Plant developmental stage drives the differentiation in ecological role of the maize microbiome.

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Abstract

Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics.

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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Fast gapped-read alignment with Bowtie 2.

Ben Langmead, Steven L Salzberg (2022)

As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

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Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Paul Shannon, Andrew Markiel, Owen Ozier … (2003)

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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Author and article information

Journal

Journal ID (iso-abbrev): Microbiome

Title: Microbiome

Publisher: Springer Science and Business Media LLC

ISSN (Electronic): 2049-2618

ISSN (Print): 2049-2618

Publication date (Electronic): Aug 13 2021

Volume: 9

Issue: 1

Affiliations

[1 ] State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.

[2 ] University of Chinese Academy of Sciences, Beijing, 100049, China.

[3 ] Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia.

[4 ] Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia.

[5 ] Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.

[6 ] College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China.

[7 ] Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, Qujing, 655000, China.

[8 ] State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. zhanglm@rcees.ac.cn.

[9 ] University of Chinese Academy of Sciences, Beijing, 100049, China. zhanglm@rcees.ac.cn.

Article

Publisher Item ID: 10.1186/s40168-021-01118-6

DOI: 10.1186/s40168-021-01118-6

PMC ID: 8364065

PubMed ID: 34389047

SO-VID: 74d6310e-0357-4736-a197-0937e84216e0

History

Keywords: Crop microbiomes,Metagenomics,Microbial interkingdom networks,Microbiome assembly,Phylloplane microbiome,Soil–plant continuum,Temporal dynamics

Data availability:

Keywords: Crop microbiomes, Metagenomics, Microbial interkingdom networks, Microbiome assembly, Phylloplane microbiome, Soil–plant continuum, Temporal dynamics

Plant developmental stage drives the differentiation in ecological role of the maize microbiome.

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Abstract

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Tick microbiome

Most cited references 99

Trimmomatic: a flexible trimmer for Illumina sequence data

Fast gapped-read alignment with Bowtie 2.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

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