Phylogenetic relationships and divergence times in bats and mammalian species.

<p>The estimated divergence time (million years ago; MYA) is given at the nodes, with the 95% confidence intervals in parentheses. The calibration times of <i>M</i>. <i>brandtii—H</i>. <i>sapiens</i> (97.5 MYA), and <i>M</i>. <i>brandtii—P</i>. <i>alecto</i> (62.6 MYA) were derived from the TimeTree database. Colored branches and circles represent bat groups (<i>blue</i>: insect-eating microbat, <i>red</i>: fruits-eating mega bat). <i>M</i>. <i>domestica</i>, used as an outgroup species, was excluded in this figure.</p

<i>Myotis</i> bats’ uAACs within melanin associated genes.

<p><i>Myotis</i> bats’ uAACs within melanin associated genes.</p

The summed PROVEAN variant score for top 20 ranked genes. The lower the more significant.

<p>The summed PROVEAN variant score for top 20 ranked genes. The lower the more significant.</p

Additional file 2: Fig. S1. of The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

Estimation of genome size using 17-mers. Fig. S2 The divergence time of avian species. Fig. S3 Specific amino acid changes in the gastric acid secretion associated genes. Fig. S4 Species distribution of BLASTx top hits of cinereous vulture transcripts. Fig. S5 NR protein database properties for the assembled unigenes. Fig. S6 Gene Ontology classifications of cinereous vulture unigenes. Fig. S7 Amino-acid sequence comparison of toll-like receptor 1 of the Griffon and cinereous vultures. (DOCX 2228 kb

Sequencing and mapping statistics of <i>M</i>. <i>rufoniger</i> genome.

<p>Sequencing and mapping statistics of <i>M</i>. <i>rufoniger</i> genome.</p

Demographic history of <i>Myotis</i> bats.

<p><i>T</i>_surf, atmospheric surface air temperature (T indicates temperature, surf indicates surface); RSL, relative sea level; 10 m.s.l.e., 10 m sea level equivalent; g, generation time (years); μ, mutation rate per base pair per year.</p

Additional file 1: Table S1. of The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

Sequencing and analysis statistics of the cinereous vulture’s WGS relative to the bald eagle genome. Table S2 17-mer statistics. Table S3 Summary of SNVs and small indel in the cinereous vulture. Table S4 PSGs list of the Accipitrimorphae using a branch-site model. Table S5 PSGs list of the Accipitrimorphae using a branch model. Table S6 Functional annotation chart of PSGs of the Accipitrimorphae. Table S7 PSGs list of the cinereous vulture using a branch-site model. Table S8 PSGs list of the cinereous vulture using a branch model. Table S9 PSGs list of the turkey vulture using a branch-site model. Table S10 PSGs list of the turkey vulture using a branch model. Table S11 Functional annotation chart of PSGs of the cinereous vulture. Table S12 Functional annotation chart of PSGs of the turkey vulture. Table S13 Unique amino acid changes of the turkey vulture. Table S14 Unique amino acid changes of the cinereous vulture Table S15 Unique amino acid changes of the Accipitridae. Table S16 Unique amino acid changes on sites between Accipitridae and Cathartidae of the digestive system-related proteins. Table S17 Unique amino acid changes on sites between Accipitridae and Cathartidae of the gastric acid secretion-related proteins. Table S18 Statistics regarding whole-transcriptome sequences and unigene construction. Table S19 GO analysis for the blood transcriptome of the cinereous vulture. Table S20 KEGG pathway analysis for the blood transcriptome of the cinereous vulture. Table S21 Gene expression in the cinereous vulture compared to the other avian species. Table S22 Immune related genes expression in the cinereous vulture compared to the other avian species. (XLSX 635 kb

NY-ESO-1 expression in DCIS: A new predictor of good prognosis

BACKGROUND: At present, it is difficult to predict which patients with ductal carcinoma-in-situ (DCIS) will subsequently develop frank invasive breast cancer (IDC). A recent survey by our group has shown that NY-ESO-1 and MAGEA are both expressed in DCIS. This study was aimed at determining whether expression of these antigens was related to the later development of IDC. RESULTS: 14 of 42 (33%) of patients developed invasive breast cancer during the follow up period. Only one of those DCIS cases that relapsed was positive for NYESO-1 at diagnosis. In contrast, DCIS samples of 15 of the 28 (54%) of those patients who remained disease-free expressed NY-ESO-1. (Permutation chi square p=0.0033). METHODS: We identified 42 patients with DCIS, and followed them up for more than 10 years. NY-ESO-1 and MAGEA were demonstrated by immunostaining as were CD8+ infiltrates on all sections together with the conventional markers, ER, PR, and HER2. CONCLUSIONS: Expression of NY-ESO-1 may predict those patients who will not subsequently develop invasive breast cancer and could therefore potentially be helpful in defining prognosis in patients with DCIS

Additional file 2: Figure S1. of Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Species and sub-species identification for three leopard samples. Figure S2. Distribution of K-mer frequency in the error-corrected reads. Figure S3. GC content distributions. Figure S4. Composition of mammalian orthologous genes. Figure S5. Divergence time estimation of 18 mammals. Figure S6. Contraction of the amylase gene families (AMY1 and AMY2) in carnivores. Figure S7. Frame-shift mutations in Felidae GCKR genes. Figure S8. Felidae-specific amino acid changes in DNA repair system. Figure S9. Felidae-specific amino acid change in MEP1A protein. Figure S10. Felidae-specific amino acid change in ACE2 protein. Figure S11. Felidae-specific amino acid change in PRCP protein. (DOCX 2024 kb

Additional file 2: Figure S1. of Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Species and sub-species identification for three leopard samples. Figure S2. Distribution of K-mer frequency in the error-corrected reads. Figure S3. GC content distributions. Figure S4. Composition of mammalian orthologous genes. Figure S5. Divergence time estimation of 18 mammals. Figure S6. Contraction of the amylase gene families (AMY1 and AMY2) in carnivores. Figure S7. Frame-shift mutations in Felidae GCKR genes. Figure S8. Felidae-specific amino acid changes in DNA repair system. Figure S9. Felidae-specific amino acid change in MEP1A protein. Figure S10. Felidae-specific amino acid change in ACE2 protein. Figure S11. Felidae-specific amino acid change in PRCP protein. (DOCX 2024 kb