From ce7f0028a510d81686284d4937bed459ee3224d3 Mon Sep 17 00:00:00 2001 From: ggserver Date: Tue, 23 Jul 2024 20:08:19 +0000 Subject: [PATCH] Add updates up until 2024-07-23 20:03:11 --- .../32/2A4D325A0259FFC2FDF956F9C7FCFC8A.xml | 938 ++++++++++++++++++ 1 file changed, 938 insertions(+) create mode 100644 data/2A/4D/32/2A4D325A0259FFC2FDF956F9C7FCFC8A.xml diff --git a/data/2A/4D/32/2A4D325A0259FFC2FDF956F9C7FCFC8A.xml b/data/2A/4D/32/2A4D325A0259FFC2FDF956F9C7FCFC8A.xml new file mode 100644 index 00000000000..7a46b7306ce --- /dev/null +++ b/data/2A/4D/32/2A4D325A0259FFC2FDF956F9C7FCFC8A.xml @@ -0,0 +1,938 @@ + + + +Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China + + + +Author + +Teng, Chao +Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, + + + +Author + +Zhou, Zhengfu +Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, + + + +Author + +Molnár, István +Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States of America, + + + +Author + +Li, Xinna +Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, + + + +Author + +Tang, Ran +Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, + + + +Author + +Chen, Ming +Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, + + + +Author + +Wang, Lin +Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, & Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, P. R. China + + + +Author + +Su, Shiyou +Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, + + + +Author + +Zhang, Wei +Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, + + + +Author + +Lin, Min +Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, + +text + + +PLoS ONE + + +2015 + +e 0122254 + + +2015-04-01 + + +10 + + +4 + + +1 +16 + + + +journal article +10.1371/journal.pone.0122254 +1932-6203 +PMC4382152 +25830331 + + + + + + +S +. +deserti + +sp. nov. + + + +The cells of strain ZW +T +are Gram-negative, non-motile, non-spore-forming, strictly aerobic + + + + +rods, approximately 0.6–1.7 μm in length and 0.3–0.6 μm in diameter ( +Fig 1 +). After 48 h of incubation on TGY, ZW +T +colonies were +3–5 mm +in diameter, lemon yellow, convex, circular, + +smooth and entire. The optimum growth temperature is 30°C (range: 5–42°C), and the opti- + +mum pH is 9 (range: pH 7.0–11.0). Growth occurs at NaCl concentrations ranging from 0 to 1%. Cells of strain ZW +T +are positive for catalase and oxidase activities, but negative for urease. Casein, starch, gelatin, Tween 20 and Tween 80 are not hydrolyzed. Cells of strain ZW +T +do not + + + + +Fig 1. Electron micrograph of the cell morphology of strain ZW +T +. + + +doi:10.1371/journal.pone.0122254.g001 + + + + +Table 1. Differential phenotypic characteristics of strain ZW +T + +and closely related + +Sphingobacterium +species. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Characteristic + +1 + +2 + +3 + +4 + +5 + +6 + +7 + +8 + +9 +
+Temperature range (°C) +5–4210–4210–4010–4210–4010–4011–3910–4215–42
+Nitrate reduction +---------
+Urease ++-++ND----
+Hydrolysis of +
+Casein +------ND--
+Gelatin +----ND+--ND
+Tween 80 +-++-+-+NDND
+Acid production from +
+D-Fructose +-++---+NDND
+D-mannitol ++-+------
+L-Arabinose +++-++-+--
+Salicin +-++-++NDNDND
+DNA GC content (mol%) +44.8542.339.044.240.240.641.038.736.6
+Strains: 1, + +Sphingobacterium deserti + +sp. nov. +ZW T; 2, + +S +. +composti + +4M24T (data from this study); 3, + +S +. +spiritivorum +JCM 1277 + +T (data from this study); 4, + +S +. +arenae + +H-12T (data from this study); 5, + +S +. +shayense +HS + +39T [ +30 +]; 6, + +S +. +nematocida + +M-SX103T [ +31 +]; 7, + +S +. +bambusae +IBFC2009 + +T [ +32 +]; 8, + +S +. +daejeonense +TR + +6-04T [ +33 +]; 9, + +S +. +kyonggiense +KEMC 2241 + +-005T [ +34 +]. +, Positive;-, negative; ND, no data available. +
+ + +doi:10.1371/journal.pone.0122254.t001 + + +show L-arginine dihydrolase activity, and are negative for citrate utilization, nitrate reduction, and the Voges-Proskauer reaction. They are able to assimilate D-glucose, D-mannose, D-maltose, and L-arabinose, but not xylose. Acid is produced from D-mannitol and L-arabinose, but not from D-fructose, D-xylose or salicin ( +Table 1 +). The cells of strain ZW +T +exhibit resistance to kanamycin (50 μg/mL), ampicillin (50 μg/mL), hygromycin (50 μg/mL) and spectinomycin (35μg/mL), but are sensitive to rifampicin (50 μg/mL), chloramphenicol (50 μg/mL) and tetracycline (50 μg/mL). The predominant cellular fatty acids are summed feature 3 (C +16:1 +ω7c +/ C +16:1 +ω6c +or C +16:1 +ω6c/ +C +16:1 +ω7c +) (39.22%), iso-C15:0 (27.91%), iso-C +17:0 +3OH (15.21%), C +16:0 +(4.98%), iso-C +15:0 +3OH (3.03%), C16:0 3OH (5.39%) and C +14:0 +(1.74%). This fatty acid profile is similar to those of several reference strains of sphingobacteria that were grown under identical conditions ( +Table 2 +), suggesting that this newly isolated bacterium belongs to the genus + +Sphingobacterium + +. The polar lipid profile of strain ZW +T +includes phosphatidylethanolamine and several unidentified polar lipids (S1 Fig). Both strain ZW +T +and + +S +. +spiritivorum + +contain sphingolipids (S2 Fig), which are a distinct feature of members of the genus + +Sphingobacterium + +. The menaquinone of strain ZW +T +is MK-7 (>99%), consistent with all known members of the family + +Sphingobacterium + +. The GC content of the DNA of strain ZW +T +is 44.9 mol%, slightly higher than that of other + +Sphingobacterium + +strains. + + +The 16S rRNA gene sequence of strain ZW +T +(= KCTC 32092T = ACCC 05744T) is 1,311 bp in length (GenBank accession number JX403964). BLAST searches in the GenBank database and the EzTaxon server (http://www.ezbiocloud.net/eztaxon; [ +35 +]) indicated that strain ZW +T +belongs to the genus + +Sphingobacterium + +of the phylum +Bacteroidetes +. The 16S rRNA gene of strain ZW +T +exhibits the highest similarity to sequences from + +S +. +bambusae +IBFC2009 + +T +(95.65%), + +S +. +composti + +4M24 +T +(95.57%), + +S +. +lactis +WCC + +4512 +T +(95.49%), + +S +. +mizutaii +DSM + +11724 +T +(95.11%), + +S +. +daejeonense +TR + +6-04 +T +(95.11%), + +S +. +kyonggiense +KEMC 2241 + +-005 +T +(94.73%) and + +S +. +nematocida + +M-SX103 +T +(93.59%). DNA–DNA relatedness between strain ZW +T +and + +S +. +composti + +4M24 +T +is 36.3%. Phylogenetic analysis confirmed that strain ZW +T +forms a coherent cluster with members of the genus + +Sphingobacterium + +, and an intra-genus clade with + +S +. +bambusae +IBFC2009 + +T +(Fig 2). According to Stackebrandt [ +36 +] and Wayne [ +37 +], 16S rRNA gene + + + + +Table 2. Fatty acid composition of strain ZW +T + +and related members of the genus + +Sphingobacterium + +. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Fatty acid + +1 2 3 4 5 6 7 8 9 +
+C +14:0 +1.7 - 1.0 1.4 1.3 0.7 2.0 - 1.2
+C +16:0 +5.0 2.2 3.5 7.3 3.5 4.5 1.8 3.4 3.2
+C +16:0 +3-OH +5.4 1.2 2.7 4.8 2.4 3.3 15.2 - 6.7
+Iso-C +15:0 +Iso-C +15:0 +3-OH Iso-C +17:0 +3-OH Summed feature 3 +27.9 29.5 30.1 27.2 28.6 33.3 22.4 45.6 27.8 3.0 2.3 2.2 3.1 2.5 2.2 5.8 1.5 1.2 15.2 19.7 12.5 15.4 13.5 13.4 12.8 16.6 12.5 39.2 37.5 42.7 37.8 37.0 35.0 34.4 - 29.6
+Strains: 1, + +Sphingobacterium deserti + +sp. nov. +ZW T; 2, + +S +. +composti + +4M24T (data from this study); 3, + +S +. +spiritivorum +JCM 1277 + +T (data from this study); 4, + +S +. +arenae + +H-12T (data from this study); 5, + +S +. +shayense +HS + +39T [ +30 +]; 6, + +S +. +nematocida + +M-SX103T [ +31 +]; 7, + +S +. +bambusae +IBFC2009 + +T [ +32 +]; 8, + +S +. +daejeonense +TR + +6-04T [ +33 +]; 9, + +S +. +kyonggiense +KEMC 2241 + +-005T [ +34 +]. Numbers represent percentages of the total fatty acids.–, not detected (<1%). Summed feature 3: C16:1ω7c / C16:1ω6c, or C16:1ω6c / C16:1ω7c. +
doi:10.1371/journal.pone.0122254.t002
+similarities that are lower than 97% and DNA–DNA relatedness values below 70% support the identification of bacterial isolates as belonging to a new species. The average nucleotide identity (ANI) of the genome sequence (see below) of strain ZW T against the four other + +Sphingobacterium +species + +for which genome sequences are publicly available ranged from 84.40% (with strain + +S +. +thalpophilum +DSM + +11723) to 84.94% (with strain + +S +. +paucimobilis +HER1398 + +). These ANI values are also considerably lower than the 95 to 96% threshold used to identify isolates as +
+belonging to the same bacterial species [ +38 +, +39 +] (S1 Table). Thus, rDNA phylogeny (S3 Fig, S4 Fig), genome relatedness and chemotaxonomic characteristics all indicate that strain ZW T +
+represents a novel species within the genus + +Sphingobacterium + +(S5 Fig). We propose the name + +S +. +deserti + +sp. nov. +(de.ser’ ti. L. gen. n. + +deserti + +of a desert), with ZW T (= KCTC 32092T = ACCC 05744T) as the type strain. +
Genome organization of strain ZW T To further characterize this novel species, we sequenced the genome of strain ZW T using WGM technology. The resulting whole genome optical map allowed the assembly of the first
+Fig 2. Neighbor-joining phylogenetic tree indicating the relationships between the strain ZW +T + +and other + +Sphingobacterium +spp. + + +Bootstrap values (expressed as percentages of 1,000 replications) of> 70% are shown at branch points. Bar, 0.01 substitutions per nucleotide position. +
+ + +doi:10.1371/journal.pone.0122254.g002 + +finished genome sequence, to the best of our knowledge, for any species within the genus + + +Sphingobacterium + +. + + +The length of the circular chromosome of strain ZW +T +was found to be 4,615,818 bp ( +Fig 3 +, + +GenBank accession number JJMU00000000). The GC content of the genome is 42.6 mol% + +( +Fig 4 +), in agreement with the value (44.9 mol%) established by DNA renaturation kinetics + + +[ +16 +]. This is within the range of the published GC contents of the four other + +Sphingobacterium + + +species for which draft genome sequences are publicly available. + + + +Fig 3. Optical mapping of the + +Sphingobacterium deserti + +sp. nov. +ZW +T +genomic DNA with +Bam +HI. + +The large chromosome restriction map was generated by shotgun optical mapping. The outer circle depicts the consensus map; the inner circles indicate the contigs from which the consensus map was generated. Colors are arbitrarily assigned to homologous overlapping fragments. + +doi:10.1371/journal.pone.0122254.g003 + + + + +Fig 4. Genome map of + +Sphingobacterium deserti + +sp. nov. +ZW +T +. + +Concentric tracks from the inside to the outside represent the GC nucleotide bias; the GC content; tRNA and rRNA genes on the reverse strand; tRNA and rRNA genes on the forward-strand; reverse-strand coding sequences (CDSs); and forwardstrand CDSs. + +doi:10.1371/journal. pone.0122254.g004 + + + + +Fig 5. Whole-genome optical mapping barcode of + +Sphingobacterium deserti + +sp. nov. +ZW +T +. + +Vertical lines represent restriction sites; distances between lines represent fragment sizes. + + +doi:10.1371/journal.pone.0122254.g005 + +The genome of strain ZW +T +contains 48 tRNA genes and several rRNA gene clusters, includ- + +ing single copies of the 16S and the 23S rRNA genes and duplicate copies of the 5S rRNA gene. +An estimated 88.6% of the genome contains coding sequences (CDSs), and these CDSs are pre- +dicted to encode 3,391 putative proteins. The predicted proteins belong to 1,238 conserved +orthologous groups (COGs) from 23 COG categories. In addition, 1,408 predicted proteins +were also annotated using the KEGG Orthology System (S2 Table). + +Although many + +Sphingobacterium + +strains have been isolated in the last 30 years, no finished + +genome assemblies have been generated for any of those strains. In addition, few chromosomal + +features have been reported for any + +Sphingobacterium + +genome. The genomic data and the + + +WGM restriction barcode of strain ZW +T +may facilitate the taxonomic characterization of fur- + + +ther members of the genus + +Sphingobacterium + +( +Fig 5 +). Strain ZW +T +can also serve as a genome + +sequencing reference strain, with its WGM sequencing and annotation data available at NCBI +for download and direct import into new draft genome sequences of other sphingobacteria. + + + \ No newline at end of file