Grass Phylogeny Working Group III: data repositoryPhylogenetic analyses of the grass family (Poaceae) using nuclear and plastid data. The data set includes 1153 accessions corresponding to 1133 accepted species. Genomic data was obtained from different sources including target capture, shotgun, transcriptomes and annotated genomes. Nuclear markers (Angiosperm353 gene set) were assembled from short read data using HybPiper or a custom assembly pipeline optimized for low coverage shotgun data. Plastid genes were either retrieved from published plastome sequences or assembled here using getOrganelle. This data set also includes the results of a gene tree-species tree reconciliation analysis using GeneRax. Contact persons:Matheus E. Bianconi ([email protected]), Jan Hackel ([email protected]), Maria S. Vorontsova ([email protected]) Content description1. MetadatagpwgIII_samples_metadata_taxonomy.tsvTab-separated file with details for all 1,702 accessions used in this study. Columns: analysis_ID - ID in nuclear analyses; analysis_ID_plastome - ID in plastome analyses; acc_species - accepted species name; acc_species_author - taxonomic species authority; acc_genus - accepted genus name; acc_genus_author - taxomomic genus authority; publication - associated prior publication; data type - type of sequence data; isolate - laboratory isolate ID; voucher_ID - herbarium voucher ID; germplasm_ID - germplasm collection ID; repo_accession - accession number in public repository; plastome_accession - accession number of assembled plastome sequence; removed_nuclear - reason for removal from nuclear tree, if applicable; removed_plastome - reason for removal from plastome tree, if applicable; soreng2022_genus - genus name in Soreng et al. 2022, https://doi.org/10.1111/jse.12847; subtribe, tribe, subfamily, major.clade - classification according to Soreng et al. 2022.2. Nuclear data- Dataset1 ("main")Number of samples: 1153Number of genes: 331Alignment trimming threshold: gt = 0.1 (removed sites > 90% missing data)Genes per sample: > 166- Dataset2 ("strict trimming")Number of samples: 1153Number of genes: 315Alignment trimming threshold: gt = 0.5 (removed sites > 50% missing data)Genes per sample: > 158- Dataset3 (dataset 1 without shotgun samples)Number of samples: 841Number of genes: 331Alignment trimming threshold: gt = 0.1 (removed sites > 90% missing data)Genes per sample: > 1662.1. Raw sequencesRaw Ang353 sequence assemblies for all samples (pre-trimming and filtering)raw_Ang353_sequences.zip2.2 Nuclear gene alignmentsTrimmed alignments from datasets 1, 2 and 3.alignments_dataset1_main_final.zipalignments_dataset2_strict_trimming_final.zipalignments_dataset3_no_shotgun_final.zip2.3. Nuclear gene treesGene trees inferred using RAxML (GTRCAT, 100 bootstraps) for the alignments from datasets 1, 2 and 3.gene_trees_dataset1_main_final.zipgene_trees_dataset2_strict_trimming_final.zipgene_trees_dataset3_no_shotgun_final.zip2.4. Multigene species treesMultigene species trees obtained using Astral-Pro3 from gene trees for datasets 1, 2 and 3. astralpro_trees.zip, which includes:trees_Ang353_grasses_dataset1_main_gtrcat.astralprotrees_Ang353_grasses_dataset2_strict_trimming_gtrcat.astralprotrees_Ang353_grasses_dataset3_no_shotgun_gtrcat.astralpro3. Gene tree–species tree reconciliationgenerax.zipCompressed zip archive with input files and results, including log files, of the GeneRax reconciliation analysis. One subfolder for each of the four analyses run: "all_tribes", "Andropogoneae", "Bambusoideae", "Triticeae".transfers_reconciliation_analyses.zip, which includes:transfers_all_all_tribes.tsv: Tab-separated file with all transfers inferred with the tribe-level Poaceae reconciliation analysis. Each line represents one transfer inferred.transfers_all_Andropogoneae.tsv: Tab-separated file with all transfers inferred with the Andropogoneae reconciliation analysis. Each line represents one transfer inferred.transfers_all_Bambusoideae.tsv: Tab-separated file with all transfers inferred with the Bambusoideae reconciliation analysis. Each line represents one transfer inferred.transfers_all_Triticeae.tsv: Tab-separated file with all transfers inferred with the Triticeae reconciliation analysis. Each line represents one transfer inferred.transfers_counts_all_tribes.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the tribe-level Poaceae reconciliation analysis.transfers_counts_Andropogoneae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Andropogoneae reconciliation analysis.transfers_counts_Bambusoideae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Bambusoideae reconciliation analysis.transfers_counts_Triticeae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Triticeae reconciliation analysis.4. Plastome dataAlignment and phylogenetic tree from plastome data.plastome_files.zip, which includesreduced_plastome_concat_CDS_trnLtrnF_trimmed.fna-out.fas: FASTA file with the final, concatenated DNA alignment of 71 plastome regions for 910 accessions, after data filtering.partitions.txt: Text file with positions of the 71 plastome regions in the concatenated alignment.plastome_concat_CDS_trnLtrnF_trimmed_TBE.raxml.support: Plastome tree with Transfer Bootstrap Expectation values as node labels.RAxML_bipartitions.plastome_concat_CDS_trnLtrnF_trimmed: Maximum likelihood plastome tree inferred with RAxML, with Felsenstein bootstrap values as node labels.RAxML_bootstrap.plastome_concat_CDS_trnLtrnF_trimmed: 100 rapid bootstrap pseudoreplicate plastome trees inferred with RAxML.RAxML_info.plastome_concat_CDS_trnLtrnF_trimmed: RAxML analysis log file.nuc_plastome_matching_tips.tab: Tab-separated file with accessions matched in nuclear-plastome comparison.5. Poaceae-specific reference Ang353 datasetReference sequence dataset used for the assembly of Ang353 sequences in this study.target_Ang353_sequences_grasses.zip6. Shotgun assembly scriptCustom script used for the assembly of Ang353 sequences from shotgun datashotgun_assembler_script.zip, which includes:shotgun_assembler_Ang353_sequences.sh: script for assembly of short reads from shotgun datatemplate_manifest_file.tsv: TAB-separated file to specify sample names and location of short read files (required by the assembly script)list_Ang353_genes_orthofinder.txt: list of Ang353 gene identifiers (required by the assembly script)7. Quartet metrics scriptR script to calculate the Quartet Concordance (QC) and Quartet Differential (QD) metrics from the gene tree frequencies/proportions for each quartet at a branch, following Pease et al. 2018 (American Journal of Botany, https://doi.org/10.1002/ajb2.1016).quartet_metrics.R

Grass Phylogeny Working Group III: data repositoryPhylogenetic analyses of the grass family (Poaceae) using nuclear and plastid data. The data set includes 1153 accessions corresponding to 1133 accepted species. Genomic data was obtained from different sources including target capture, shotgun, transcriptomes and annotated genomes. Nuclear markers (Angiosperm353 gene set) were assembled from short read data using HybPiper or a custom assembly pipeline optimized for low coverage shotgun data. Plastid genes were either retrieved from published plastome sequences or assembled here using getOrganelle. This data set also includes the results of a gene tree-species tree reconciliation analysis using GeneRax. Contact persons:Matheus E. Bianconi ([email protected]), Jan Hackel ([email protected]), Maria S. Vorontsova ([email protected]) Content description1. MetadatagpwgIII_samples_metadata_taxonomy.tsvTab-separated file with details for all 1,702 accessions used in this study. Columns: analysis_ID - ID in nuclear analyses; analysis_ID_plastome - ID in plastome analyses; acc_species - accepted species name; acc_species_author - taxonomic species authority; acc_genus - accepted genus name; acc_genus_author - taxomomic genus authority; publication - associated prior publication; data type - type of sequence data; isolate - laboratory isolate ID; voucher_ID - herbarium voucher ID; germplasm_ID - germplasm collection ID; repo_accession - accession number in public repository; plastome_accession - accession number of assembled plastome sequence; removed_nuclear - reason for removal from nuclear tree, if applicable; removed_plastome - reason for removal from plastome tree, if applicable; soreng2022_genus - genus name in Soreng et al. 2022, https://doi.org/10.1111/jse.12847; subtribe, tribe, subfamily, major.clade - classification according to Soreng et al. 2022.2. Nuclear data- Dataset1 ("main")Number of samples: 1153Number of genes: 331Alignment trimming threshold: gt = 0.1 (removed sites > 90% missing data)Genes per sample: > 166- Dataset2 ("strict trimming")Number of samples: 1153Number of genes: 315Alignment trimming threshold: gt = 0.5 (removed sites > 50% missing data)Genes per sample: > 158- Dataset3 (dataset 1 without shotgun samples)Number of samples: 841Number of genes: 331Alignment trimming threshold: gt = 0.1 (removed sites > 90% missing data)Genes per sample: > 1662.1. Raw sequencesRaw Ang353 sequence assemblies for all samples (pre-trimming and filtering)raw_Ang353_sequences.zip2.2 Nuclear gene alignmentsTrimmed alignments from datasets 1, 2 and 3.alignments_dataset1_main_final.zipalignments_dataset2_strict_trimming_final.zipalignments_dataset3_no_shotgun_final.zip2.3. Nuclear gene treesGene trees inferred using RAxML (GTRCAT, 100 bootstraps) for the alignments from datasets 1, 2 and 3.gene_trees_dataset1_main_final.zipgene_trees_dataset2_strict_trimming_final.zipgene_trees_dataset3_no_shotgun_final.zip2.4. Multigene species treesMultigene species trees obtained using Astral-Pro3 from gene trees for datasets 1, 2 and 3. astralpro_trees.zip, which includes:trees_Ang353_grasses_dataset1_main_gtrcat.astralprotrees_Ang353_grasses_dataset2_strict_trimming_gtrcat.astralprotrees_Ang353_grasses_dataset3_no_shotgun_gtrcat.astralpro3. Gene tree–species tree reconciliationgenerax.zipCompressed zip archive with input files and results, including log files, of the GeneRax reconciliation analysis. One subfolder for each of the four analyses run: "all_tribes", "Andropogoneae", "Bambusoideae", "Triticeae".transfers_reconciliation_analyses.zip, which includes:transfers_all_all_tribes.tsv: Tab-separated file with all transfers inferred with the tribe-level Poaceae reconciliation analysis. Each line represents one transfer inferred.transfers_all_Andropogoneae.tsv: Tab-separated file with all transfers inferred with the Andropogoneae reconciliation analysis. Each line represents one transfer inferred.transfers_all_Bambusoideae.tsv: Tab-separated file with all transfers inferred with the Bambusoideae reconciliation analysis. Each line represents one transfer inferred.transfers_all_Triticeae.tsv: Tab-separated file with all transfers inferred with the Triticeae reconciliation analysis. Each line represents one transfer inferred.transfers_counts_all_tribes.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the tribe-level Poaceae reconciliation analysis.transfers_counts_Andropogoneae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Andropogoneae reconciliation analysis.transfers_counts_Bambusoideae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Bambusoideae reconciliation analysis.transfers_counts_Triticeae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Triticeae reconciliation analysis.4. Plastome dataAlignment and phylogenetic tree from plastome data.plastome_files.zip, which includesreduced_plastome_concat_CDS_trnLtrnF_trimmed.fna-out.fas: FASTA file with the final, concatenated DNA alignment of 71 plastome regions for 910 accessions, after data filtering.partitions.txt: Text file with positions of the 71 plastome regions in the concatenated alignment.plastome_concat_CDS_trnLtrnF_trimmed_TBE.raxml.support: Plastome tree with Transfer Bootstrap Expectation values as node labels.RAxML_bipartitions.plastome_concat_CDS_trnLtrnF_trimmed: Maximum likelihood plastome tree inferred with RAxML, with Felsenstein bootstrap values as node labels.RAxML_bootstrap.plastome_concat_CDS_trnLtrnF_trimmed: 100 rapid bootstrap pseudoreplicate plastome trees inferred with RAxML.RAxML_info.plastome_concat_CDS_trnLtrnF_trimmed: RAxML analysis log file.nuc_plastome_matching_tips.tab: Tab-separated file with accessions matched in nuclear-plastome comparison.5. Poaceae-specific reference Ang353 datasetReference sequence dataset used for the assembly of Ang353 sequences in this study.target_Ang353_sequences_grasses.zip6. Shotgun assembly scriptCustom script used for the assembly of Ang353 sequences from shotgun datashotgun_assembler_script.zip, which includes:shotgun_assembler_Ang353_sequences.sh: script for assembly of short reads from shotgun datatemplate_manifest_file.tsv: TAB-separated file to specify sample names and location of short read files (required by the assembly script)list_Ang353_genes_orthofinder.txt: list of Ang353 gene identifiers (required by the assembly script)7. Quartet metrics scriptR script to calculate the Quartet Concordance (QC) and Quartet Differential (QD) metrics from the gene tree frequencies/proportions for each quartet at a branch, following Pease et al. 2018 (American Journal of Botany, https://doi.org/10.1002/ajb2.1016).quartet_metrics.R

Grass Phylogeny Working Group III: data repositoryPhylogenetic analyses of the grass family (Poaceae) using nuclear and plastid data. The data set includes 1153 accessions corresponding to 1133 accepted species. Genomic data was obtained from different sources including target capture, shotgun, transcriptomes and annotated genomes. Nuclear markers (Angiosperm353 gene set) were assembled from short read data using HybPiper or a custom assembly pipeline optimized for low coverage shotgun data. Plastid genes were either retrieved from published plastome sequences or assembled here using getOrganelle. This data set also includes the results of a gene tree-species tree reconciliation analysis using GeneRax. Contact persons:Matheus E. Bianconi ([email protected]), Jan Hackel ([email protected]), Maria S. Vorontsova ([email protected]) Content description1. MetadatagpwgIII_samples_metadata_taxonomy.tsvTab-separated file with details for all 1,702 accessions used in this study. Columns: analysis_ID - ID in nuclear analyses; analysis_ID_plastome - ID in plastome analyses; acc_species - accepted species name; acc_species_author - taxonomic species authority; acc_genus - accepted genus name; acc_genus_author - taxomomic genus authority; publication - associated prior publication; data type - type of sequence data; isolate - laboratory isolate ID; voucher_ID - herbarium voucher ID; germplasm_ID - germplasm collection ID; repo_accession - accession number in public repository; plastome_accession - accession number of assembled plastome sequence; removed_nuclear - reason for removal from nuclear tree, if applicable; removed_plastome - reason for removal from plastome tree, if applicable; soreng2022_genus - genus name in Soreng et al. 2022, https://doi.org/10.1111/jse.12847; subtribe, tribe, subfamily, major.clade - classification according to Soreng et al. 2022.2. Nuclear data- Dataset1 ("main")Number of samples: 1153Number of genes: 331Alignment trimming threshold: gt = 0.1 (removed sites > 90% missing data)Genes per sample: > 166- Dataset2 ("strict trimming")Number of samples: 1153Number of genes: 315Alignment trimming threshold: gt = 0.5 (removed sites > 50% missing data)Genes per sample: > 158- Dataset3 (dataset 1 without shotgun samples)Number of samples: 841Number of genes: 331Alignment trimming threshold: gt = 0.1 (removed sites > 90% missing data)Genes per sample: > 1662.1. Raw sequencesRaw Ang353 sequence assemblies for all samples (pre-trimming and filtering)raw_Ang353_sequences.zip2.2 Nuclear gene alignmentsTrimmed alignments from datasets 1, 2 and 3.alignments_dataset1_main_final.zipalignments_dataset2_strict_trimming_final.zipalignments_dataset3_no_shotgun_final.zip2.3. Nuclear gene treesGene trees inferred using RAxML (GTRCAT, 100 bootstraps) for the alignments from datasets 1, 2 and 3.gene_trees_dataset1_main_final.zipgene_trees_dataset2_strict_trimming_final.zipgene_trees_dataset3_no_shotgun_final.zip2.4. Multigene species treesMultigene species trees obtained using Astral-Pro3 from gene trees for datasets 1, 2 and 3. astralpro_trees.zip, which includes:trees_Ang353_grasses_dataset1_main_gtrcat.astralprotrees_Ang353_grasses_dataset2_strict_trimming_gtrcat.astralprotrees_Ang353_grasses_dataset3_no_shotgun_gtrcat.astralpro3. Gene tree–species tree reconciliationgenerax.zipCompressed zip archive with input files and results, including log files, of the GeneRax reconciliation analysis. One subfolder for each of the four analyses run: "all_tribes", "Andropogoneae", "Bambusoideae", "Triticeae".transfers_reconciliation_analyses.zip, which includes:transfers_all_all_tribes.tsv: Tab-separated file with all transfers inferred with the tribe-level Poaceae reconciliation analysis. Each line represents one transfer inferred.transfers_all_Andropogoneae.tsv: Tab-separated file with all transfers inferred with the Andropogoneae reconciliation analysis. Each line represents one transfer inferred.transfers_all_Bambusoideae.tsv: Tab-separated file with all transfers inferred with the Bambusoideae reconciliation analysis. Each line represents one transfer inferred.transfers_all_Triticeae.tsv: Tab-separated file with all transfers inferred with the Triticeae reconciliation analysis. Each line represents one transfer inferred.transfers_counts_all_tribes.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the tribe-level Poaceae reconciliation analysis.transfers_counts_Andropogoneae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Andropogoneae reconciliation analysis.transfers_counts_Bambusoideae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Bambusoideae reconciliation analysis.transfers_counts_Triticeae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Triticeae reconciliation analysis.4. Plastome dataAlignment and phylogenetic tree from plastome data.plastome_files.zip, which includesreduced_plastome_concat_CDS_trnLtrnF_trimmed.fna-out.fas: FASTA file with the final, concatenated DNA alignment of 71 plastome regions for 910 accessions, after data filtering.partitions.txt: Text file with positions of the 71 plastome regions in the concatenated alignment.plastome_concat_CDS_trnLtrnF_trimmed_TBE.raxml.support: Plastome tree with Transfer Bootstrap Expectation values as node labels.RAxML_bipartitions.plastome_concat_CDS_trnLtrnF_trimmed: Maximum likelihood plastome tree inferred with RAxML, with Felsenstein bootstrap values as node labels.RAxML_bootstrap.plastome_concat_CDS_trnLtrnF_trimmed: 100 rapid bootstrap pseudoreplicate plastome trees inferred with RAxML.RAxML_info.plastome_concat_CDS_trnLtrnF_trimmed: RAxML analysis log file.nuc_plastome_matching_tips.tab: Tab-separated file with accessions matched in nuclear-plastome comparison.5. Poaceae-specific reference Ang353 datasetReference sequence dataset used for the assembly of Ang353 sequences in this study.target_Ang353_sequences_grasses.zip6. Shotgun assembly scriptCustom script used for the assembly of Ang353 sequences from shotgun datashotgun_assembler_script.zip, which includes:shotgun_assembler_Ang353_sequences.sh: script for assembly of short reads from shotgun datatemplate_manifest_file.tsv: TAB-separated file to specify sample names and location of short read files (required by the assembly script)list_Ang353_genes_orthofinder.txt: list of Ang353 gene identifiers (required by the assembly script)

Phylogenetic analyses of the grass family (Poaceae) using nuclear and plastid data.  The data set includes 1153 accessions corresponding to 1133 accepted species. Genomic data was obtained from different sources including target capture, shotgun, transcriptomes and annotated genomes. Nuclear markers (Angiosperm353 gene set) were assembled from short read data using HybPiper or a custom assembly pipeline optimized for low coverage shotgun data. Plastid genes were either retrieved from published plastome sequences or assembled here using getOrganelle. This data set also includes the results for a gene tree-species tree reconciliation analysis using GeneRax.

PREMISE OF THE STUDY: The grass tribe Paniceae includes important food, forage, and bioenergy crops such as switchgrass, napiergrass, various millet species, and economically important weeds. Paniceae are also valuable for answering scientific and evolutionary questions about C4 photosynthetic evolution, drought tolerance, and spikelet variation. However, the phylogeny of the tribe remains incompletely resolved. METHODS: Forty-five taxa were selected from across the tribe Paniceae and outgroups for genome survey sequencing (GSS). These data were used to build a phylogenetic tree of the Paniceae based on 102 markers (78 chloroplast, 22 mitochondrial, 2 nrDNA). Ancestral state reconstruction analyses were also performed within the Paniceae using both the traditional and two subtype classification systems to test hypotheses of C4 subtype evolution. KEY RESULTS: The phylogenetic tree resolves many areas of the Paniceae with high support and provides insight into the origin and number of C4 evolution events within the tribe. The recovered phylogeny and ancestral state reconstructions support between four and seven independent origins of C4 photosynthesis within the tribe and indicate which species are potentially the closest C3 sister taxa of each of these events. CONCLUSIONS: Although the sequence of evolutionary events that produced multiple C4 subtypes within the Paniceae remains undetermined, the results presented here are consistent with only a subset of currently proposed models. The species used in this study constitute a panel of C3 and C4 grasses that are suitable for further studies on C4 photosynthesis, bioenergy, food and forage crops, and various developmental features of the Paniceae.