Abstract
BackgroundIt is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field.ResultsUsing the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls.ConclusionsThe donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent.
Highlights
It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture
Because the horse genome was constructed according to genetic physical mapping [11], we identified the cytogenetic nomenclature and adjusted the direction of the donkey chromosome-length sequence according to the subchromosomal painting results between donkey and horse [13, 29, 30]
Here we used the donkey genome as an example to prove the availability of DNA Zoo chromosome-level assembly data through the assessment of continuity and gene integrity and the collinearity analysis between horse and donkey genomes
Summary
It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. Owing to the lowering of the cost associated with sequencing, an increasing number of species genome scaffolds have reached chromosome length, contig N50 still needs to be improved. This allows the inference of most of the inversions, translocations, fusions, and fissions that occurred during evolution by simple observational comparisons on a sequence-based whole-genome scale [9, 10]. We will focus on some chromosomes of perissodactyls, especially the horse and the donkey
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