Additional file 1 of Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management
Creators: name: Samaha, Georgina
name: Wade, Claire M.
name: Mazrier, Hamutal
name: Grueber, Catherine E.
name: Haase, Bianca
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology

description: Additional file 1: Table S1. Sequencing and alignment performance for all individual samples and species pools. Cheetah_pool, tiger_pool and snowleopard_pool refer to species pools consisting of 4 multiplexed individuals each. Figure S1. Mapped and total reads across WGS samples and pools. Total number of mapped reads (black) includes singletons and pairs. Number of paired reads mapped indicated by the grey line. Tiger_zoo, snowleopard_zoo and cheetah_zoo refer to multiplexed pool samples. Figure S2. Plots of genome coverage for each sample .bam file aligned to the felCat9 reference assembly for a. cheetah, b. Sumatran tiger and c. snow leopard cohorts. On each panel, the key indicates coloured line of each sample and their sequencing depth in brackets. Table S2. Functional annotation of all fixed and within-species SNPs for each species. Table S3a. Top 20 gene ontology terms (GOterms) enriched for species-specific SNV within cheetahs. P-values were adjusted for multiple testing using Benjamini-Hochberg false discovery rate. Table S3b. Top 20 gene ontology terms (GOterms) enriched for species specific SNVs within Sumatran tigers. P-values were adjusted for multiple testing using Benjamini-Hochberg false discovery rate. Table S4. Genes under positive selection identified as those displaying elevated πNπSratios across all three species. Table S5a. Top 20 gene ontology terms (GOterms) enriched across fixed SNVs in snow leopards. P-values were adjusted for multiple testing using Benjamini-Hochberg FDR (false discovery rate). Table S5b. Top 20 gene ontology terms (GOterms) enriched across fixed SNVs in Sumatran tigers. P-values were adjusted for multiple testing using Benjamini-Hochberg FDR (false discovery rate). Table S6. Multi-species alignment of LCORL (ENSFCAG00000029474) revealed Panthera-specific conservation of six missense variants. Cheetah, snow leopard and Sumatran tiger refer to samples aligned to the domestic cat (felCat9) reference assembly. Protein positions are reported relative to the Ensembl transcript ENSFCAT00000081895.1. Table S7. Protocadherin genes containing fixed non-synonymous SNVs common to all big cat species relative to the domestic cat (felCat9) reference assembly. Table S8. Genes containing deleterious SNVs implicated in heritable conditions affecting big cats grouped by species. Figure S3a. Gene ontology annotation of clinically significant GOterms in cheetahs. Deleterious variants were observed in 201 genes included in custom list of GO terms relevant to known heritable conditions, immune and reproductive function. These genes were annotated for terms relevant to reproductive and immune function. Network interaction graph produced by GOnet ( https://tools.dice-database.org/GOnet/ ). Figure S3b. Gene ontology annotation of clinically significant GOterms in Sumatran tigers. Deleterious variants were observed in 44 genes included in custom list of GO terms relevant to known heritable conditions, immune and reproductive function. These genes were annotated for terms relevant to cilium structure. Network interaction graph produced by GOnet ( https://tools.dice-database.org/GOnet/ ). Table S9. Samples downloaded from Sequence Read Archive (SRA) comprised six cheetahs, one snow leopard and seven Sumatran tigers. Table S10.Genes associated with size in domestic species identified from a literature search. Table S11. Selected GO enrichment terms used to classify deleterious variants potentially implicated in reproductive success and overall health of captive bred big cats. Table S12. Known heritable conditions affecting captive bred big cat species and relevant GO terms.