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 M. melodia. 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 M. melodia genome. Supplemental Figure S3 contains comparison of M. melodia genome assembly with genome assemblies of related birds.补充文件S1收录了RepeatModeler的提交运行脚本。补充文件S2包含运行GMATA所用的主配置文件（default_cfg.txt）。补充文件S3收录了MAKER的提交运行脚本。补充文件S4包含MAKER可执行文件配置文件（maker_exe.ctl）。补充文件S5包含BLAST与Exonerate比对结果的下游过滤标准（maker_bopts.ctl）。补充文件S6收录了MAKER专属选项的主配置文件（maker_opts.ctl）。补充文件S7包含用于训练SNAP的脚本。补充文件S8收录了用于训练Augustus的脚本。补充文件S9包含用于对预测基因开展功能注释的BLASTP与InterProScan运行脚本，以及将功能注释信息添加至基因注释文件的配套脚本。补充文件S10收录了BUSCO的提交运行脚本。补充文件S11包含JupiterPlot流程的提交运行脚本。补充文件S12收录了tRNAscan-SE的提交运行脚本。补充文件S13包含Infernal的提交运行脚本。补充文件S14收录了预测转座因子的分类结果。补充文件S15包含微卫星的基因组位置注释信息。补充文件S16收录了基因组中不同类型微卫星的占比数据。补充文件S17包含基因组各支架（scaffold）中微卫星的出现频率数据。补充文件S18收录了微卫星的长度分布数据。补充文件S19包含通过BLASTP分析得到的预测基因功能注释结果。补充文件S20收录了通过InterProScan分析得到的预测基因蛋白质结构域、基因本体（GO）注释及通路注释结果。补充文件S21收录了歌带鹀（song sparrow）基因组中鉴定得到的转运RNA（tRNA）序列与结构信息。补充文件S22收录了预测tRNA的分类结果。补充文件S23包含通过Infernal预测得到的基因组内各类非编码RNA（ncRNA）的分类结果。补充文件S24收录了用于筛查歌带鹀基因组重复序列的定制化重复序列库。补充表S1收录了与歌带鹀（M. melodia）相关的鸟类基因组大小数据。补充图S1展示了携带对应AED评分的注释基因的占比分布情况。补充图S2展示了歌带鹀基因组内微卫星基序的优势碱基组成分布情况。补充图S3展示了歌带鹀基因组组装结果与近缘鸟类基因组组装结果的对比情况。