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Additional file 4: Supplementary material 4. The details of multi-omics analysis.

Additional file 2: Figure S1. Volcano plot of differentially expressed genes in (A) liver and (B) pancreas. Each dot represents one gene. Red dots represent up-regulated differentially expressed genes, and blue dots represent down-regulated differentially expressed genes. Grey dots represent no significantly biased gene. The number at the top right represented the number of DEGs in pairwise comparison. Figure S2. The expression level of genes calculated by qRT-PCR.Y-axis represents relative expression levels of each gene by using 2−ΔΔCT method. Figure S3. (A) The methylation degree in promoters for convergently expressed nutrition metabolism-related genes in liver samples. (B) The methylation degree in promoters for convergently expressed nutrition metabolism-related genes inpancreas samples. Y-axis represents methylation levels in promoters. * indicates P < 0.05 between the comparison, ** indicates P < 0.01 between the comparison, *** indicates P < 0.001 between the comparison, **** indicates P < 0.0001 between the comparison. Figure S4. Distributions of coefficient of variance of gene expression levels among liver and pancreas samples before and after normalization, for all 1:1 single-copy orthologues. Histogram was created with a density scale. A normal density curve was added to the histogram to make the distribution of CV more appealing. Figure S5. The ORF and amino acid sequence of giant panda NR3C1 gene.

Nocardiosis is a rare but life-threatening infection particularly affecting immuno-compromised hosts, causing localized or systemic suppurative disease usually in human beings. Nocardia species, as the pathogen of nocardiosis, are difficult to differentiate because of their complex colony morphological features. In this study, we describe two patients who had been misdiagnosed for a long time infected with Nocardia cyriacigeorgica with completely different morphology were accurately diagnosed. Single colonies were analyzed by Gram staining, acid-fast stain, mass spectrometry and whole genome resequencing (WGRS). These two bacterial, strains L5.53 and L5.54, were found to be Gram-negative and acid-fast-weak positive. Blood sample culturing of strain L5.53 yielded white colonies, which were like a layer of hoarfrost, while colonies of L5.54 were yellow, rough, slightly convex. The two strains were identified as Nocardia sp. by mass spectrometry, and WGRS accurately determined them as N. cyriacigeorgica. After medical treatment, one patient was cured and the other was still receiving treatment in the hospital. It can be seen that Nocardia sp. cannot be accurately classified and identified only by phenotypic tests such as bacterial morphological differences, so it is necessary to identify Nocardia spp. with phenotypic tests in combination with other molecular biology technologies, such as WGRS.

Additional file 1: Table S1. The summary of information of RMs. Table S2. The antibiotic resistant profiles of isolates from RMs

Additional file 2: Figure S1. The gut microbiome of chronic diarrhea RMs and asymptomatic RMs. Figure S2. The functional comparison of gut microbiome. Figure S3. The gut bacterial composition of NHPs and human. Figure S4. The antibiotic resistance in gut microbiome of asymptomatic and chronic diarrhea RMs.

The grey wolf (Canis lupus) is one of the most widely distributed mammals in which a variety of distinct populations have been described. However, given their currently fragmented distribution and recent history of human-induced population decline, little is known about the events that led to their differentiation. Based on the analysis of whole canid genomes, we examined the divergence times between Southern European wolf populations and their ancient demographic history. We found that all present-day Eurasian wolves share a common ancestor ca 36 000 years ago, supporting the hypothesis that all extant wolves derive from a single population that subsequently expanded after the Last Glacial Maximum. We also estimated that the currently isolated European populations of the Iberian Peninsula, Italy and the Dinarics-Balkans diverged very closely in time, ca 10 500 years ago, and maintained negligible gene flow ever since. This indicates that the current genetic and morphological distinctiveness of Iberian and Italian wolves can be attributed to their isolation dating back to the end of the Pleistocene, predating the recent human-induced extinction of wolves in Central Europe by several millennia.

Robinson_et_al_IslandFox_2016_author_version.pdf: Author's version of manuscript, "Genomic Flatlining in the Endangered Island Fox" by Robinson et al. Robinson_et_al_IslandFox_2016_supplement.pdf: Supplemental figures, tables, and text. Robinson_et_al_IslandFox_DataS1_speciespi.xlsx: Supplemental table containing previously published estimates of pi across 159 eukaryotic species, used for Figure 1C of main text. Robinson_et_al_IslandFox_DataS2_peakcoordinates.xlsx: Supplemental table containing coordinates of peaks of heterozygosity in sevenisland foxes and one gray fox. Citation:Robinson, J.A., Ortega-Del Vecchyo, D., Fan, Z., Kim, B.Y., vonHoldt, B.M., Marsden, C.D., Lohmueller, K.E. and Wayne, R.K., 2016. Genomic Flatlining in the Endangered Island Fox. Current Biology, 26(9), pp.1183-1189. Note: Raw sequence reads (fastq files) have been deposited in the NCBI Sequence Read Archive under BioProject PRJNA312115.