2021/12/10 by Simon Hellemans, Menglin Wang, Nonno Hasegawa +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · Agricultural and Biological Sciences · Mathematics · #Insect and Arachnid Ecology and Behavior #Plant and animal studies #Animal Behavior and Reproduction #Phylogenetic tree #Biology #Evolutionary biology #Genome #Tree (set theory) #Phylogenetics #In silico #Set (abstract data type) #Transcriptome #Computational biology #Gene #Genetics #Computer science #Mathematics
paper · pdf · doi:10.1101/2021.12.09.472027
openalex publication_date 2021/12/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
Abstract The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting 50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of Cryptocercus , for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted in silico between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: https://github.com/oist/TER-UCE-DB/ .