Additional file 4: of Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Supplementary datasets S8–S11. (XLS 395 kb

Additional file 5: of Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Supplementary datasets S12–S24. (XLS 2190 kb

Additional file 3: of Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Supplementary datasets S5–S7. (XLS 20553 kb

Additional file 2: of Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Supplemental datasheets. Datasheet S1: Summary of the annotation of the human and felid degradomes. Datasheet S2: List of orphan genes with expression levels in different organs. Datasheet S3: List of potential chromosomal rearrangements with respect to domestic cat. Datasheet S4: Gene Ontology terms enriched in proteins that duplicated at specific points in the lynx, cat, and tiger phylogeny. Datasheet S5: List of putative pseudogenes. Datasheet S6: Partitions identified by Saguaro as yielding alternative topologies from a whole genome alignment of Felidae. Datasheet S7: List of genes with signatures of positive selection. Datasheet S8: List of Gene Ontology terms significantly enriched in windows of high and low diversity in Iberian lynx populations or of high of low difference with respect to Eurasian. (XLSX 340 kb

Additional file 1: of Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Supplemental information. Additional details on methods and results, including additional tables (Tables S1–S37) and figures (Figures S1–S45). Section 1: Samples, libraries and sequencing. Section 2: Genome assembly. Section 3: Genome annotation. Section 4: Functional annotation. Section 5: Manual annotation and comparative analysis of lynx protease genes. Section 6: Transcriptome characterization. Section 7: Evolutionary profiling and expression of lncRNAs. Section 8: Lynx orphan genes. Section 9: Eurasian and Iberian lynx divergence Section 10: Demographic history. Section 11: Karyotype. Section 12: Genome alignments and synteny analysis. Section 13: Phylogenomics. Section 14: Positive selection. Section 15: Transposable elements dynamics. Section 16: Substitution patterns. Section 17: Segmental duplications. Section 18: Variant discovery and genotype calling. Section 19: Runs of homozygosity (ROH) and individual inbreeding. Section 20: Genomic averages of population genetics parameters. Section 21: Variation and divergence at coding sequences. Section 22: X chromosome versus autosomes genetic diversity. Section 23: Patterns of diversity across the genome. Section 24: Linkage disequilibrium. Section 25: The Iberian lynx genome browser. Section 26: References. (PDF 10 MB