Supporting data for “Chromosome-length genome assembly and linkage map of a Critically Endangered Australian bird: the helmeted honeyeater”. Robledo-Ruiz et al. (2022)

Supporting data for the manuscript: Robledo-Ruiz D. A., Gan H. M., Kaur P., Dudchenko O., Weisz D., Khan R., Lieberman Aiden E., Osipova E., Hiller M., Morales H. E., Magrath M. J. L., Clarke R. H., Sunnucks P. & Pavlova A. (2022) Chromosome-length genome assembly and linkage map of a Critically Endangered Australian bird: the helmeted honeyeater. Data usage: Helmeted honeyeater (Lichenostomus melanops cassidix) nuclear genome annotation GFF and GP files containing the predictive gene annotation of the Helmeted honeyeater nuclear genome. Helmeted_honeyeater_annotation.gff.gz Helmeted_honeyeater_annotation.gp.gz Helmeted honeyeater mitochrondrial genome FASTA file containing the assembly of the Helmeted honeyeater mitochondrial genome. Helmeted_honeyeater_mitogenome.fasta Helmeted honeyeater mitochrondrial genome annotation TBL file containing the predictive gene annotation of the Helmeted honeyeater mitochondrial genome. Helmeted_honeyeater_mitogenome_annotation.tbl Helmeted honeyeater mitochrondrial genome tree Neighbour-joining tree and subtree in newick format of the helmeted honeyeater mitogenome to closest matches based on BLASTn analysis.Helmeted_honeyeater_mitogenome_tree.nwkHelmeted_honeyeater_mitogenome_subtree.nwk Helmeted honeyeater linkage map Pedigree-based linkage map of the Helmeted honeyeater estimated using 53,111 SNPs with Lep-MAP3. Includes chromosomes, sex-averaged genetic distances (cM), sex-specific genetic distances (cM), sex-averaged recombination rates (cM/Mb) and sex-specific recombination rates (cM/Mb). We make available the original genetic map and the map for which negative recombination rates were converted to zeros. Helmeted_honeyeater_geneticMap.txt Helmeted_honeyeater_geneticMap_notConverted.txt Helmeted honeyeater genetic map with sliding window recombination rate Genetic map with sex-averaged genetic distances (cM) and recombination rates (cM/Mb) for non-overlapping windows of width 50Kb, 100Kb and 200Kb inferred from smoothing the Marey Map produced by Lep-MAP3. Helmeted_honeyeater_recombinationRate_50Kb.txt Helmeted_honeyeater_recombinationRate_100Kb.txt Helmeted_honeyeater_recombinationRate_200Kb.txt Helmeted honeyeater BUSCO completeness results Full results of BUSCO completeness (including summary table, full results table, and table of missing genes) for the draft genome, the chromosome-length genome, and the annotation of the chromosome-length genome.Helmeted_honeyeater_BUSCO_DraftGenome.zip Helmeted_honeyeater_BUSCO_ChrLengthGenome.zipHelmeted_honeyeater_BUSCO_annotation.zip 0.GeneticMap_rawDArTs_HiC_HelmetedHoneyeater_Robledo-Ruiz-etal.docxDocument with the process done to produce the linkage and recombination maps for the helmeted honeyeater, including the scripts used. 1.Pedigree.zip Folder containing the pedigree file used as input for Lep-MAP3, and the files and scripts used to assembled it. 2.Lep-MAP3_Genotypes.zip The genotype posterior probabilities file and the called genotypes file obtained with Lep-MAP3. 3.Lep-MAP3_LOD.zip The files produced by Lep-MAP3 modules SeparateChromosomes2 and JoinSingles2All testing different LOD scores. Scripts and plots produces are also included. 4.LASTZ_Mapping_ZF.zip Scripts, output and plots from the synteny analysis by aligning the helmeted honeyeater genome to zebra finch, collared flycatcher and superb fairy-wren genomes using LASTZ. 5.MareyMap_LG.zip Files and scripts from processing the Marey maps per Linkage Group.

本数据集为论文《Robledo-Ruiz D.A.、Gan H.M.、Kaur P.、Dudchenko O.、Weisz D.、Khan R.、Lieberman Aiden E.、Osipova E.、Hiller M.、Morales H.E.、Magrath M.J.L.、Clarke R.H.、Sunnucks P. 与 Pavlova A.（2022）：极度濒危澳大利亚鸟类——盔吸蜜鸟（Helmeted honeyeater, *Lichenostomus melanops cassidix*）的染色体级基因组组装与连锁图谱》的配套支撑数据。
1. 盔吸蜜鸟核基因组注释文件：包含盔吸蜜鸟核基因组预测基因注释的通用特征格式（General Feature Format, GFF）文件与GP文件，对应文件为`Helmeted_honeyeater_annotation.gff.gz`与`Helmeted_honeyeater_annotation.gp.gz`。
2. 盔吸蜜鸟线粒体基因组FASTA格式文件：包含盔吸蜜鸟线粒体基因组组装序列的FASTA格式文件，对应文件为`Helmeted_honeyeater_mitogenome.fasta`。
3. 盔吸蜜鸟线粒体基因组注释TBL文件：包含盔吸蜜鸟线粒体基因组预测基因注释的TBL格式文件，对应文件为`Helmeted_honeyeater_mitogenome_annotation.tbl`。
4. 盔吸蜜鸟线粒体基因组系统发育树：基于BLASTn分析与近缘物种比对得到的盔吸蜜鸟线粒体基因组邻接系统发育树与子树，格式为Newick，对应文件为`Helmeted_honeyeater_mitogenome_tree.nwk`与`Helmeted_honeyeater_mitogenome_subtree.nwk`。
5. 盔吸蜜鸟连锁图谱：基于家系构建的连锁图谱，通过Lep-MAP3软件对53111个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）位点进行分析得到。该图谱包含染色体信息、性别平均遗传距离（单位：cM）、性别特异性遗传距离（单位：cM）、性别平均重组率（单位：cM/Mb）与性别特异性重组率（单位：cM/Mb）。本数据集提供两份遗传图谱：原始遗传图谱，以及将负重组率转换为0后的遗传图谱，对应文件分别为`Helmeted_honeyeater_geneticMap.txt`与`Helmeted_honeyeater_geneticMap_notConverted.txt`。
6. 盔吸蜜鸟滑动窗口重组率遗传图谱：基于Lep-MAP3生成的Marey图进行平滑处理得到的非重叠窗口遗传图谱，窗口宽度分别设置为50Kb、100Kb与200Kb，包含性别平均遗传距离（单位：cM）与重组率（单位：cM/Mb），对应文件分别为`Helmeted_honeyeater_recombinationRate_50Kb.txt`、`Helmeted_honeyeater_recombinationRate_100Kb.txt`与`Helmeted_honeyeater_recombinationRate_200Kb.txt`。
7. 盔吸蜜鸟BUSCO完整度分析结果：包含草图基因组、染色体级基因组以及染色体级基因组注释的单拷贝同源基因通用基准评估（Benchmarking Universal Single-Copy Orthologs, BUSCO）完整度分析全部结果，包括汇总表、完整结果表与缺失基因表，对应压缩文件分别为`Helmeted_honeyeater_BUSCO_DraftGenome.zip`、`Helmeted_honeyeater_BUSCO_ChrLengthGenome.zip`与`Helmeted_honeyeater_BUSCO_annotation.zip`。
8. 辅助分析文件：
0. `GeneticMap_rawDArTs_HiC_HelmetedHoneyeater_Robledo-Ruiz-etal.docx`：记录盔吸蜜鸟连锁图谱与重组率图谱构建流程的文档，包含所用分析脚本。
1. `Pedigree.zip`：包含用于Lep-MAP3分析的输入家系文件，以及用于组装该家系的相关文件与脚本的压缩文件夹。
2. `Lep-MAP3_Genotypes.zip`：包含通过Lep-MAP3得到的基因型后验概率文件与基因型调用文件的压缩文件夹。
3. `Lep-MAP3_LOD.zip`：包含Lep-MAP3模块SeparateChromosomes2与JoinSingles2All在不同LOD评分下生成的结果文件，以及所用脚本与生成的绘图结果的压缩文件夹。
4. `LASTZ_Mapping_ZF.zip`：包含通过LASTZ软件将盔吸蜜鸟基因组与斑胸草雀、领姬鹟、华丽细尾鹩莺基因组进行比对以完成共线性分析所用的脚本、输出结果与绘图结果的压缩文件夹。
5. `MareyMap_LG.zip`：包含针对每个连锁群处理Marey图所用的文件与脚本的压缩文件夹。