Genome sequences of four Ixodes species expands understanding of tick evolution
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Abstract
Ticks, hematophagous acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genus Ixodes , which includes the main vectors of Lyme disease. Here, we present the complete genome sequences of four tick species, derived from a single female individual, with a particular focus on the European species Ixodes ricinus , achieving a chromosome-level assembly. Additionally, draft assemblies were generated for the three other Ixodes species, I. persulcatus, I. pacificus and I. hexagonus . The quality of the four genomes and extensive annotation of several important gene families have allowed us to study the evolution of gene repertoires at the level of the genus Ixodes and of the tick group. We have determined gene families that have undergone major amplifications during the evolution of ticks, while an expression atlas obtained for I. ricinus reveals striking patterns of specialization both between and within gene families. Notably, several gene family amplifications are associated with a proliferation of single-exon genes. The integration of our data with existing genomes establishes a solid framework for the study of gene evolution, improving our understanding of tick biology. In addition, our work lays the foundations for applied research and innovative control targeting these organisms.
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Materials and Methods
I may have missed it, but I didn't see a methods section for peptide discovery/annotation. Would you be willing to add this?
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especially regarding taxon sampling and filtering of sites/genes.
Is it possible to be more specific about the sequencing data that would be needed to answer this question? I think that could be value-added for the community to have this clearly spelled out
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post-assembly errors.
would these be post-assembly errors or assembly errors? If post-assembly, can you add details about what this means?
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The completeness (% of complete BUSCOs) of the four new gene catalogs generated in this study fell within the range of recently sequenced tick genomes as shown in Table 2. Completeness was lowest in I. pacificus (81%), and highest in I. ricinus and I. hexagonus (about 91%), which is somewhat lower than the 98% observed for the recently improved genome of I. scapularis (De et al. 2023). For I. pacificus, we also note a relatively high percentage of “duplicated” genes in the BUSCO analysis, suggesting that heterozygosity might have not been fully resolved and that our assembly still contains duplicate alleles, which is supported by the higher heterozygosity estimate for this genome (supplementary Fig. S1).
It isn't clear in this section whether you ran BUSCO on the genomes in genome or protein mode. I think it would be helpful to see …
The completeness (% of complete BUSCOs) of the four new gene catalogs generated in this study fell within the range of recently sequenced tick genomes as shown in Table 2. Completeness was lowest in I. pacificus (81%), and highest in I. ricinus and I. hexagonus (about 91%), which is somewhat lower than the 98% observed for the recently improved genome of I. scapularis (De et al. 2023). For I. pacificus, we also note a relatively high percentage of “duplicated” genes in the BUSCO analysis, suggesting that heterozygosity might have not been fully resolved and that our assembly still contains duplicate alleles, which is supported by the higher heterozygosity estimate for this genome (supplementary Fig. S1).
It isn't clear in this section whether you ran BUSCO on the genomes in genome or protein mode. I think it would be helpful to see both sets of results -- the genome alone would tell us how many single copy genes are in the assembly, while the proteins compared with this will tell us how well annotation went for these genomes as well.
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