Dipylidium caninum draft genome - a new resource for comparative genomic and genetic explorations of flatworms

Li, Guohua; Korhonen, Pasi K.; Young, Neil D.; Jiang, Lu; Wang, Tao; Fu, Yi-Tian; Koehler, Anson V.; Hofmann, Andreas; Chang, Bill C.H.; Wang, Shuai; Li, Nan; Lin, Chuyu; Zhang, Hui; Xiangli, Lingzi; Lin, Lin; Liu, Weimin; Li, Huawei; Gasser, Robin B.; Zhu, Xingquan

doi:10.1016/j.ygeno.2021.02.019

Cited by 8 publications

(16 citation statements)

References 75 publications

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“…The present study is the first to provide additional proof to the two species proposal using whole genome data. Average depth of coverage of the Canine FL1 and Feline KS1 isolates from this study was 46.5x and 25.8x (Figure 1), which was lower than the coverage obtained by [16](200x) due to the different Illumina technologies used. The genomes from this study were mapped against the reference genome to determine the presence and positions of genetic variants such as SNPs, insertions and deletions.…”

Section: Discussioncontrasting

confidence: 68%

“…D. caninum Canine FL1 and Feline KS1 isolates from this study generated 18,886,666 and 17,928,712 raw reads (SRA Accessions: SRX12485835, SRX12485836), of which 18,827,832 (99.68%) and 17,870,800 (99.71%) reads were paired, with index trimmed mean insert lengths of 137.4 bp and 138.6 bp respectively. Trimmed reads were aligned with the D. caninum canine reference draft genome (Assembly Accession number: GCA_017562135.1) [16], which has 1686 scaffolds (Figure 1). Average depth of coverage of the D. caninum canine FL1 and feline KS1 genomes generated in this study were 46.5x and 25.8x with a GC% of 47.71% and 47.33% respectively.…”

Section: Resultsmentioning

confidence: 99%

“…Labuschagne et al used 28S rDNA variation and the complete mitochondrial genomes of canine and feline derived D. caninum to propose that the two host associated genotypes be considered distinct species. A 110Mb draft nuclear genome of a canine isolate of D. caninum from China is available [16].…”

Section: Discussionmentioning

confidence: 99%

“…Completeness of the draft genomes were measured using BUSCO genes [35]. BUSCO completeness in the draft Canine FL1 genome (63.1% complete single copy; 3.4% duplicated single copy) was similar to the reference genome (63.5% % complete single copy; 1.3% duplicated single copy) [16]. BUSCO completeness of the draft feline KS1 genome was lower (57.9% complete single copy; 0.7% duplicated single copy).…”

Section: Discussionmentioning

confidence: 99%

“…Our objectives in this study were to sequence the genomes of D. caninum isolated from a dog and a cat from the United States using the Illumina platform and to compare them to the reference D. caninum genome isolated from a dog in China [16]. We hypothesized that the genomes of D. caninum canine isolates would be similar despite the geographical distance of the sites of isolation, and that D. caninum feline isolates would have significant differences.…”

Section: Introductionmentioning

confidence: 99%

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Genomic differences and species delimitation: a case for two species in the zoonotic cestodeDipylidium caninum

Chelladurai

Abraham

Quintana

et al. 2023

Preprint

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Dipylidium caninum (Linnaeus, 1758) is a common zoonotic cestode of dogs and cats worldwide. Previous studies have demonstrated the existence of largely host associated canine and feline genotypes based on infection studies, genetic differences at the nuclear 28S rDNA gene and complete mitochondrial genomes. There have been no comparative studies at a genome-wide scale. Here, we sequenced the genomes of a dog and cat isolate of Dipylidium caninum from the United States using the Illumina platform and conducted comparative analyses with the reference draft genome. Complete mitochondrial genomes were used to confirm the genotypes of the isolates. D. caninum canine and feline genomes generated in this study had mean coverage depths of 45x and 26x and an average identity of 98% and 89% respectively when compared to the reference genome. SNPs were 20 times higher in the feline isolate. Comparison and species delimitation using universally conserved orthologs and protein coding mitochondrial genes revealed that the canine and feline isolates are different species. Data from this study builds a base for future integrative taxonomy. Further genomic studies from geographically diverse populations are necessary to understand implications for taxonomy, epidemiology, veterinary clinical medicine, and anthelmintic resistance.

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Section: Discussioncontrasting

confidence: 68%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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