Supplemental Material for Louha et al., 2020

Supplemental File S1 contains submission script for RepeatModeler. Supplemental File S2 contains primary configuration file used to run GMATA (default_cfg.txt). Supplemental File S3 contains submission script for MAKER. Supplemental File S4 contains MAKER executable file (maker_exe.ctl). Supplemental File S5 contains specifications for downstream filtering of BLAST and Exonerate alignments (maker_bopts.ctl). Supplemental File S6 contains primary configuration of MAKER specific options (maker_opts.ctl). Supplemental File S7 contains scripts for training SNAP. Supplemental File S8 contains scripts for training Augustus. Supplemental File S9 contains scripts for running BLASTP and InterProScan for functional annotation of predicted genes; and scripts for adding the functional annotations to gene annotation files. Supplemental File S10 contains submission script for BUSCO. Supplemental File S11 contains submission scripts for JupiterPlot pipeline. Supplemental File S12 contains submission script for tRNAscan-SE. Supplemental File S13 contains submission script for Infernal. Supplemental File S14 contains classification of predicted transposable elements. Supplemental File S15 contains annotation of microsatellites with their genomic locations. Supplemental File S16 contains percentage of different microsatellites present in the genome. Supplemental File S17 contains frequency of occurrence of microsatellites in each scaffold of the genome. Supplemental File S18 contains the distribution of the length of microsatellites. Supplemental File S19 contains predicted function of annotated genes by BLASTP. Supplemental File S20 contains prediction of protein domains, GO annotations and pathway annotations of predicted genes by InterProScan. Supplemental File S21 contains sequence and structure of tRNAs identified in the song sparrow genome. Supplemental File S22 contains classification of predicted tRNAs. Supplemental File S23 contains classification of different ncRNAs predicted in the genome with Infernal. Supplemental File S24 contains custom repeat library used to screen for repeats in the song sparrow genome. Supplemental Table S1 contains genome sizes of birds related to <i>M. melodia</i>. Supplemental Figure S1 contains the distribution of the percentage of annotated genes with their corresponding AED scores. Supplemental Figure S2 contains the distribution of the top base-pair composition of microsatellite motifs in the <i>M. melodia</i> genome. Supplemental Figure S3 contains comparison of <i>M. melodia</i> genome assembly with genome assemblies of related birds.