DOI: 10.26180/16695607.v9
title: Supporting data for “Chromosome-length genome assembly and linkage map of a Critically Endangered Australian bird: the helmeted honeyeater”. Robledo-Ruiz et al. (2022)

description: <br>Supporting data for the manuscript:<br> 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) <b>Chromosome-length genome assembly and linkage map of a Critically Endangered Australian bird: the helmeted honeyeater.</b><i><br></i><br><br><br>Data usage:<br><br><b>Helmeted honeyeater (<i>Lichenostomus melanops cassidix</i>) nuclear genome annotation</b><br>GFF and GP files containing the predictive gene annotation of the Helmeted honeyeater nuclear genome.<br>Helmeted_honeyeater_annotation.gff.gz<br>Helmeted_honeyeater_annotation.gp.gz<br><b>Helmeted honeyeater mitochrondrial genome</b><br>FASTA file containing the assembly of the Helmeted honeyeater mitochondrial genome.<br>Helmeted_honeyeater_mitogenome.fasta<br><b>Helmeted honeyeater mitochrondrial genome annotation</b><br>TBL file containing the predictive gene annotation of the Helmeted honeyeater mitochondrial genome.<br>Helmeted_honeyeater_mitogenome_annotation.tbl<br><b>Helmeted honeyeater mitochrondrial genome tree</b><br>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<b><br></b><b>Helmeted honeyeater linkage map</b><br>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.<br>Helmeted_honeyeater_geneticMap.txt<br>Helmeted_honeyeater_geneticMap_notConverted.txt<br><br><b>Helmeted honeyeater genetic map with sliding window recombination rate</b><br>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.<br>Helmeted_honeyeater_recombinationRate_50Kb.txt<br>Helmeted_honeyeater_recombinationRate_100Kb.txt<br>Helmeted_honeyeater_recombinationRate_200Kb.txt<br><b>Helmeted honeyeater BUSCO completeness results</b><br>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<br>Helmeted_honeyeater_BUSCO_ChrLengthGenome.zipHelmeted_honeyeater_BUSCO_annotation.zip<br><b>0.GeneticMap_rawDArTs_HiC_HelmetedHoneyeater_Robledo-Ruiz-etal.docx</b>Document with the process done to produce the linkage and recombination maps for the helmeted honeyeater, including the scripts used.<br><br><b>1.Pedigree.zip</b><br>Folder containing the pedigree file used as input for Lep-MAP3, and the files and scripts used to assembled it.<br><br><b>2.Lep-MAP3_Genotypes.zip</b><br>The genotype posterior probabilities file and the called genotypes file obtained with Lep-MAP3.<br><br><b>3.Lep-MAP3_LOD.zip</b><br>The files produced by Lep-MAP3 modules SeparateChromosomes2 and JoinSingles2All testing different LOD scores. Scripts and plots produces are also included.<br><br><b>4.LASTZ_Mapping_ZF.zip</b><br>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.<br><br><b>5.MareyMap_LG.zip</b><br>Files and scripts from processing the Marey maps per Linkage Group.<br>