Additional file 1 of Primary orthologs from local sequence context
Creators: name: Gao, Kun
name: Miller, Jonathan
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences

description: Additional file 1: Figure S1. Match length distributions (MLDs) exhibited by histograms of maxmers for real genome sequences, as well as for synthetic sequences created by the model described in [46, 47]. Red curves in the figure exhibit the MLDs of the given real genome sequences, without any repeat-masking: (a) human whole-genome protein-coding sequences, (b) mouse whole-genome protein-coding sequences, (c) human whole-genome sequences, both protein-coding and non-protein-coding, and (d) mouse whole-genome sequences, both protein-coding and non-protein-coding. Other curves in the figure show MLDs for the synthetic sequences of the same length and the same maximal duplication length as the corresponding real genome sequence; different synthetic sequences are created with different μ/ν ratios. In each subfigure, by comparing the MLD of the real genome sequence to the MLDs of the synthetic sequences, we estimate the μ/ν ratio for the real genome sequence as following: (a) for human protein-coding genes, μ/ν ≈ 1; (b) for mouse protein-coding genes μ/ν ≈ 0.1; (c) and (d), for human and mouse whole-genome sequences, μ/ν is between 0.01 and 0.1. Figure S2. Match length distributions (MLDs) for different chromosomes of human and mouse, as well as for synthetic sequences of the same length and the same maximal duplication length, created by the model described in [46, 47] with different μ/ν ratios. As shown in the figure, the μ/ν ratio is significantly heterogenous within and across genomes; different chromosomes of human and mouse show very different μ/ν ratios, varying from 0.001 (as mouse chromosome Y in subfigure (i)) to over 0.1 (as human chromosome 5 in subfigure (a)). Therefore, the μ/ν ratios selected for the numerical simulations exhibited in Fig. 5 of the main text (μ/ν = 0.001, 0.01, 0.1 and 1) should be typical and realistic for mammalian genomes. Figure S3. Standard deviations indicated by error bars for the Lastz net alignment exhibited in Fig. 5 of the main text. Figure S4. Standard deviations indicated by error bars for the BLAST RBHs exhibited in Fig. 5 of the main text. Figure S5. Standard deviations indicated by error bars for the non-nested EDMs exhibited in Fig. 5 of the main text. Figure S6. Precision and recall of our method derived from numerical simulations, in which each segmental duplication is inserted into the genome rather than substitutes another sequence of the same length in the same genome. Due to computation burden, we only simulate diverged lineages whose similarity is above 20% in a single realization. The result is essentially consistent with that in Fig. 5 of the main text Figure S7. Venn diagrams among non-nested RBHs, BLAST RBHs and Ensembl CBGs between the genomes of human against four different species: (a) gorilla (Gorilla gorilla), (b) cat (Felis catus), (c) chicken (Gallus gallus), (d) anole lizard (Anolis carolinensis), (e) frog (Xenopus tropicalis), (f) zebrafish (Danio rerio), and (g) drosophila (Drosophila melanogaster). From (a) to (g), species are more and more distantly related to human; in this figure we use MUMs longer than 15 nucleotide bases to determine the non-nested RBHs. Estimated by the proportion of non-nested RBHs validated by either BLAST RBHs or Ensembl CBGs, the precision of our method in each subfigure is: (a) 94.5%, (b) 89.6%, (c) 93.8%, (d) 87.5%, (e) 84.7%, (f) 67.6% and (g) 27.8%. Table S1. Statistics for figure S7, exhibiting the precision and recall of non-nested RBHs and BLAST RBHs, benchmarked by Ensembl CBGs. Numbers in the brackets indicate the numbers of RBHs shared between the corresponding sets. Table S2. Performance of a “control experiment” in which mmRBHs are determined by all exact matches (both non-nested and nested). Parameters Lmin refers to the minimal length of exact matches, and P refers to the proportion of hits on genes contributed by non-nested exact matches over those contributed by all exact matches, both weighted by lengths in bases. Precisions and recalls are defined as same as those in Table 3 of the main text, except non-nested RBHs are substituted by mmRBHs determined by all exact matches: “Precision 1:” mmRBHs validated by either BLAST RBHs or Ensembl CBGs; “Precision 2:” mmRBHs validated by both BLAST RBHs and Ensembl CBGs; “Recall 1:” Ensembl CBGs recovered by mmRBHs; “Recall 2:” BLAST RBHs recovered by mmRBHs. Numbers in the brackets indicate the numbers of RBHs (or CBGs) shared by the corresponding sets. For human-chimpanzee, with large Lmin, non-nested exact matches overwhelmingly dominate nested ones in terms of hits on genes; mmRBHs determined by all exact matches and those solely by non-nested exact matches are nearly equivalent. For human-mouse, non-nested exact matches are not as dominant as for human-chimpanzee; therefore, for human-mouse, mmRBHs RBHs determined by all exact matches exhibit much lower precision and recall than those determined by non-nested exact matches. Supplementary Material 1. How to identify non-nested and nested maximal matches with SEQANALYSIS. Supplementary Material 2. Ensembl annotations for human and chimpanzee genes that constitute nonnested RBHs but are not annotated as orthologs by Ensembl Compara.