<i>Alnus rubra</i> root nodule metagenome data analysis
Creators: name: Bell, Callum
name: Lewis, Norman G.
name: Davin, Laurence B.
name: Sena, Johnny A.
name: Fajardo, Diego
name: Lavelle, Evan
name: Costa, Michael A.
name: Herman, Barrington
name: Berry, Alison M.
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310509
subject: Genomics

description: There have been frequent reports of more than one strain of the nitrogen-fixing symbiont, <i>Frankia</i>, in the same root nodule of plants in the genus <i>Alnus</i>, but quantitative assessments of their relative contributions have not been made to date. Neither has the diversity of other microbes, having potential functional roles in symbiosis been systematically evaluated. <i>Alnus rubra</i> root nodule microbiota were studied using Illumina short read sequencing and kmer-based read classification. Single end 76 bp sequencing was done to a median depth of 96 million reads per sample. Reads were assigned to taxa using KrakenUniq, with taxon abundances being estimated using its companion program Bracken. This was the first high resolution study of <i>Alnus</i> root nodules using next generation sequencing (NGS), quantifying multiple Cluster 1A <i>Frankia</i> strains in single nodules, and in some cases, a Cluster 4 strain. Root nodules were found to contain diverse bacteria, including several genera containing species known to have growth-promoting effects. Evidence was found for partitioning of some bacterial strains in older versus younger lobes.This repository contains root nodule metagenome sequence analysis related to the project described above. The sequence reads and assembled metagenomes have been placed in NCBI under BioProject PRJNA924029. This repository contains tables too large to be included in the manuscript.The KrakenUniq index is impractical to upload here. Instead, we have included the fasta headers of the sequences (headers.txt) and the NCBI taxonomy files (nodes.dmp and names.dmp) used to construct the index. Combined, these contain all of the information required to replicate our work.<br>Table Descriptions:Table_S1_krakenuniq_frankia_0_kmers.xlsx: kmers assigned by krakenuniq to Frankia strains applying no kmer thresholdTable_S2_krakenuniq_frankia_0_reads.xlsx: reads assigned by krakenuniq to Frankia strains applying no kmer thresholdTable_S3_krakenuniq_frankia_2000_kmers.xlsx: kmers assigned by krakenuniq to Frankia strains applying the 2000 kmers/million reads thresholdTable_S4_krakenuniq_frankia_2000_reads.xlsx: reads assigned by krakenuniq to Frankia strains applying the 2000 kmers/million reads thresholdTable_S5_bracken_frankia_2000_reads.xlsx: reads assigned by bracken to Frankia strains applying the 2000 kmers/million reads thresholdTable_S6_krakenuniq_genus_0_reads.xlsx: kmers assigned by krakenuniq to bacterial genera applying no kmer thresholdTable_S7_krakenuniq_genus_0_kmers.xlsx: reads assigned by krakenuniq to bacterial genera applying no kmer thresholdTable_S8_krakenuniq_genus_2000_reads.xlsx: kmers assigned by krakenuniq to bacterial genera applying the 2000 kmers/million reads thresholdTable_S9_krakenuniq_genus_2000_kmers.xlsx: reads assigned by krakenuniq to bacterial genera applying the 2000 kmers/million reads thresholdTable_S10_bracken_genus_2000_reads.xlsx: reads assigned by bracken to bacterial genera applying the 2000 kmers/million reads thresholdTable_S11_krakenuniq_species_0_kmers.xlsx: kmers assigned by krakenuniq to bacterial species applying no kmer thresholdTable_S12_krakenuniq_species_0_reads.xlsx: reads assigned by krakenuniq to bacterial species applying no kmer thresholdTable_S13_krakenuniq_species_2000_reads.xlsx: reads assigned by krakenuniq to bacterial species applying the 2000 kmers/million reads thresholdTable_S14_krakenuniq_species_2000_kmers.xlsx: kmers assigned by krakenuniq to bacterial species applying the 2000 kmers/million reads thresholdTable_S15_bracken_species_2000_reads.xlsx: kmers assigned by bracken to bacterial species applying the 2000 kmers/million reads thresholdTable_S16_metagenome_glna1_reciprocal_hits.xlsx: metagenome contigs matching glnA1 and their reciprocal best BLASTN hitsTable_S17_genes_cluster_2_only.emapper.annotations.xlsx: eggNOG-Mapper annotations of these Cluster 2-specific gene setsTable_S18_genes_cluster_3_only.emapper.annotations.xlsx: eggNOG-Mapper annotations of these Cluster 3-specific gene setsTable_S19_genes_cluster_4_only.emapper.annotations.xlsx: eggNOG-Mapper annotations of these Cluster 4-specific gene setsTable_S20_Frankia_cluster_2_reciprocal_best_hit_annotations.xlsx: eggNOG-Mapper annotations of Cluster 2 reciprocal best hitsTable_S21_Frankia_cluster_3_reciprocal_best_hit_annotations.xlsx: eggNOG-Mapper annotations of Cluster 3 reciprocal best hitsTable_S22_Frankia_cluster_4_reciprocal_best_hit_annotations.xlsx: eggNOG-Mapper annotations of Cluster 4 reciprocal best hits