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Supplemental Data

File Name Description Download Link
Figure S1 Supplemental microscope images for all chicken-scarlet macaw Zoo-FISH experiments, including the identification of telometric (TTAGGG) sequences and the 18S, 28S and 5.8S rRNA genes in the scarlet macaw genome, localization of telometric repeat sequences and inverted DAPI-banding, and lastly, the location of NORs in 2 pairs of microchromosomes (arrows,left) and inverted DAPI-banding (right) Download PPTX (4.74 MB)
Table S1 Scarlet macaw simple de novo assembly statistics Download XSLX (34.27 MB)
Table S2 Scarlet macaw scaffolded de novo assembly statistics Download XSLX (22.68 MB)
Table S3 Scarlet macaw simple de novo contig positions in the scaffolded assembly Download XSLX (18.21 MB)
Table S4 Summary of the simple de novo scarlet macaw comparative genome alignments using blastn Download XLSX (54.13MB)
Table S5 Summary of the scaffolded de novo scarlet macaw comparative genome alignments using blastn Download XLSX (37.42MB)
Table S6 Summary of repeats predicted in the scarlet macaw simple de novo assembly using RepeatMasker Download ZIP (10.16 MB)
Table S7 Summary of repeats predicted in the scarlet macaw scaffolded de novo assembly using RepeatMasker Download ZIP (8.74 MB)
Table S8 Summary of scarlet macaw predicted microsatellites within the simple de novo assembly using PHOBOS. The table was split into two parts (S8a,S8b) to reduce file size. Download ZIP (44.26 MB)
Table S9 Summary of scarlet macaw predicted microsattelites within the scaffolded de novo assembly using PHOBOS. The table was split into two parts (S9a, S9b) to reduce file size. Download ZIP (36.64 MB)
Table S10 Summary of scarlet macaw putative SNPs predicted within the simple de novo assembly Download CSV (77.61 MB)
Table S11 Summary of scarlet macaw putative SNPs predicted within the scaffolded de novo assembly Download CSV (75.96 MB)
Table S12 Summary of scarlet macaw putative annotation models and corresponding proteins Download XLSX (13.55 MB)
Table S13 Summary of scarlet macaw functional annotation analysis using DAVID Download XLSX (0.27 MB)
Table S14 Summary of nucleotide-based analysis of divergence Download DOC(0.19 MB)
Table S15 Summary of conserved outlier quality control analysis Download XLSX (0.12 MB)
Table S16 Example of running sum method for quality trimming Download XLSX (0.03 MB)
Dataset S1 GlimmerHMM predictions are available on the genome project website Go to project website