in off-shore oil recovery fields. When nitrate was added to this column unde- sirable hydrogen sulfide production was stopped because the sulfate reducing populations were superseded by these nitrate reducing bacteria. Here we describe the features of this ma- rine, mesophilic, obligately anaerobic organism respiring by nitrate reduction, together with the complete genome sequence, and annotation. This is the second complete genome se- quence of the order Deferribacterales and the class Deferribacteres, which is the sole class in the phylum Deferribacteres. The 3,222,077 bp genome with its 3,034 protein-coding and 51 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)

Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)

various secondary transporters belonging to the sodium:solute symporter family (Tagg_0251, Tagg_0258), the sodium:neurotransmitter sym- porter family (Tagg_0418) and the so- dium:dicarboxylate symporter family (Tagg_0524). The sodium-motive force required for the uptake of small solutes is possibly generated by sodium ion- proton antiporters (e.g., Tagg_0296), whereas no genes encoding any of the known sodium ion- translocating decarboxylases could be identified. Within the cell oligopeptides are degraded by sev- eral distinct peptidases, represented by Tagg_0523 (trypsin-like serine protease), Tagg_0073 (amino- peptidase), Tagg_1142 (Xaa-Pro aminopeptidase), Tagg_0908 (zinc-dependent peptidase), Tagg_0282 (thermophilic metallo-aminopeptidase), and Tagg_0456 (thermostable zinc-dependent carboxy- peptidase). On the other hand, glycosidases might be involved in the degradation of complex oligo- saccharides. Three different types of glycoside hy- drolases were identified, which belong to family 1 (Tagg_1110), family 4 (Tagg_1191) and family 57 (Tagg_0640). A beta-glycosidase represented by the gene locus Tagg_1110 has been already identi- fied before the here reported complete genome sequencing and was expressed in Escherichia coli as a recombinant protein. A crystal structure of this T. aggregans enzyme was determined in order to identify factors which could be responsible for its thermostability [36,37].
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Complete genome sequence of Conexibacter woesei type strain (ID131577T)

Complete genome sequence of Conexibacter woesei type strain (ID131577T)

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All gen- eral aspects of library construction and sequenc- ing can be found at Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 6,955 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q- scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Perfor- mance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher [28] or transpo- son bombing of bridging clones (Epicentre Bio- technologies, Madison, WI). Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 1,608 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The error rate of the
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Complete genome sequence of Spirosoma linguale type strain (1T)

Complete genome sequence of Spirosoma linguale type strain (1T)

Large Newbler contigs were broken into 9,401 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q- scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Perfor- mance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher [29] or transpo- son bombing of bridging clones (Epicentre Bio- technologies, Madison, WI). Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 974 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. Illumina reads were used to improve the final consensus quality using an in- house developed tool (the Polisher). The error rate of the completed genome sequence is less than 1 in 100,000. Together all sequence types provided 28.5× coverage of the genome. The final assembly contains 87,186 Sanger and 666,973 pyrosequence reads.
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Complete genome sequence of Acidaminococcus fermentans type strain (VR4T)

Complete genome sequence of Acidaminococcus fermentans type strain (VR4T)

Genes were identified using Prodigal [36] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [37]. The predicted CDSs were translated and used to search the National Center for Biotechnology In- formation (NCBI) nonredundant database, Uni- Prot, TIGRFam, Pfam, PRIAM, KEGG, COG, and In- terPro databases. Additional gene prediction anal- ysis and manual functional annotation was per- formed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform [38].

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Complete genome sequence of Meiothermus ruber type strain (21T)

Complete genome sequence of Meiothermus ruber type strain (21T)

Eastern China [10], Northern Taiwan [11] and Iceland [12]. Interestingly, the genus Meiothermus is heterogeneous with respect to pigmentation. The yellow pigmented species also form a distinct group on the basis of the 16S rRNA gene sequence similarity, with the red/orange pigmented strains forming two groups, one comprising M. silvanus and the other the remaining species [9,10]. Like all members of the Deinococci the lipid composition of the cell membrane of members of the genus Meiothermus is based on unusual and characteris- tic structures. Here we present a summary classi- fication and a set of features for M. ruber 21 T , to-
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Complete genome sequence of Cellulomonas flavigena type strain (134T)

Complete genome sequence of Cellulomonas flavigena type strain (134T)

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All gen- eral aspects of library construction and sequenc- ing can be found at th ing reads were assembled using the Newbler as- sembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 4,499 overlapping frag- ments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quali- ty scores based on Newbler consensus q-scores with modifications to account for overlap redun- dancy and adjust inflated q-scores. A hybrid 454/Sanger assembly was made using PGA as- sembler. Possible mis-assemblies were corrected and gaps between contigs were closed by primer walks off Sanger clones and bridging PCR frag- ments and by editing in Consed. A total of 704 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. 12,171,379 Illu- mina reads were used to improve the final con- sensus quality using an in-house developed tool (the Polisher [41]). The error rate of the com- pleted genome sequence is less than 1 in 100,000.
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Complete genome sequence of Archaeoglobus profundus type strain (AV18T)

Complete genome sequence of Archaeoglobus profundus type strain (AV18T)

A widespread phenomenon among Archaea and Bacteria is their ability to sense environmental conditions by the chemotaxis system and actively move towards more favorable locations by the activity of the flagellum. The archaeal flagella are non-homologous to those of Bacteria , and their components are encoded by one or two well- conserved gene clusters ( fla clusters) [85], which have been subject to extensive phylogenetic stu- dies [86]. A. profundus is reported to be non- motile [1,43], showing no flagellation, in contrast to most Archaeoglobi , including A. fulgidus [3] and F. placidus [4]. Unexpectedly, the genome se- quence revealed the presence of a complete fla gene cluster (Arcpr_1384 – Arcpr_1391) and the preflagellin peptidase FlaK gene (Arcpr_0277), [85]. The situation in A. fulgidus (AF_1048– AF_1055, flaK -gene: AF_0936) and F. placidus (Ferp_1456–Ferp_1463, flaK -gene: Ferp_0061) is virtually identical in content, order and orienta- tion of genes of the fla cluster, therefore the dif- ferent phenotypes are unexpected. However, a conflict between presence of the flagella genes and the phenotypically observed lack of motility is not unique for A. profundus , but has also been re- ported for Methanosarcina species [86]. Also the reverse, even more surprising case – observed motility, but lacking homologues of the genes cod- ing for flagellum components – has been reported for Pyrobaculum aerophilum and M. kandleri [86]. Some of our electron micrograph images (data not shown) displayed structures which might be fla- gella on few A. profundus cells, mainly observed in larger cell clots. This indicates that A. profundus might be flagellated under certain conditions, not necessarily for motility reasons, but also functions such as cell-cell adhesion to form cell aggregates (as reported for Methanosarcinales ) are thinkable.
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Complete genome sequence of Thermobispora bispora type strain (R51T)

Complete genome sequence of Thermobispora bispora type strain (R51T)

somal protein AT-L30 [8], Microbispora bispora was subsequently removed from the genus Mi- crobispora to be the type species of the new ge- nus Thermobispora [1]. T. bispora is currently the only species in the genus Thermobispora [1]. In 1997 T. bispora gained interest, as it was de- scribed as the first organism to have two distinct (6.4% of total nucleotides) types of transcrip- tionally active 16S rRNA genes (GenBank acces- sions U83909 and U83912) [9]. Based on the two copies of the 16S rRNA genes that match best to sequence U83909 the closest related type strain (9% sequence difference [10]) is Micromonospo- ra pattaloongensis [11] of the family Micromo- nosporaceae ; based on the two copies of the 16S rRNA genes that match best to sequence U83912 the closest related type strain (8% sequence dif- ference [10]) is Planotetraspora silvatica [12] of the family Streptosporangiaceae . Neither fit to the taxonomic position as shown in the List of Proca- ryotic names with Standing in Nomenclature that shows the genus Thermobispora as a member of the family Pseudonocardiaceae , reflecting the current uncertainty of the taxonomic position of T. bispora [13]. In their recent review of Actino- bacteria taxonomy, Zhi et al. [14] suggested to
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Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T)

Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T)

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All gen- eral aspects of library construction and sequenc- ing can be found at Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 2,525 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q- scores. A hybrid 454/Sanger assembly was made using the phrap assembler. Possible mis- assemblies were corrected with Dupfinisher or transposon bombing of bridging clones [32]. Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 471 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The er- ror rate of the completed genome sequence is less
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Complete genome sequence of Tsukamurella paurometabola type strain (no. 33T)

Complete genome sequence of Tsukamurella paurometabola type strain (no. 33T)

Tsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of the genus Tsukamurella, which is the type genus to the family Tsukamurellaceae. The spe- cies is not only of interest because of its isolated phylogenetic location, but also because it is a human opportunistic pathogen with some strains of the species reported to cause lung in- fection, lethal meningitis, and necrotizing tenosynovitis. This is the first completed genome sequence of a member of the genus Tsukamurella and the first genome sequence of a mem- ber of the family Tsukamurellaceae. The 4,479,724 bp long genome contains a 99,806 bp long plasmid and a total of 4,335 protein-coding and 56 RNA genes, and is a part of the Ge- nomic Encyclopedia of Bacteria and Archaea project.
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Complete genome sequence of Treponema succinifaciens type strain (6091T)

Complete genome sequence of Treponema succinifaciens type strain (6091T)

13475) is the type strain of Treponema succinifa- ciens [1,2]. Currently, there are 25 species placed in the genus Treponema [3]. The species epithet is derived from the Latin noun acidum succinicum meaning succinic acid and the Latin verb facio meaning to make, produce , referring to the succin- ic acid-producing property of the species [1]. T. succinifaciens was isolated from the colon of swine, and first described as small spirochete by Harris et al. in 1972 [4]. In 1974 it was published that strain 6091 T belonged to a group of harmless

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Complete genome sequence of Haliscomenobacter hydrossis type strain (OT)

Complete genome sequence of Haliscomenobacter hydrossis type strain (OT)

Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Halisco- menobacter, which belongs to order "Sphingobacteriales". The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically un- charted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The ge- nome of H. hydrossis is the first completed genome sequence reported from a member of the family "Saprospiraceae". The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Complete genome sequence of Rhodospirillum rubrum type strain (S1T)

Complete genome sequence of Rhodospirillum rubrum type strain (S1T)

Rhodospirillaceae. The 16S rRNA accessions were selected from the most recent release of the All-Species-Living-Tree- Project [4] as far as possible. The tree was inferred from 1,361 aligned characters [5,6] of the 16S rRNA gene sequence under the maximum likelihood criterion [7]. Rooting was done initially using the midpoint method [8] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers to the right of bifurcations are support values from 550 bootstrap replicates [9] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [10] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks.
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Complete genome sequence of Bacteroides salanitronis type strain (BL78T)

Complete genome sequence of Bacteroides salanitronis type strain (BL78T)

bly and quality assessment in the subsequent fi- nishing process. After the shotgun stage, reads were assembled with parallel phrap (High Per- formance Software, LLC). Possible mis-assemblies were corrected with gapResolution [34], Dupfi- nisher [37], or sequencing cloned bridging PCR fragments with subcloning or transposon bomb- ing (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F.Chang, unpublished). A total of 193 additional reactions and four shatter libraries were neces- sary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase con- sensus quality using a software Polisher devel- oped at JGI [38]. The error rate of the completed genome sequence is less than 1 in 100,000. To- gether, the combination of the Illumina and 454 sequencing platforms provided 320.7 × coverage of the genome. The final assembly contained 393,135 pyrosequence and 25,576,764 Illumina reads.
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Complete genome sequence of Veillonella parvula type strain (Te3T)

Complete genome sequence of Veillonella parvula type strain (Te3T)

from porcine intestine (EU728725, Hojberg and Jensen, unpublished, 99.9% identity). The other type strains of the genus Veillonella vary from 94.1% ( V. ratti ) to 99.2% ( V. dispar ). A vast number of phylotypes with significant 16S rRNA sequence similarity to V. parvula were observed from intubated patients [9], carious dentine from advanced caries (AY995757; 99.7% identity), and the human skin microbiome [10]. Curiously, only one sample from a human gut metagenome analysis [11] scored above 96% sequence similarity in screenings of environmental samples (status September 2009).
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Complete genome sequence of Haloterrigena turkmenica type strain (4kT)

Complete genome sequence of Haloterrigena turkmenica type strain (4kT)

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All gen- eral aspects of library construction and sequenc- ing performed at the JGI can be found at the bled using the Newbler assembler version 1.1.03.24 (Roche). Large Newbler contigs were broken into 6,060 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifica- tions to account for overlap redundancy and ad- just inflated q-scores. A hybrid 454/Sanger as- sembly was made using the parallel phrap as- sembler (High Performance Software, LLC). Possi- ble misassemblies were corrected with Dupfinish- er or transposon bombing of bridging clones [35]. A total of 1,183 Sanger finishing reads were pro- duced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. Illumina reads were used to improve the final consensus quality using an in-house developed tool (the Polisher). The error rate of the com- pleted genome sequence is less than 1 in 100,000.
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Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T)

Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T)

Xylanimonas cellulosilytica Rivas et al. 2003 is the type species of the genus Xylanimonas of the actinobacterial family Promicromonosporaceae. The species X. cellulosilytica is of interest because of its ability to hydrolyze cellulose and xylan. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large family Promicromonosporaceae, and the 3,831,380 bp long genome (one chromosome plus an 88,604 bp long plasmid) with its 3485 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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