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On the hybrid origin of the C2 Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages

Citation

Tefarikis, Delphine T. et al. (2022), On the hybrid origin of the C2 Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages , Dryad, Dataset, https://doi.org/10.5061/dryad.xsj3tx9hh

Abstract

C2 photosynthesis is characterized by recapturing photorespiratory CO2 by RuBisCO in Kranz-like cells and is therefore physiologically intermediate between C3 and C4 photosynthesis. C2 can be interpreted as an evolutionary precursor of C4 and/or as the result of hybridization between a C3 and C4 lineage.

We compared the expression of photosynthetic traits among populations of the Salsola divaricata agg. (C2) from humid subtropical to arid habitats on the coasts of the Canary Islands and Morocco and subjected them to salt and drought treatments. We screened for enhanced C4-like expression of traits related to habitat or treatment. We estimated species trees with a transcriptome dataset of Salsoleae and explored patterns of gene tree discordance. With phylogenetic networks and hybridization analyses we tested for hybrid origin of the Salsola divaricata agg.

We observed distinct independent variation of photosynthetic traits within and among populations and no clear evidence for selection towards C4-like trait expression in more stressful habitats or treatments. We found reticulation and gene tree incongruence in Salsoleae supporting a putative hybrid origin of the Salsola divaricata agg.

C2 photosynthesis in the Salsola divaricata agg. combines traits inherited from its C3 and C4 parental lineages and seems evolutionarily stable, possibly well adapted to a wide climatic amplitude.

Usage Notes

DATA PACKAGE FROM TEFARIKIS ET AL (New Phytologist)

On the hybrid origin of the C2 Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages

This package contains the data and software outputs (i.e. fasta files, alignments, trees, etc).

1_transcriptomes_and_genomes:

- final_filtered_transcriptomes:
Coding sequence (CDS) fasta files (*.cds.fa)
Coding sequence (CDS) fasta files clustered with CD-HIT (*cdhitest)
Protein translated (PEP) fasta files (*.pep.fa)     

- genomes:
CDS and PEP fasta files (*.fasta) of Beta vulgaris genome

- original_transcriptome_assemblies:
Fasta files of original Trinity transcriptome assemblies
            
2_final_homologs:

- Tree files (*.tre) of homologs in newick format inferred with RAxML after monophyletic clades and paraphyletic grades of same species were masked, and spurious tips removed with TreeShrink.

3_MO_orthologs:

- Tree files (*.tre) of final MO orthologs in newick format. Orthologs were obtained from final homologs (2_final_homologs)

4_MO_fasta_files_17tx_aln:

- Ortholog DNA alignments (*.aln) obtained with MAFFT in fasta format
- Clean ortholog DNA alignmentsalignments (*aln-cln) from pxclsq in fasta format.

5_concatenated_matrices: Concatenated alignment from 4_MO_fasta_files_17tx_aln

- concatenate_MO_orthologs_300_17_taxon_occupancy_stats - taxon occupancy stats
- concatenate_MO_orthologs_300_17.fa - alignment in fasta format
- concatenate_MO_orthologs_300_17.model - partition file in RAxML format
- concatenate_MO_orthologs_300_17.nex - alignment in nexus format
- concatenate_MO_orthologs_300_17.phy - alignment in phylip format

6_phylogenetic_analyses

- ASTRAL:
all_orthologs_trees.tre - Input tree containing all ortholog trees
astral_all_orthologs_trees_lpp.tre - Species tree output from ASTRAL

- HyDe:
run_hyde_individuals.sh - command used to run HyDe
ind_level_all_sites-out-filtered.txt - filtered output of HyDe
ind_level_all_sites-out.txt - raw output of HyDe
map_ind_level.txt - map file at individual label
concatenate_MO_orthologs_300_17_for_hyde.phy - concatenated alignment of ortholog alignments in phylip format.
    
- Phylonet:
    
1(3)-5_hyb.nex - best networks from each analyses (see Table 2)
astral_fit.nex - nexus file to calculate the ML score of the ASTRAL tree with CalGTProb in PhyloNet
astral_fit.out - ML score of the ASTRAL tree with CalGTProb in PhyloNet
cpdna_fit.nex - nexus file to calculate the ML score of the cpDNA tree
cpdna_fit.out - ML score of the cpDNA tree tree with CalGTProb in PhyloNet
raxml_fit.nex - nexus file to calculate the ML score of the RAxML tree with CalGTProb in PhyloNet
raxml_fit.out - ML score of the RAxML tree with CalGTProb in PhyloNet
phylonet_mpl_(1-5)hyb.nex - PhyloNet nexus input files for searches with 1 to 5 reticulation events.
phylonet_mpl_(1-5)hyb.out - Phylogenetic networks output from PhyloNet for searches with 1 to 5 reticulation events.

- Phyparts:
ASTRAL: output files from Phyparts from the analysis using the ASTRAL tree
directory_of_ortholog_MO_trees_rooted: rerooted orthologs trees in newick format (*.rr)
RAxML: output files from Phyparts from the analysis using the RAxML tree

- QuartetSampling:   
raxml_quartet_sampling: QuartetSampling output files from the analysis using the RAxML tree
astral_quartet_sampling: QuartetSampling output files from the analysis using the ASTRAL tree
    
- RAxML_concatenated

Output files from RAxML for the concatenated alignment.
    
- RAxML_invidivual_gene_trees

Tree files in newick format (*.tre) from RAxML for the individual MO ortholog alignments.

- cpDNA: Input and output files from plastome data set.
IQtree - Input and output files from IQ-Tree for the contiguous cpDNA alignment.
QuartetSampling: Input and output files from Quartet Sampling
aln: Contiguous cpDNA alignment with MAFFT (*aln) and also masked alignment with GBlocks (*.aln-cln)
filtered_contigs_from_cp_assemblies: filtered contigs form partial assemblies in fasta format (*.fasta) for five species of Salsola

- photosynthetic_gene_trees
gene_trees: unrooted (*.ur) and rooted (*reroot) baited gene trees in newick format
AT_baits: Arabidopsis references for baited homology of C4 genes of interest
       
If you have any questions about the data, please do not hesitate to contact Diego F. Morales-Briones at dfmoralesb@gmail.com

Funding