• Mycobiology
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• 제50권6호
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• pp.448-456
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• 2022

In this study, the roots and rhizosphere soil of Abies koreana and Taxus cuspidata were collected from sites at two different altitudes on Mt. Halla. Ectomycorrhizal fungi (EMF) were identified by Illumina MiSeq sequencing. The proportion of EMF from the roots was 89% in A. koreana and 69% in T. cuspidata. Among EMF in rhizosphere soils, the genus Russula was the most abundant in roots of A. koreana (p < 0.05). The altitude did not affect the biodiversity of EMF communities but influenced fungal community composition. However, the host plants had the most significant effect on EMF communities. The result of the EMF community analysis showed that even if the EMF were isolated from the same altitudes, the EMF communities differed according to the host plant. The community similarity index of EMF in the roots of A. koreana was higher than that of T. cuspidata (p < 0.05). The results show that both altitude and host plants influenced the structure of EMF communities. Conifers inhabiting harsh sub-alpine environments rely strongly on symbiotic relationships with EMF. A. koreana is an endangered species with a higher host specificity of EMF and climate change vulnerability than T. cuspidata. This study provides insights into the EMF communities, which are symbionts of A. koreana, and our critical findings may be used to restore A. koreana.

• 미생물학회지
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• 제55권3호
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• pp.283-285
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• 2019

이 연구에서는 Illumina Hiseq platform을 사용하여 동해 심층 해양수로부터 분리된 Pelagicola sp. DSW4-44 (= KCTC 62762 = KCCM 43261)의 초안 유전체 염기서열 해독을 수행하였다. 그 결과, 유전체는 대략 4.85 Mbp의 길이 및 54.3%의 G + C 함량으로 구성되었고, 전체 4,566개의 단백질 암호 유전자, 3개의 rRNA 유전자, 48개의 tRNA 유전자, 3개의 non-coding RNA 유전자 및 67개의 위유전자(pseudo gene)가 확인되었다. 초안 유전체에서 균주 DSW4-44는 Pelagicola 속의 다른 균주에서 발견되지 않는 이화적 질산염의 암모늄 환원과 탈질화의 질소대사 유전자를 가지고 있었다.

• 미생물학회지
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• 제54권4호
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• pp.480-482
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• 2018

이 연구에서는 Illumina Hiseq platform을 사용하여 동해 심층 해양수로부터 분리된 Zhongshania marina $DSW25-10^T$의 유전체 염기서열 해독을 수행하였다. 그 결과, 유전체는 대략 4.08 Mbp의 길이 및 49.0%의 G + C 함량으로 구성되었고, 전체 3,702개의 단백질 암호 유전자, 3개의 rRNA 유전자, 39개의 tRNA 유전자, 4개의 non-coding RNA 유전자 및 36개의 위 유전자(pseudogenes)가 확인되었다. 또한, 지방족 및 방향족 화합물의 대사 경로가 확인되었다. 이러한 대사 경로들로 비추어 Zhongshania marina $DSW25-10^T$는 유용한 생물 정화 자원으로 사용될 수 있을 것으로 기대된다.

• Genomics & Informatics
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• 제18권3호
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• pp.32.1-32.7
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• 2020

The mitochondrial genome of a species is an essential resource for its effective conservation and phylogenetic studies. In this article, we present sequencing and characterization of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba collected from Khulna region of Bangladesh. The complete mitochondrial genome was 16,597 bp in size, which formed a circular double-stranded DNA molecule containing a total of 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes) with two non-coding regions, an origin of light strand replication (OL) and a displacement loop (D-loop), similar structure with other fishes of Teleostei. The phylogenetic tree demonstrated its close relationship with labeonine fishes. The complete mitogenome of Cirrhinus reba (GenBank no. MN862482) showed 99.96% identity to another haplotype of Cirrhinus reba (AP013325), followed by 90.18% identity with Labeo bata (AP011198).

• 한국미생물·생명공학회지
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• 제51권3호
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• pp.325-327
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• 2023

This paper presents the complete genome sequence of a novel marine actinomycete, Streptomyces sp. MMBL 11-1. The genome of Streptomyces sp. MMBL 11-1 was obtained through next-generation sequencing using the PacBio Sequel system and Illumina platform provided by Macrogen, Korea. The assembled genome consists of five contigs, with a total length of 8,496,900 bp and a G+C content of 71.6%. The genome harbors multiple biosynthetic gene clusters (BGCs) associated with producing microbial natural products (MNPs). The comprehensive genomic information of this type of strain will serve as a valuable resource for identifying other marine actinomycetes strains.

• Journal of Microbiology and Biotechnology
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• 제28권7호
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• pp.1168-1177
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• 2018

The aim of this study was to investigate the microbial community of three tannery wastewater treatment plants (WWTPs) involved in nitrification by Illumina MiSeq sequencing. The results showed that highly diverse communities were present in tannery wastewater. A total of six phyla, including Proteobacteria (37-41%), Bacteroidetes (6.04-16.80), Planctomycetes (3.65-16.55), Chloroflexi (2.51-11.48), Actinobacteria (1.91-9.21), and Acidobacteria (3.04-6.20), were identified as the main phyla, and Proteobacteria dominated in all the samples. Within Proteobacteria, Beta-proteobacteria was the most abundant class, with the sequence percentages ranging from 9.66% to 17.44%. Analysis of the community at the genus level suggested that Thauera, Gp4, Ignavibacterium, Phycisphaera, and Arenimonas were the core genera shared by at least two tannery WWTPs. A detailed analysis of the abundance of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) indicated that Nitrosospira, Nitrosomonas, and Nitrospira were the main AOB and NOB in tannery wastewater, respectively, which exhibited relatively high abundance in all samples. In addition, real-time quantitative PCR was conducted to validate the results by quantifying the abundance of the AOB and total bacteria, and similar results were obtained. Overall, the results presented in this study may provide new insights into our understanding of key microorganisms and the entire community of tannery wastewater and contribute to improving the nitrogen removal efficiency.

• Mycobiology
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• 제46권4호
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• pp.421-428
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• 2018

The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.

• Genomics & Informatics
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• 제13권2호
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• pp.31-39
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• 2015

Sequencing depth, which is directly related to the cost and time required for the generation, processing, and maintenance of next-generation sequencing data, is an important factor in the practical utilization of such data in clinical fields. Unfortunately, identifying an exome sequencing depth adequate for clinical use is a challenge that has not been addressed extensively. Here, we investigate the effect of exome sequencing depth on the discovery of sequence variants for clinical use. Toward this, we sequenced ten germ-line blood samples from breast cancer patients on the Illumina platform GAII(x) at a high depth of ${\sim}200{\times}$. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of $120{\times}$. Furthermore, investigation using a diagnostic gene set showed that the number of clinical variants identified using exome sequencing reached a plateau at an average sequencing depth of about $120{\times}$. Moreover, the phenomena were consistent across the breast cancer samples.

• International Journal of Oral Biology
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• 제46권3호
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• pp.146-153
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• 2021

Accurate identification of microbes facilitates the prediction, prevention, and treatment of human diseases. To increase the accuracy of microbiome data analysis, a long region of the 16S rRNA is commonly sequenced via paired-end sequencing. In paired-end sequencing, a sufficient length of overlapping region is required for effective joining of the reads, and high-quality sequencing reads are needed at the overlapping region. Trimming sequences at the reads distal to a point where sequencing quality drops below a specific threshold enhance the joining process. In this study, we examined the effect of trimming conditions on the number of reads that remained after quality control and chimera removal in the Illumina paired-end reads of the V3-V4 hypervariable region. We also examined the alpha diversity and taxa assigned by each trimming condition. Optimum quality trimming increased the number of good reads and assigned more number of operational taxonomy units. The pre-analysis trimming step has a great influence on further microbiome analysis, and optimized trimming conditions should be applied for Divisive Amplicon Denoising Algorithm 2 analysis in QIIME2 platform.

• 한국미생물·생명공학회지
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• 제48권4호
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• pp.574-581
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• 2020

Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is commonly used to analyze the microbiome due to its relatively long read length. However, recently, Illumina introduced the 250x2 chip for HiSeq 2500. The purpose of this study was to compare the performance of MiSeq and HiSeq in the context of oral microbiome samples. The MiSeq Reagent Kit V3 and the HiSeq Rapid SBS Kit V2 were used for MiSeq and HiSeq 2500 analyses, respectively. Total read count, read quality score, relative bacterial abundance, community diversity, and relative abundance correlation were analyzed. HiSeq produced significantly more read sequences and assigned taxa compared to MiSeq. Conversely, community diversity was similar in the context of MiSeq and HiSeq. However, depending on the relative abundance, the correlation between the two platforms differed. The correlation between HiSeq and MiSeq sequencing data for highly abundant taxa (> 2%), low abundant taxa (2-0.2%), and rare taxa (0.2% >) was 0.994, 0.860, and 0.416, respectively. Therefore, HiSeq 2500 may also be compatible for microbiome studies. Importantly, the HiSeq platform may allow a high-resolution massive parallel sequencing for the detection of rare taxa.