Additional file 1 of Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis
Creators: name: Liu, Jian
name: Lindstrom, Anders J.
name: Gong, Xun
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: TableS1. Collectioninformation, morphological classification, vouchers, characteristics andplastome NCBI accessions of the Cycas samples used in this study. Allspecimens are identified by the authors of this study (Anders J. Lindstrom,Jian Liu, and Xun Gong). TableS2. Thebest nucleotide substitution model for the whole plastome (WP) and the partitioned protein-codinggenes (PCGs) datasetsused in Bayesian Inference as determined by PartitionFinder2. TableS3. Plastid genes and functional groups included in the analyses. Genesindicated with asterisk are those with estimated nonsynonymous substitutionrates (dN) lower than 0.0003. TableS4. Theestimated substitution rates, nucleotide diversity, aligned length and numberof variable sites (segregates) and percent of variationsof 82 protein-coding genes in 47 Cycas of this study. Order is ranked bypercent of variation. TableS5. Treedistance between concatenated dataset and gene cluster datasets as inferred bydifferent methods (Bayesian and MaximumLikelihood: ML). Genenames of different clusters can be referred in Table 1. FigureS1. Chloroplastgenome graph of Cycas wadei. Genes on the outside of the large circleare transcribed clockwise and those on the inside are transcribedcounterclockwise. The genes are color-coded based on their function. The dashedarea represents the GC composition of the chloroplast genome. IR (a &amp; b):inverted repeat region a &amp; b; LSC: large single-copy region; SSC: smallsingle-copy region. FigureS2. Globalalignment of 11 Cycas genomes and using mVISTA. Alignment was performedusing C. aenigma as a reference. Grey arrows above thealignment indicate the orientation of genes. Purple bars represent exons, blueones represent introns, and pink ones represent non-coding sequences (CNS). Acut-off of 50% identity was used for the plots. The Y-scale axis represents thepercent identity within 50–100%. FigureS3. Comparison of inverted-repeat (IR) andsingle-copy (SC) borders among 11 Cycas chloroplast genomes from sixsections. Gene annotation or portions are represented by colored boxes. JSA:junction between SSC and IRa; JSB: junction between SSC and IRb; JLA: junctionbetween LSC and Ira; JLB: junction between LSC and IRb. FigureS4. Thetype and distribution of SSRs in the 47 Cycas chloroplast genomes. (a) Theproportion of SSR distribution in different species (b) Number of identifiedSSR motifs in different repeat class types. FigureS5. CombinedML topology inferred by ASTRAL (species tree) for Cycas, with summary ofconflicting and concordant genes. For each branch, the top number indicates thenumber of homologs concordant with the species tree at that node, and thebottom number indicates the number of homologs in conflict with that clade in thespecies tree. The pie charts at each node present the proportion of homologsthat support that clade (blue), the proportion that support the mainalternative for that clade (pink), the proportion that support the remainingalternatives (orange), and the proportion that inform (conflict or support)this clade that have no bootstrap support (grey). FigureS6. Principalcoordinate analyses depicting ordinations of rooted tree topologies (Robinson-Foulds)of four species trees versus six gene-cluster trees. (a): Plots for the firsttwo principal coordinates; (b) Plots for the first and third principalcoordinates. In both plots, a total of 10 trees were obtained from different phylogeneticinference methods (ML: maximum likelihood, BY: Bayesian method) based on allprotein-coding genes (Concatenate_ML: inferred ML tree based onconcatenated genes; Concatenate_BY: inferred Bayesian treebased on concatenated genes; Astral_ML: inferred species tree using ASTRAL-IIIbased on ML gene trees, Astral_BY: inferred species tree using ASTRAL-III basedon Bayesian gene trees), and different gene tree clusters (Clusters 1–3) areplotted. The inset dendrograms reflect the tree distances between the speciestree and the cluster trees revealed by TREESPACE. FigureS7. Inferredphylogenies of Cycas using RaxML based on different concatenated plastidgene clusters obtained by Maximum likelihood and Bayesian gene trees (clusters1-3, see Table 1 for the genes grouped by different methods). FigureS8. Principalcoordinate analyses depicting ordinations of rooted tree topologies (Robinson-Foulds)of two species trees (ASTRAL species tree and concatenated gene tree) versus 11gene trees based on different gene functional groups (see Figure 2 and Table S3 for the group information). (a): Plots for the first two principal coordinates;(b) Plots for the first and third principal coordinates. FigureS9. Inferredphylogenies of Cycas using RaxML based on different concatenatedfunctional gene groups (see Figure 2 and Table S3 for the information of 11genes groups). The three indicated groups correspond to the clusters revealedin Fig. S8.