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original-paper | 31-May-2021

Environmental Factors Associated with the Eukaryotic Microbial Community and Microalgal Groups in the Mountain Marshes of South Korea

nephelometric turbidity of the samples were measured on-site using a multiparameter instrument (U-50 Multiparameter Water Quality Meter, HORIBA, Kyoto, Japan). A water test kit (HUMAS, Daejeon, South Korea) was used to measure total nitrogen (TN) and total phosphorus (TP) in each sample. Microbial community analysis. Illumina MiSeq analyses of the microbial communities were performed by the Macrogen (Macrogen, Seoul, South Korea, https://dna.macrogen.com/kor/), as described previously (Yun et al. 2019). DNA

YOUNG-SAENG KIM, HYUN-SIK YUN, JEA HACK LEE, HAN-SOON KIM, HO-SUNG YOON

Polish Journal of Microbiology, Volume 70 , ISSUE 2, 215–233

Research Article | 03-September-2018

Nematode Genome Announcement: A Draft Genome for Rice Root-Knot Nematode, Meloidogyne graminicola

The rice root-knot nematode Meloidogyne graminicola has emerged as a devastating pest of rice in South-East Asian countries. Here we present a draft genome sequence for M. graminicola, assembled using data from short and long insert libraries sequenced on Illumina GAIIx sequencing platform.

Vishal Singh Somvanshi, Madhura Tathode, Rohit Nandan Shukla, Uma Rao

Journal of Nematology, Volume 50 , ISSUE 2, 111–116

research-article | 30-November-2020

Nematode genome announcement: The draft genome sequence of entomopathogenic nematode Heterorhabditis indica

). DNA was fragmented by sonication using Bioruptor (Diagenode, Seraing (Ougrée), Belgium). The size distribution was checked by running an aliquot of the fragmented DNA sample on an Agilent high sensitivity bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Illumina TruSeq DNA sample preparation guide (Illumina, San Diego, CA, USA) was followed to prepare two high-quality libraries of insert sizes 300 bp and 600 bp. Illumina Nextera Mate Pair Library Prep Kit was used to prepare a mate-pair

Chaitra G. Bhat, Vishal S. Somvanshi, Roli Budhwar, Jeffrey Godwin, Uma Rao

Journal of Nematology, Volume 53 , 1–3

short-communication | 28-June-2019

Bacterial Diversity in Soybean Rhizosphere Soil at Seedling and Mature Stages

nodules of leguminous plants lacking hydrogenase. Experiments have shown that bacteria remove hydrogen (Mclearn and Dong 2002), and these bacteria were beneficial to the growth of plants (Dong et al. 2003; Abdellatif et al 2017). Therefore, studying the rhizosphere microbial diversity of legumes will improve our understanding of microbes that promote the growth of legumes. Accordingly, in this study, Illumina high-throughput sequencing was used to investigate the microbial communities of rhizosphere

LIN WANG, ZHIYING LI, RUIRUI LIU, LULU LI, WEIWEI WANG

Polish Journal of Microbiology, Volume 68 , ISSUE 2, 281–284

original-paper | 08-September-2020

Characteristics and Diversity of Endophytic Bacteria in Endangered Chinese Herb Glehnia littoralis Based on Illumina Sequencing

°40′16.68″). Three sampling locations, approximately 1000 m apart, were selected, and four single healthy plant samples, were randomly gathered from each sampling location in September 2018. Samples collected included leaves, stems, and roots. All the plant samples were placed into the aseptic sample box immediately and stored at –80°C. The plant tissues were surface-sterilized following the previously described method (Correa-Galeote et al. 2014). DNA isolation, PCR amplification, and Illumina

XIAOWEI HUO, YUE WANG, DAWEI ZHANG, TING GAO, MENGMENG LIU

Polish Journal of Microbiology, Volume 69 , ISSUE 3, 283–291

original-paper | 05-December-2019

Illumina MiSeq Analysis and Comparison of Freshwater Microalgal Communities on Ulleungdo and Dokdo Islands

producer and consumer trophic levels (Berner 1992; Vitousek et al. 2002; Cardinale et al. 2011). However, microalgal community research based solely on the culturing faces certain limitations, particularly the difficulty in identifying and analyzing unculturable microorganisms (Handelsman 2004; Streit and Schmitz 2004). Consequently, amplicon sequencing analysis using Illumina MiSeq can be a powerful tool for the investigation of unculturable microorganisms in their natural environment (Knight 2000

HYUN-SIK YUN, YOUNG-SAENG KIM, HO-SUNG YOON

Polish Journal of Microbiology, Volume 68 , ISSUE 4, 527–539

original-paper | 11-March-2020

Oligotrophic Nitrification and Denitrification Bacterial Communities in a Constructed Sewage Treatment Ecosystem and Nitrogen Removal of Delftia tsuruhatensis NF4

known from their culturable microorganisms. We know that traditional pure-culture methods can identify only a few microorganisms (Ward et al. 1990). Recently, the culture-independent molecular biological methods, such as Illumina HiSeq DNA sequencing has been used besides conventional isolation techniques for the analysis of microbial community structures (Watson et al. 2014). So far, there has been no report on the bacterial community in STE using both the Illumina HiSeq DNA sequencing and

RUILAN YANG, JING LI, LUYAO WEI-XIE, LIN SHAO

Polish Journal of Microbiology, Volume 69 , ISSUE 1, 99–108

original-paper | 31-May-2021

Diversity of Endophytic Fungal Community in Leaves of Artemisia argyi Based on High-throughput Amplicon Sequencing

at 72°C for 7 min. The PCR products were qualitatively detected by electrophoresis using 2% agarose gel in 1 × TAE solution, purified, quantified, and a test library was constructed using Qubit 3.0. Subsequently, the test DNA library was subjected to high-throughput amplicon sequencing performed by Sangon Bioengineering Co., Ltd. (Shanghai) using the Illumina MiSeq sequencing platform (Liao et al. 2020). The raw data of high-throughput amplicon sequencing was uploaded to the NCBI SRA database

QIU-FANG WU, LING-MIN HE, XIN-QIANG GAO, MEI-LING ZHANG, JING-SHUN WANG, LI-JIANG HOU

Polish Journal of Microbiology, Volume 70 , ISSUE 2, 273–281

research-article | 17-September-2019

Genome Announcement: The Draft Genomes of Two Radopholus similis populations from Costa Rica

using NEBNext Ultra II DNA Library Prep Kit for Illumina (San Diego, CA). Whole genome sequencing was performed on the Illumina HiSeq 3000 at the Center for Genome Research and Biocomputing at Oregon State University (Corvallis, OR). Raw reads were screened for sequencing adapters, trimmed and filtered for quality (Q = 20) using BBDuk (https://github.com/BioInfoTools/BBMap) and resulted in 5,376,812 and 14,006,275 paired-end 150 reads for Rd and Rv, respectively. Quality-filtered reads were

Catherine L. Wram, Cedar N. Hesse, Sulochana K. Wasala, Dana K. Howe, Amy B. Peetz, Dee R. Denver, Danny Humphreys-Pereira, Inga A. Zasada

journal of nematology, Volume 51 , 1–4

research-article | 23-April-2019

A genomic resource for the sedentary semi-endoparasitic reniform nematode, Rotylenchulus reniformis Linford & Oliveira

provided by Illumina (San Diego, CA). Additionally, a single R. reniformis egg was isolated, its DNA was amplified by whole genome amplification (WGA) using the Qiagen Repli-G single cell kit (Valencia, CA) and short-read small-insert libraries (400- and 600-bp) were constructed and sequenced using standard protocols provided by Illumina (San Diego, CA). Paired-end sequencing was conducted on Illumina GAIIx and Illumina MiSeq systems. We obtained 19.17 Gb and 29.85 Gb from the pooled population short

Kurt C. Showmaker, William S. Sanders, Sebastian Eves-van den Akker, Brigitte E. Martin, Roy N. Platt, John V. Stokes, Chuan-Yu Hsu, Benjamin D. Bartlett, Daniel G. Peterson, Martin J. Wubben

Journal of Nematology, Volume 51 , 1–2

Research Article | 24-July-2017

The Draft Genome of Globodera ellingtonae

Globodera ellingtonae is a newly described potato cyst nematode (PCN) found in Idaho, Oregon, and Argentina. Here, we present a genome assembly for G. ellingtonae, a relative of the quarantine nematodes G. pallida and G. rostochiensis, produced using data from Illumina and Pacific Biosciences DNA sequencing technologies.

WENDY S. PHILLIPS, DANA K. HOWE, AMANDA M. V. BROWN, SEBASTIAN EVES-VAN DEN AKKER, LEVI DETTWYLER, AMY B. PEETZ, DEE R. DENVER, INGA A. ZASADA

Journal of Nematology, Volume 49 , ISSUE 2, 127–128

research-article | 17-March-2020

Genome sequence of the root-knot nematode Meloidogyne luci

positions of different populations of M. ethiopica group species within Clade I Meloidogyne are incompletely resolved. Isolated specimens of M. luci in Europe were previously misidentified as M. ethiopica due to their high similarity (Gerič Stare et al., 2017). We used long-read Pacific Biosciences Sequel and short-read Illumina HiSeqX sequencing data to produce a high-quality Meloidogyne luci genome assembly. The M. luci population SI-Smartno was isolated from tomato plants grown in a commercial

Nik Susič, Georgios D. Koutsovoulos, Cristian Riccio, Etienne G. J. Danchin, Mark L. Blaxter, David H. Lunt, Polona Strajnar, Saša Širca, Gregor Urek, Barbara Gerič Stare

Journal of Nematology, Volume 52 , 1–5

research-article | 30-November-2020

Genome sequence of the coffee root-knot nematode Meloidogyne exigua

of which may help in the development of new strategies for its management. We used long-read Oxford Nanopore Technology (ONT) and short-read Illumina HiSeq sequencing data to generate the genome assembly. The population ‘Mex1’ was isolated from coffee roots collected in Hacienda Aquiares located in Turrialba, Cartago, Costa Rica (9°56′18.09′′N, 83°43′43.86′′W). A single juvenile was inoculated and multiplied on tomato (Solanum lycopersicum var. Moneymaker). The procedures for sequencing of M

Ngan Thi Phan, Guillaume Besnard, Rania Ouazahrou, William Solano Sánchez, Lisa Gil, Sophie Manzi, Stéphane Bellafiore

Journal of Nematology, Volume 53 , 1–6

Original Paper | 09-March-2018

High-Throughput Sequencing Analysis of Endophytic Bacteria Diversity in Fruits of White and Red Pitayas from Three Different Origins

Pitaya contains various types of polyphenols, flavonoid and vitamins which are beneficial for health and it is among the most important commercial tropical fruits worldwide. Endophytic bacteria might be beneficial for plant growth and yield. However, bacterial diversity in pitaya is poorly characterized. In this study, fruits of white and red pitayas from three different origins (Thailand, Vietnam and China) were chosen for endophytic bacteria diversity investigation by using Illumina HiSeq

Zhen Ren, Shukun Tang, Yi Jiang, Mingxing Jiang, Shangyong Zheng, Wenjing Liu, Zhili Yang, Shuping Sang, Zebin Chen, Tiyuan Xia, Min Yin

Polish Journal of Microbiology, Volume 67 , ISSUE 1, 27–35

original-paper | 17-September-2021

Hydrolytic Enzymes Producing Bacterial Endophytes of Some Poaceae Plants

% agarose gel in 1 × TBE buffer. The 16S rRNA gene amplicon sequencing was performed by the Sentebiolab Biotechnology Company (Turkey) using the Miseq (Illumina) next-generation sequencing platform. The sequences obtained were analyzed using the database on the website (https://www.ezbiocloud.net), and then the sequences were logged in to the GenBank site and accessed “GenBank accession” numbers (Table II). The phylogenetic tree was created by the GGDC web server at http://ggdc.dsmz.de using the

GOKHAN DOGAN, BILGIN TASKIN

Polish Journal of Microbiology, Volume 70 , ISSUE 3, 297–304

original-paper | 05-December-2019

The Composition of Fungal Communities in the Rumen of Gayals (Bos frontalis), Yaks (Bos grunniens), and Yunnan and Tibetan Yellow Cattle (Bos taurs)

included abundance and structure of rumen fungi using MEGAN and NCBI databases. Venn and Heatmap diagrams were built using the R language (Jami et al. 2013). Results A total of 622 176 original sequences were obtained from four cattle breeds by Illumina sequencing of which 297 745 sequences remained after quality control measures, and 285 092 sequences were used for phylogenetic analyses. The average length of trim sequences used for analyses was 317.6 bp. The average number of sequences from the

HOUFU WANG, PENGFEI LI, XUCHUAN LIU, CHUNYONG ZHANG, QIONGFEN LU, DONGMEI XI, RENHUI YANG, SHULING WANG, WENSHUN BAI, ZHEN YANG, RONGKANG ZHOU, XIAO CHENG, JING LENG

Polish Journal of Microbiology, Volume 68 , ISSUE 4, 505–514

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