Table 1 Recent studies employing holo-omics in the field of plant microbiome research. This table lists twenty recent publications from the period of 2014 through 2020 that employ a holo-omics approach to explore plant and microbial interactions within the above or below ground plant microbiome. A subset of these studies is also indicated in Fig. 2. The first column lists the first author, year, and reference number within this review, while the second third and fourth columns indicate the plant host, sample type, and specific omics techniques employed
From: Holo-omics for deciphering plant-microbiome interactions
Refs | Plant host | Sample type(s) | Approaches |
|---|---|---|---|
Deng et al. 2020 [61] | Sorghum | Rhizosphere | 16S, host genomic |
Horton et al. 2014 [62] | Arabidopsis | Leaf | 16S, ITS, host genomic |
Wallace et al. 2018 [63] | Maize | Leaf | 16S, host genomic |
Walters et al. 2018 [65] | Maize | Rhizosphere | 16S, host genomic |
Bergelson et al. 2019 [64] | Arabidopsis | Root | 16S, host genomic |
Castrillo et al. 2017 [55] | Arabidopsis | Root | 16S, host RNA-seq |
Zolti et al. 2020 [51] | Tomato, lettuce | Root | Shotgun metagenome, metatranscriptome, host RNA-seq |
Chialva et al. 2019 [52] | Tomato | Root | Metatranscriptome, host rna-seq |
Ofek-Lalzar et al. 2014 [53] | Wheat, cucumber | Root | Metagenomics, host rna-seq, metatranscriptomic |
Li et al. 2019 [54] | Peanut | Root, rhizosphere | Shotgun metagenome, metatranscriptome, host RNA-seq |
Kudjordjie et al. 2019 [59] | Maize | Soil, rhizosphere, root, shoot | Plant extracts, 16S |
Hu et al. 2018 [58] | Maize | Root | 16S, root metabolites |
Huang et al. 2019 [13] | Arabidopsis, Wheat, rice and N. benthamiana | Root, leaf | Metabolites, 16S |
Xu et al. 2018 [7] | Sorghum | Root, rhizosphere | Host metabolites, 16S, metatranscriptome |
Varoquaux et al. 2019 [45] | Sorghum | Root, leaf | Host rna-seq, ITS |
Gao et al. 2020 [44] | Sorghum | Soil, rhizosphere, root, leaf | Host rna-seq, ITS |
VÃlchez et al. 2020 [66] | Arabidopsis | Root | Plant and bacteria RNA quantification with qPCR, root exudates, host methylation |
Ichihashi et al. 2020 [67] | Brassica rapa | Soil, rhizosphere, root | Ionomics, metabolomics, phenome, 16S |
Zhalnina et al. 2018 [68] | Avena barbata | Rhizosphere | 16S, isolates genomes, root exudates, exometabolomics, bacterial metabolites |
Harbort et al. 2020 [15] | Arabidopsis | Root | 16S, host RNA-seq |
Finkel et al. 2019 [9] | Arabidopsis | Shoot, root, seedling | 16S, host RNA-seq |