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.nwk

Helmeted_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.zip

Helmeted_honeyeater_BUSCO_annotation.zip

Document 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.