|
| Status |
Public on Apr 26, 2021 |
| Title |
Dissecting the co-transcriptome landscape of plants and microbiota |
| Organisms |
Arabidopsis thaliana; Plantibacter sp. Leaf1; Acinetobacter sp. Leaf130; Rhizobium sp. Leaf155; Pedobacter sp. Leaf176; Burkholderia sp. Leaf177; Exiguobacterium sp. Leaf187; Chryseobacterium sp. Leaf404; Arthrobacter sp. Soil763; Flavobacterium sp. Root935 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Interactions between plants and each neighboring microbial species are fundamental building blocks that collectively determine the structure and function of the plant microbiota, but the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant-associated bacteria from all major phyla of the plant microbiota and profiled co-transcriptomes of plants and bacteria. These strains elicited quantitatively different plant transcriptional responses including typical pattern-triggered immunity responses. Genes of non-pathogenic bacteria involved in general metabolism and energy production were commonly suppressed in planta in contrast to a virulent pathogen. Various nutrient acquisition pathways that are frequently encoded in the genomes of plant-associated bacteria were induced in planta in a strain-specific manner, shedding light on bacterial adaptation to the plant environment and identifying a potential driving force of niche separation. Integrative analyses of plant and bacterial transcriptomes suggested that the transcriptional reprogramming of plants is largely uncoupled from that of bacteria at an early stage of interactions. This study provides insights into how plants discriminate among bacterial strains and sets the foundation for in-depth mechanistic dissection of plant-microbiota interactions.
|
| |
|
| Overall design |
Plant RNA-seq: 20 conditions (19 commensal strains and mock control) with 3 biological replicates. Bacterial RNA-seq: 9 commensal strains both in vitro and in planta (18 conditions in total), each condition contains 3 biological replicates.
|
| |
|
| Contributor(s) |
Nobori T, Tsuda K |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 12, 2020 |
| Last update date |
Apr 26, 2021 |
| Contact name |
Tatsuya Nobori |
| E-mail(s) |
tnobori@salk.edu
|
| Phone |
+49-(0)221-5062-302
|
| Organization name |
Max-Planck Institute for Plant Breeding Research
|
| Street address |
Carl-von-Linne Weg 10, Max-Planck Institute for Plant Breeding Research
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platforms (10)
|
| GPL21179 |
Illumina HiSeq 3000 (Arabidopsis thaliana) |
| GPL28522 |
Illumina HiSeq 3000 (Plantibacter sp. Leaf1) |
| GPL28523 |
Illumina HiSeq 3000 (Rhizobium sp. Leaf155) |
| GPL28524 |
Illumina HiSeq 3000 (Pedobacter sp. Leaf176) |
| GPL28525 |
Illumina HiSeq 3000 (Chryseobacterium sp. Leaf404) |
| GPL28526 |
Illumina HiSeq 3000 (Exiguobacterium sp. Leaf187) |
| GPL28527 |
Illumina HiSeq 3000 (Acinetobacter sp. Leaf130) |
| GPL28528 |
Illumina HiSeq 3000 (Burkholderia sp. Leaf177) |
| GPL28529 |
Illumina HiSeq 3000 (Flavobacterium sp. Root935) |
| GPL28530 |
Illumina HiSeq 3000 (Arthrobacter sp. Soil763) |
|
| Samples (125)
|
|
| Relations |
| BioProject |
PRJNA632011 |
| SRA |
SRP261329 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150422_GCA_001423205.1_Leaf130_cds_from_genomic.fna.gz |
1.2 Mb |
(ftp)(http) |
FNA |
| GSE150422_GCF_001421315.1_Leaf1_cds_from_genomic.fna.gz |
1.2 Mb |
(ftp)(http) |
FNA |
| GSE150422_GCF_001423925.1_Leaf187_cds_from_genomic.fna.gz |
1.0 Mb |
(ftp)(http) |
FNA |
| GSE150422_GCF_001424145.1_Leaf404_cds_from_genomic.fna.gz |
1.2 Mb |
(ftp)(http) |
FNA |
| GSE150422_GCF_001424245.1_Leaf155_cds_from_genomic.fna.gz |
1.5 Mb |
(ftp)(http) |
FNA |
| GSE150422_GCF_001424305.1_Leaf176_cds_from_genomic.fna.gz |
1.4 Mb |
(ftp)(http) |
FNA |
| GSE150422_GCF_001424345.1_Leaf177_cds_from_genomic.fna.gz |
2.0 Mb |
(ftp)(http) |
FNA |
| GSE150422_GCF_001428365.1_Soil763_cds_from_genomic.fna.gz |
1.1 Mb |
(ftp)(http) |
FNA |
| GSE150422_GCF_001429295.1_Root935_cds_from_genomic.fna.gz |
1.5 Mb |
(ftp)(http) |
FNA |
| GSE150422_L130_combined.txt.gz |
38.4 Kb |
(ftp)(http) |
TXT |
| GSE150422_L155_combined.txt.gz |
45.4 Kb |
(ftp)(http) |
TXT |
| GSE150422_L176_combined.txt.gz |
43.7 Kb |
(ftp)(http) |
TXT |
| GSE150422_L177_combined.txt.gz |
57.8 Kb |
(ftp)(http) |
TXT |
| GSE150422_L187_combined.txt.gz |
29.3 Kb |
(ftp)(http) |
TXT |
| GSE150422_L1_combined.txt.gz |
32.7 Kb |
(ftp)(http) |
TXT |
| GSE150422_L404_combined.txt.gz |
37.1 Kb |
(ftp)(http) |
TXT |
| GSE150422_R935_combined.txt.gz |
40.3 Kb |
(ftp)(http) |
TXT |
| GSE150422_S763_combined.txt.gz |
32.4 Kb |
(ftp)(http) |
TXT |
| GSE150422_annotation_comb_Leaf1.txt.gz |
76.0 Kb |
(ftp)(http) |
TXT |
| GSE150422_annotation_comb_Leaf130.txt.gz |
79.5 Kb |
(ftp)(http) |
TXT |
| GSE150422_annotation_comb_Leaf155.txt.gz |
98.4 Kb |
(ftp)(http) |
TXT |
| GSE150422_annotation_comb_Leaf176.txt.gz |
81.6 Kb |
(ftp)(http) |
TXT |
| GSE150422_annotation_comb_Leaf177.txt.gz |
130.5 Kb |
(ftp)(http) |
TXT |
| GSE150422_annotation_comb_Leaf187.txt.gz |
73.2 Kb |
(ftp)(http) |
TXT |
| GSE150422_annotation_comb_Leaf404.txt.gz |
70.2 Kb |
(ftp)(http) |
TXT |
| GSE150422_annotation_comb_Root935.txt.gz |
85.1 Kb |
(ftp)(http) |
TXT |
| GSE150422_annotation_comb_Soil763.txt.gz |
71.3 Kb |
(ftp)(http) |
TXT |
| GSE150422_plant_count.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...