A guide for the analysis of plant microbial communities through high-throughput sequencing methods
Plant microbiome research allows an understanding of microbial functions and their ecology. This knowledge can be applied to develop efficient biofertilizers based on the most relevant taxa or functions of the microbiome. Nowadays, the advance of high-throughput sequencing methods have enabled us to get sequences from (meta)genomes, (meta)transcriptomes, and marker genes from complete microbial communities. To reach this goal, several programs allow the decoding of many features of the plant microbiome, such as its taxonomic composition and its functions. However, the analysis of this kind of data is not so easy and requires some expertise in bioinformatics. Here we aim to provide a brief introduction to the analysis of high-throughput sequencing data to help researchers be immersed in these methodologies. We include key steps and common workflows in plant microbiome research, including many examples of bioinformatic tools and databases, and mention their inherent biases. We hope this chapter allows researchers that are not used to utilizing next-generation sequencing to be started with these methods easily.
| Main Authors: | , , , , , , |
|---|---|
| Format: | capítulo de libro biblioteca |
| Language: | English |
| Published: |
Elsevier
2024
|
| Subjects: | Amplicon sequencing, Bioinformatics, Metagenomic, Metatranscriptomics, Microbial communities, NGS, Plant microbiome, Plant-microbe interactions, Tutorial, bioinformatics, |
| Online Access: | http://hdl.handle.net/10261/358470 https://api.elsevier.com/content/abstract/scopus_id/85193394763 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Summary: | Plant microbiome research allows an understanding of microbial functions and their ecology. This knowledge can be applied to develop efficient biofertilizers based on the most relevant taxa or functions of the microbiome. Nowadays, the advance of high-throughput sequencing methods have enabled us to get sequences from (meta)genomes, (meta)transcriptomes, and marker genes from complete microbial communities. To reach this goal, several programs allow the decoding of many features of the plant microbiome, such as its taxonomic composition and its functions. However, the analysis of this kind of data is not so easy and requires some expertise in bioinformatics. Here we aim to provide a brief introduction to the analysis of high-throughput sequencing data to help researchers be immersed in these methodologies. We include key steps and common workflows in plant microbiome research, including many examples of bioinformatic tools and databases, and mention their inherent biases. We hope this chapter allows researchers that are not used to utilizing next-generation sequencing to be started with these methods easily. |
|---|