Supporting data for "Taxonomic structure and functional association of foxtail millet root microbiome"

Dataset type: Metagenomic
Data released on September 11, 2017

Jin T; Wang Y; Huang Y; Xu J; Zhang P; Wang N; Liu X; Chu H; Liu G; Jiang H; Li Y; Xu J; Kristiansen K; Xiao L; Zhang Y; Zhang G; Du G; Zhang H; Zou H; Zhang H; Jie Z; Liang S; Jia H; Wan J; Lin D; Li J; Fan G; Yang H; Wang J; Bai Y; Xu X (2017): Supporting data for "Taxonomic structure and functional association of foxtail millet root microbiome" GigaScience Database. http://dx.doi.org/10.5524/100342

DOI10.5524/100342

The root microbes play pivotal roles in plant productivity, nutrient uptakes and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity.
We determined the bacterial composition of 2,882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from two well-separated geographic locations by 16S rRNA gene amplicon sequencing. We identified 16,109 OTUs, and defined 187 OTUs as shared rhizoplane core OTUs. The β-diversity analysis revealed that microhabitat was the major factor shaping foxtail millet root bacterial community, followed by geographic locations. Large-scale association analysis identified the potential beneficial bacteria correlated with plant high productivity. Besides, the functional prediction revealed specific pathways enriched in foxtail millet rhizoplane bacterial community.

Keywords:

Additional details

Read the peer-reviewed publication(s):

(PubMed: 29050374)

Accessions (data generated as part of this study):

ENA: PRJEB16061





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
YL.BS.B1410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
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YL.BS.B2410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
+
YL.BS.B3410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
+
YL.BS.B4410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
+
YL.BS.B5410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
+
YL.BS.B6410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
+
YL.BS.B7410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
+
YL.BS.B8410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
+
YL.RP.1410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
+
YL.RP.10410658Soil Metagenome soil metagenome Description:Metagenome sequences from foxtail mill...
Analyte type:DNA
Geographic location (country and/or sea,region):Ch...
...
+
Displaying 1-10 of 2882 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Coding sequenceFASTA136.58 MB2017-08-23
TextTEXT9.58 MB2017-08-23
OtherUNKNOWN117.04 KB2017-08-23
OtherUNKNOWN23.05 KB2017-08-23
Mixed archiveTAR1.25 GB2017-08-23
OtherUNKNOWN0.76 KB2017-08-23
Coding sequenceFASTA15.22 MB2017-08-23
TextTEXT244.67 KB2017-08-23
Tabular dataUNKNOWN17.6 KB2017-08-23
TextTEXT179.93 MB2017-08-23
Displaying 1-10 of 16 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China G Chen U1301252
Chinese Academy of Sciences Y Bai XDB11020700 Strategic Priority Research Program
Chinese Academy of Sciences Y Bai QYZDB-SSW-SMC021 Priority Research Program
Date Action
September 11, 2017 Dataset publish
October 17, 2017 Manuscript Link added : 10.1093/gigascience/gix089
May 1, 2020 File size of tools.tar.gz updated
May 1, 2020 File size of clean_data.tar.gz updated
May 1, 2020 gold.fa: additional file attribute added
May 1, 2020 pathway.info: additional file attribute added
May 1, 2020 All_map_ko.list: additional file attribute added
May 1, 2020 degration_maplist: additional file attribute added
May 1, 2020 97_otu_taxonomy.txt: additional file attribute added
May 1, 2020 module.info: additional file attribute added
May 1, 2020 All_module_ko.list: additional file attribute added
May 1, 2020 97_otus.fasta: additional file attribute added
May 1, 2020 File location of gold.fa updated
May 1, 2020 File location of pathway.info updated
May 1, 2020 File location of All_map_ko.list updated
May 1, 2020 File location of degration_maplist updated
May 1, 2020 File location of 97_otu_taxonomy.txt updated
May 1, 2020 File location of module.info updated
May 1, 2020 File location of All_module_ko.list updated
May 1, 2020 File location of 97_otus.fasta updated
June 2, 2021 Link updated : ENA:PRJEB16061
November 9, 2022 Manuscript Link updated : 10.1093/gigascience/gix089
November 14, 2022 Update data type for File 97_otus.fasta updated
November 14, 2022 Data type for File gold.fa updated