Additional file 2: of NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

Detailed results for Table 1. (TXT 472 kb

Additional file 1: of NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

Figure S1. Reference fragments placement order depending on query fragment orientations during detection of local differences. Figure S2. Circular genome alignment alternatives. Figure S3. Number of differences in each category obtained by NucDiff with the default parameter settings for all assemblers. Figure S4. Comparison of multiple assemblies against one reference using NucDiff. Figure S5. Examples of detection of long deletions located in all assemblies at the same place in the reference sequence. Table S1. Alignment fragmentation cases caused by simple differences. Table S2. Genome modifications implemented during the simulation process. Table S3. List of E. coli genomes used in the Comparison of genomes from different strains of the same species section. Table S4. Parameter values used for each parameter settings. Table S5. Correspondence between the QUAST difference types and the simulated difference types. Table S6. Correspondence between the QUAST, dnadiff and NucDiff difference types and the expected difference types. (PDF 989 kb

Additional file 2: of Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish

Data showing full length analysis of the Illumina de novo brain and intestine transcriptome assembly using BLAST+ and Uniprot as a reference database (release). The metric analysis examines the number of assembled transcripts that appeared to be full length or nearly full length. The first column (#hit_pct_cov_bin %) shows the present coverage in the database. The second column (count_in_bin) shows the number proteins that match a trinity assembly transcript by more than the present given in the table >%. E.g 1554 proteins match a transcript by > 80% and <= 90% of their protein lengths. The third column (>bin_below) shows the number of protein in the reference database that are represented by nearly full length transcripts with a % alignment coverage. (PDF 285 kb

Additional file 9: of Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish

Top ten differentially expressed genes based on fold change (positive or negative) between segment 1 and 4 (Upregulated and downregulated genes in segment 1 compared to 4. The table shows Gene_ID, gene_symbol, Fold change and p-adjust values. (PDF 258 kb

Additional file 1: of Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish

Illumina de novo brain and intestine transcriptome assembly statistics. (PDF 154 kb

Additional file 4: of Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish

The figures shows the genomic region with Ensembl coordinates and flanking genes (Synteny) for mboat4, motilin receptor (mlnr), peptide y a (pyya), peptide y b (pyyb), cholecystokinin a (ccka), cholecystokinin b (cckb). (PDF 333 kb

Additional file 6: of Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish

The table shows the differentially expressed genes between the different segments. Segment 2 versus (vs) 1, 3 vs 1, 4 vs 1, 3 vs 4 and 3 vs 2. Gene IDs, gene symbol, P-values, P-adjust values and Log2 fold change are given in the table. Expression values are given in the sheet labeled “transcriptome” (XLSX 5003 kb

Additional file 7: of Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish

Excel file showing the statistics of the functional enrichment analysis using the DAVID tool. Number of genes counted for each term (count) P-values, list of genes counted (Genes), p adjust values (Benjamini) and % false discovery rate (FDR) are given in the tables. The figure shows enriched gene ontology terms (GOs) (biological function (BF), cellular compartment (CC) and molecular function (MF)) and KEGG pathways in segment 4 (seg4 vs seg1), segment 1 (seg1 vs 4) and segment 3 vs segment 2. It also shows the complete list of terms used for the Revigo analysis. (XLSX 112 kb

Additional file 3: of Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish

Schematic figure showing the strategy for gene search and for deciding whether a gene is present (“Present”) in the wrasse genome or not (“Not present”). (PNG 322 kb

Additional file 1: of Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats

Note S1 and Table S1-S10. (PDF 595 kb