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The AllPaths contigs were aligned on the Gallus_gallus-5.0 assembly (GCF_000002315.4) to obtain an assembly at the chromosome level, taking into account the rare known inter-chromosomal rearrangements detected by cytogenetic mapping. Comparison of cytogenetic and genetic maps from several gallo-anseriformes ... showed very limited number of inter-chromosomal rearrangements, all distinguishable by cytogenetics methods. No inter-chromosomal rearrangements between ducks and galliforme chromosomes were detected to date. Therefore, a chromosome assignment of Numida scaffolds based on Gallus_gallus-5.0 is correct. However, many intra-chromosomal rearrangements will be missed in regions composed of small scaffolds. Linkage of gaps in the assembly can therefore be informed by paired-end or mate-pair information in which case the number of Ns corresponds to the estimated size of the gap, or by alignment to Gallus_gallus-5.0 in which case we inserted 100 Ns. However, there are a few cases in which the paired-ends (or mate-pairs) gaps have 100 Ns. Following the alignment of the Numida scaffolds on the Gallus_gallus-5.0 genome, a few scaffolds had to be split and are thus named scaffoldXXA and scaffoldXXB. The mitochondrial chromosome is in GenBank accession number KY865420.  more

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