In this study, we present the draft genome of Aureobasidium pullulans strain MHAU2101, which is the first strain to effectively control fire blight caused by Erwinia amylovora in Korea. The genome of ...strain MHAU2101 was composed of 28,669,322 base pairs, with a C+G content of 50.4%. The assembly comprised 17 contigs and had 99.22% completeness. The results of this study will be a valuable resource for future research on the biocontrol mechanism of A. pullulans strain MHAU2101. KCI Citation Count: 0
Two Gram-stain-negative, moderately halophilic, non-motile, rod-shaped, pale yellow, and aerobic strains, designated WDS1C4
T
and WDS4C29
T
, were isolated from a marine solar saltern in Weihai, ...Shandong Province, PR China. Growth of strain WDS1C4
T
occurred at 10–45 °C (optimum, 37 °C), with 4–16 % (w/v) NaCl (optimum, 8 %) and at pH 6.5–9.0 (optimum, pH 7.5). Growth of strain WDS4C29
T
occurred at 10–45 °C (optimum, 40 °C), with 2–18 % (w/v) NaCl (optimum, 6 %) and at pH 6.5–9.0 (optimum, pH 7.5). Q-10 was the sole respiratory quinone of the two strains. The major polar lipids of strains WDS1C4
T
and WDS4C29
T
were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major cellular fatty acid in strains WDS1C4
T
and WDS4C29
T
was C
18 : 1
ω
7
c
, and the genomic DNA G+C contents of strains WDS1C4
T
and WDS4C29
T
were 67.6 and 63.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains WDS1C4
T
and WDS4C29
T
were members of the family
Rhodobacteraceae
and showed 94.3 and 95.3 % similarities to their closest relative,
Celeribacter indicus
, respectively. The similarity between WDS1C4
T
and WDS4C29
T
was 97.3 %. Differential phenotypic and genotypic characteristics of the two isolates from recognized genera showed that the two strains should be classified as representing two novel species in a new genus for which the names
Salibaculum halophilum
gen. nov., sp. nov. (type species, type strain WDS1C4
T
=MCCC 1H00179
T
=KCTC 52542
T
) and
Salibaculum griseiflavum
sp. nov. (WDS4C29
T
=MCCC 1H00175
T
=KCTC 52541
T
) are proposed.
A Gram-stain-negative, rod-shaped, facultative anaerobic bacterium, designated strain 3539
, was isolated from coastal sediment of Weihai, PR China. Optimal growth occurred at 28 °C, pH 7.5-8.0 and ...in the presence of 3.0 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 3539
formed a robust clade with members of the genus
and was closely related to
JCM 16154
,
F2
and
sw153
with 97.7, 96.2 and 95.4 % sequence similarity, respectively. The average amino acid identity, percentage of conserved proteins, average nucleotide identity and digital DNA-DNA hybridization values between strain 3539
and
JCM 16154
were 64.9, 68.3, 72.8 and 18.9 %, respectively. The genomic DNA G+C content of strain 3539
was 42.0 mol%. The dominant respiratory quinone was ubiquinone-8, and the major fatty acids were iso-C
and summed feature 3 (C
ω7
/C
ω6
). The polar lipids of strain 3539
consisted of phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified lipid and three unidentified phospholipids. Based on the combination of phylogenetic, phenotypic and chemotaxonomic data, strain 3539
is considered to represent a novel species within the genus
in he family
, for which the name
sp. nov. is proposed. The type strain of the new species is 3539
(=KCTC 72414
=MCCC 1H00388
).
The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is ...an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.
Prasiola crispa , an aerial green alga, exhibits remarkable adaptability to the extreme conditions of Antarctica by forming layered colonies capable of utilizing far-red light for photosynthesis. ...Despite a recent report on the structure of P. crispa ’s unique light-harvesting chlorophyll (Chl)-binding protein complex (Pc-frLHC), which facilitates far-red light absorption and uphill excitation energy transfer to photosystem II, the specific genes encoding the subunits of Pc-frLHC have not yet been identified. Here, we report a draft genome sequence of P. crispa strain 4113, originally isolated from soil samples on Ongul Island, Antarctica. We obtained a 92 Mbp sequence distributed in 1,045 scaffolds comprising 10,244 genes, reflecting 87.1% of the core eukaryotic gene set. Notably, 26 genes associated with the light-harvesting Chl a / b binding complex (LHC) were identified, including four Pc-frLHC genes, with similarity to a noncanonical Lhca gene with four transmembrane helices, such as Ot_Lhca6 in Ostreococcus tauri and Cr_LHCA2 in Chlamydomonas reinhardtii . A comparative analysis revealed that Pc-frLHC shares homology with certain Lhca genes found in Coccomyxa and Trebouxia species. This similarity indicates that Pc-frLHC has evolved from an ancestral Lhca gene with four transmembrane helices and branched out within the Trebouxiaceae family. Furthermore, RNA-seq analysis conducted during the initiation of Pc-frLHC gene induction under red light illumination indicated that Pc-frLHC genes were induced independently from other genes associated with photosystems or LHCs. Instead, the genes of transcription factors, helicases, chaperones, heat shock proteins, and components of blue light receptors were identified to coexpress with Pc-frLHC. Those kinds of information could provide insights into the expression mechanisms of Pc-frLHC and its evolutional development.
As close relatives,
is often wrongly identified as
. In this study, two genetic markers are presented based on
and
from the fengycin operon of
to rapidly distinguish it from
. The fengycin operon is ...one of the few present in
but absent in
up to date. Using these markers, two presumptive
isolates each were recovered from a set of isolates previously identified as
by Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) or identified only to genus level as
by 16S ribosomal RNA (rRNA) gene sequencing, respectively. Whole genome sequencing of the four isolates confirmed their identity as
having the closest similarity with
ATCC 9945a (GenBank: CP005965.1) with a 7,682 k-mer score and 97.22% Average Nucleotide Identity (ANI). ANI of 100% suggests that the four isolates are highly similar. Further analysis will be necessary to determine if finer differences exist among these isolates at the level of single nucleotide polymorphisms.
A novel Gram-stain-negative, rod-shaped marine bacterium, designated strain F02
, was isolated from a marine saltern in Weihai, PR China. The cells of strain F02
were approximately 0.8-1.0×3.0-4.0 µm ...and motile by means of a polar flagellum. Strain F02
grew optimally at 33-35 °C, pH 7.5 and in the presence of 3.0 % (w/v) NaCl. Strain F02
showed oxidase- and catalase-positive activities. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain F02
belonged to the family Halieaceae and exhibited 16S rRNA gene sequence similarities of 96.6 and 96.4 % to the type strains of Chromatocurvus halotolerans and Parahaliea mediterranea, respectively. The major cellular fatty acids of strain F02
were C18 : 1ω7c, C16 : 1ω7c, C15 : 0 and C18 : 1ω9c. The major polar lipids of strain F02
were phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Strain F02
contained Q-8 as the sole respiratory quinone. The genomic DNA G+C content was 58.4 mol%. The genome sequences of strain F02
and Chromatocurvus halotolerans DSM 23344
had an OrthoANI value of 70.5 %, and the average amino acid identity value between the two genomes was 62.6 %. The sequence similarity value between the rpoB genes of strain F02
and Chromatocurvus halotolerans DSM 23344
was 79.5 %. On the basis of polyphasic analysis, strain F02
represents a novel species in a new genus, for which the name Kineobactrum sediminis gen. nov., sp. nov. is proposed. The type strain is F02
(=KCTC 52616
=MCCC 1H00224
).
A Gram-stain-negative, non-motile, fine rod or short filament shaped, jacinth pigmented bacterium, designated strain WDS2C27
, was isolated from a marine solar saltern in Wendeng, Weihai, PR China ...(37°31'5″ N, 122°1'47″ E). Growth of WDS2C27
occurred at 20-42 °C (optimum 37 °C) and pH 6.5-8.5 (optimal pH 7.0-8.0). Optimal growth occurred in modified marine broth containing 6 % (w/v) NaCl. The major polar lipids in WDS2C27
were phosphatidylethanolamine, two unidentified aminolipids and one unidentified lipid. The major respiratory quinone of WDS2C27
was MK-6. The dominant fatty acids were iso-C
and anteiso
C
. The DNA G+C content was 35.0 mol%. The nucleotide sequence of the 16S rRNA gene indicated that the most closely related strain was
X15M-8
(92.0 % over 1452 bp). WDS2C27
showed 60.7 % average amino acid identity, 55.6 % percentage of conserved proteins, 75.0 % average nucleotide identity and 13.1 % digital DNA-DNA hybridization identity with the type species of the genus
,
ATCC 700755
. The phenotypic and genotypic properties and phylogenetic inference indicated that WDS2C27
could be assigned to a novel species within a novel genus, for which the name
gen. nov., sp. nov. is proposed. Strain WDS2C27
(=MCCC 1H00133
=KCTC 52044
) is the type strain.
Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the ...potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution.
Strains chi3
T
and sf7
T
were collected from a tidal mudflat around Dongmak beach in Ganghwa, Republic of Korea. Both strains were Gram-stain-negative, aerobic or facultatively anaerobic, and ...rod-shaped. Results of phylogenetic tree analysis based on 16S rRNA and whole-genome sequences suggested that strains chi3
T
and sf7
T
belong to the genera
Alteromonas
and
Erythrobacter
, respectively. The cells of strain chi3
T
were non-motile and grew at 15–45 °C (optimum, 38 °C), at pH 6.0–10.0 (optimum, pH 8.0) and in the presence of 0–9.0 % (w/v) NaCl (optimum, 2.0 %). The cells of strain sf7
T
were motile as they had flagella and grew at 20–48 °C (optimum, 38 °C), at pH 6.0–10.0 (optimum, pH 9.0) and in the presence of 0–5.0 % (w/v) NaCl (optimum, 1.0 %). Strains chi3
T
and sf7
T
have average nucleotide identity values (70.0–70.4% and 78.9–81.7 %) and digital DNA–DNA hybridization values (21.8–22.3% and 21.0–25.6 %) with reference strains in the genera
Alteromonas
and
Erythrobacter
, respectively. Data from digital DNA–DNA hybridization, as well as phylogenetic, biochemical and physiological analyses, indicated the distinction of the two strains from the genera
Alteromonas
and
Erythrobacter
, respectively, and we thus propose the names
Alteromonas gilva
sp. nov. (type strain chi3
T
=KACC 22866
T
=TBRC 16612
T
) and
Erythrobacter fulvus
sp. nov. (type strain sf7
T
=KACC 22865
T
=TBRC 16611
T
).
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