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  • Polish Journal Of Microbiology
  • Journal Of Nematology

 

Research Article

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 , ISSUE 2, 111–116

short-communication

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 , ISSUE 2, 281–284

original-paper

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 , ISSUE 4, 527–539

original-paper

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 , ISSUE 1, 99–108

research-article

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 , 1–4

research-article

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 , 1–2

Research Article

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 , ISSUE 2, 127–128

research-article

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 , 1–5

Original Paper

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 , ISSUE 1, 27–35

original-paper

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 , ISSUE 4, 505–514

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