An aerobic and Gram-stain-negative bacterial strain, designated UKS-15
, was isolated from lake water in the Republic of Korea. Results of 16S rRNA gene sequence and phylogenetic analyses indicated ...that the novel isolate belongs to the genus
and was most closely related to
RCML-52
(98.0 %),
9 NM-14
(97.4 %) and
FJY8
(97.2 %). The DNA G+C content was 69.1 mol%. Strain UKS-15
possessed ubiquinone-8 (Q-8) as the sole respiratory quinone and the fatty acid profile comprised iso-C
, iso-C
and summed feature 9 (iso-C
ω9
and/or C
10-methyl) as its major components. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unidentified aminophospholipid. Moreover, the physiological and biochemical results and low level of DNA-DNA relatedness (<22.0 %) allowed the phenotypic and genotypic differentiation of strain UKS-15
from other
species. Therefore, on the basis of the data from this polyphasic taxonomic study, strain UKS-15
should represent a novel species of the genus
, for which the name
sp. nov. is proposed. The type strain is UKS-15
(=JCM 30983
=KACC 18719
).
A Gram-stain-negative, aerobic, non-motile, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated 1KV19
, was isolated from a surface sediment sample collected near a bay in the ...Arctic. Growth of strain 1KV19
occurred in 1-4 % (w/v) NaCl (optimum, 2 %), at 4-35 °C (optimum, 25-30 °C) and at pH 6.5-8.0 (optimum, pH 7.0-7.5). The phylogenetic trees based on the 16S rRNA gene sequences showed that strain 1KV19
was associated with the genus
and had the highest 16S rRNA gene sequence similarity to
325-5
with 98.1 % similarity. Similarity values between strain 1KV19
and the type strains of other
species were in the range 95.9-97.6 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain 1KV19
and related species of the genus
were 76.4-79.1 and 19.9-22.3 %, respectively. The major cellular fatty acids of strain 1KV19
were iso-C
3-OH, iso-C
and iso-C
H. The respiratory quinone was MK-6. The major polar lipids of strain 1KV19
were phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids. The phenotypic, genotypic and chemotaxonomic differences between strain 1KV19
and its phylogenetic relatives indicate that strain 1KV19
should be regarded as representing a novel species in the genus
, for which the name
sp. nov. is proposed. The type strain is 1KV19
(=KCTC 62595
=MCCC 1H00307
).
Four novel bacterial strains, designated as RG327
, SE158
, RB56-2
and SE220
, were isolated from wet soil in the Republic of Korea. To determine their taxonomic positions, the strains were fully ...characterized. On the basis of genomic information (16S rRNA gene and draft genome sequences), all four isolates represent members of the genus
. The draft genomes of RG327
, SE158
, RB56-2
and SE220
consisted of circular chromosomes of 2 226 119, 2 507 338, 2 593 639 and 2 548 888 base pairs with DNA G+C contents of 64.6, 63.6, 63.0 and 63.1 %, respectively. All the isolates contained ubiquinone Q-10 as the predominant quinone compound and a fatty acid profile with C
, C
ω6
, C
2-OH
summed feature 3 (C
ω7
/C
ω6c) and summed feature 8 (C
ω
/C
ω6
) as the major fatty acids, supporting the affiliation of strains RG327
, SE158
, RB56-2
and SE220
to the genus
. The major identified polar lipids in all four novel isolates were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Moreover, the physiological, biochemical results and low level of DNA-DNA relatedness and average nucleotide identity values allowed the phenotypic and genotypic differentiation of RG327
, SE158
, RB56-2
and SE220
from other species of the genus
with validly published names and indicated that they represented novel species of the genus
, for which the names
sp. nov. (RG327
= KACC 22409
= LMG 32497
),
sp. nov. (SE158
= KACC 224408
= LMG 324498
),
(RB56-2
= KACC 22410
= LMG 32496
) and
sp. nov., (SE220
= KACC 22406
= LMG 32499
) are proposed.
Abstract
Land plants produce specialized low molecular weight metabolites to adapt to various environmental stressors, such as UV radiation, pathogen infection, wounding and animal feeding damage. ...Due to the large variety of stresses, plants produce various chemicals, particularly plant species-specific alkaloids, through specialized biosynthetic pathways. In this study, using a draft genome sequence and querying known biosynthetic cytochrome P450 (P450) enzyme-encoding genes, we characterized the P450 genes involved in benzylisoquinoline alkaloid (BIA) biosynthesis in California poppy (Eschscholzia californica), as P450s are key enzymes involved in the diversification of specialized metabolism. Our in silico studies showed that all identified enzyme-encoding genes involved in BIA biosynthesis were found in the draft genome sequence of approximately 489 Mb, which covered approximately 97% of the whole genome (502 Mb). Further analyses showed that some P450 families involved in BIA biosynthesis, i.e. the CYP80, CYP82 and CYP719 families, were more enriched in the genome of E. californica than in the genome of Arabidopsis thaliana, a plant that does not produce BIAs. CYP82 family genes were highly abundant, so we measured the expression of CYP82 genes with respect to alkaloid accumulation in different plant tissues and two cell lines whose BIA production differs to estimate the functions of the genes. Further characterization revealed two highly homologous P450s (CYP82P2 and CYP82P3) that exhibited 10-hydroxylase activities with different substrate specificities. Here, we discuss the evolution of the P450 genes and the potential for further genome mining of the genes encoding the enzymes involved in BIA biosynthesis.
A Gram-stain-negative, aerobic, gliding, rod-shaped (0.2-0.5×1.0-13.0 µm) and yellow-pigmented bacterium, designated PLHSN227
, was isolated from seawater collected near the coast of Yantai, PR ...China. PLHSN227
was found to grow at 15-37 °C (optimum, 28-30 °C) and pH 6.0-8.5 (optimum, 6.5-7.5) in the presence of 2-14 % (w/v) NaCl (optimum, 5.0 %). Phylogenetic analysis of the 16S rRNA gene sequences revealed that PLHSN227
represented a member of the family
and exhibited the highest sequence similarity (94.6 %) to the type strain
NBRC 100249
. The chemotaxonomic analysis revealed that the sole respiratory quinone was menaquinone 6 (MK-6) and the major fatty acids included C
ω8
, iso-C
, anteiso-C
, C
and summed feature 8 (C
ω7
and/or C
ω6
). The major polar lipids included phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The DNA G+C content of PLHSN227
was 35.6 mol%. PLHSN227
showed the highest average amino acid identity value of 67.2 %, the average nucleotide identity value of 75.6 and 14.5 % digital DNA-DNA hybridization identity with
DSM 15361
. According to the phylogenetic data, PLHSN227
formed a distinct clade in the phylogenetic tree. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is considered that PLHSN227
represents a novel genus within the family
, for which the name
gen. nov., sp. nov. is proposed. The type strain is PLHSN227
(=KCTC 72159
=MCCC 1H00371
).
Genome sequencing became one of the important tools for diagnosis of microorganisms. Proteus mirabilis is an enteric Gramnegative bacterium causes gastrointestinal and urinary tract infections in ...human and animals. Here, the draft sequencing of Proteus mirabilis (MAD23) strain was performed. The strain was collected from Chinese duck cecum suffering from diarrhea. Bacteria was identified by biochemical tests and characteristic swarming pattern on the plate. Antimicrobial susceptibility test was performed by VITEC-2 MS system. Also, draft genome sequencing was conducted using the Illumina platform NovaSeq sequencer. The genome is about 3,729,695 bp long, GC content is of 38.9%., number of contigs is 123, largest contig is 137547pb, smallest contig is 513, total of protein-coding sequences (CDSs) is 3410, and number of RNA genes is 72. Genome Pairwise comparisons of Proteus mirabilis MAD23 with other vs. type strain was detected based on is DDH, GC content, δ- value, genome size and number of proteins. Neighbour-Joining phylogenetic trees show relationship between Proteus mirabilis MAD23 and the close strains of Proteus species based on 16S rRNA sequences. In addition, analysis of the sequence reveals presence of many antibiotic resistance genes as dfrA1, sul2, dfrA32, aadA2b, aph(3’)-Ia, aadA1, aph(6)-Id, aph(3’’)-Ib, ere(A), aadA1, aadA2b, tet(J), tet(C), floR, and Cat genes.These genes encoding the resistance to different antibiotics including Aminoglycosides, Macrolides, Aminocyclitol, Tetracycline and Amphenicol. This work is considered as an important study can help in more understanding of WGS in Proteus spp. and recognize the genes that related to antibiotic resistance in this pathogen.
Spodoptera is an agriculturally important pest insect and studies in understanding its biology have been limited by the unavailability of its genome. In the present study, the genomic DNA was ...sequenced and assembled into 37,243 scaffolds of size, 358Mb with N50 of 53.7kb. Based on degree of identity, we could anchor 305Mb of the genome onto all the 28 chromosomes of Bombyx mori. Repeat elements were identified, which accounts for 20.28% of the total genome. Further, we predicted 11,595 genes, with an average intron length of 726bp. The genes were annotated and domain analysis revealed that Sf genes share a significant homology and expression pattern with B. mori, despite differences in KOG gene categories and representation of certain protein families. The present study on Sf genome would help in the characterization of cellular pathways to understand its biology and comparative evolutionary studies among lepidopteran family members to help annotate their genomes.
•Genomic DNA isolated from Sf21 cells was sequenced and assembled.•The genomic assembly contains 37,243 scaffolds of size, 358Mb with N50 of 53.7kb.•The Spodoptera genome contains an approximate 20.28% of repeat elements.•11,595 genes were predicted from the Spodoptera draft genome sequence.•The genes were annotated and protein families unique to Spodoptera were identified.
Rice bean is a less-known underutilized legume crop with a high nutritional value among members of the Vigna family. As an initiative to compose rice bean (
Vigna umbellata
) genomic resource, the ...size of 414 mega-base pairs with an estimated identification of 31,276 high confidence index genes via 15,521 scaffolds generated from Illumina and PacBio platform 30X coverage data has achieved 96.08% functional coverage data from Illumina and PacBio platform. Rice bean genome assembly was found to be exquisitely close to
Vigna angularis
(experimental control/outgroup),
Vigna radiata
, and
Vigna unguiculata
, however,
Vigna angularis
being the closest. The assembled genome was further aligned with 31 leguminous plants (13 complete genomes and 18 partial genomes), by collinearity block mapping. Further, we predicted similar discriminant results by complete coding sequence (CDS) alignment. In contrast, 17 medically influential genomes from the National Institute of General Medical Sciences-National Institutes of Health NIGMS-NIH, when compared to rice bean assembly for LCB clusters, led to the identification of more than 18,000 genes from the entire selected medicinal genomes. Empirical construction of all genome comparisons revealed symplesiomorphic character in turn uncovering the lineage of genetic and functional features of rice beans. Significantly, we found deserving late-flowering genes, palatably indexed uncommon genes that regulate various metabolite pathways, related to abiotic and biotic stress pathways and those that are specific to photoperiod and disease resistance and so on. Therefore, the findings from this report address the genomic value of rice bean to be escalated
via
breeding by allied and applied approaches.
Members of the genus Aspergillus are extensively studied ascomycetes because of their ability to synthesize high value-added compounds and enzymes of industrial interest. Precise whole genome ...assembly and gene annotation are significant for gene functional analyses. Here, we report the draft genome sequencing, assembly and whole genome analysis of Aspergillus terreus P14_T3, isolated from rumen sample of cattle fed with coconut-coir. A total of 13,340 protein-coding genes were predicted, among them 493 are involved in degradation of complex carbohydrate polysaccharides. Further, it was found that 29 genes, encoding β-glucosidase belong to Glycosyl hydrolase (GH) family 1 (3 gene), 3 (17 gene), 5 (4 gene), 17 (3 gene), 132 (2 gene). The tertiary structure of all the β-glucosidases was designed by homology modeling; modeled structure AtBgl1.3 (GH1), AtBgl3.1 (GH3), AtBgl5.4 (GH5), AtBgl17.1 (GH17) show classical (α/β) TIM-like barrel motif. Molecular docking of different β-glucosidases with cellobiose revealed that conserved amino acids i.e. Glu, Trp, Arg, His, Tyr and Asp are taking part in substrate hydrolysis. Moreover, some other amino acids i.e. Ser, Phe, Gln and Asn are found to be involved in hydrogen bond formation and catalysis. These findings may provide valuable insights in designing β-glucosidases with higher cellulose-hydrolyzing efficiency.
•Draft genome of Aspergillus terreus sequenced from fungal strain isolated from cattle rumen fed with lignin rich diet.•13,340 protein coding genes with 493 CAZymes including 29 β-glucosidases reported.•4 refined modeled structures of β-glucosidases of GH1, GH3, GH5 and GH17 family shows classical TIM-like barrel motif.•Molecular docking of different β-glucosidases with cellobiose shows conserved amino acids for substrate hydrolysis.•Aspergillus terreus represents model fungi for studying ligno-cellulolytic enzyme machinery.
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