Dataset Information

Whole-Genome Sequence of the Trypoxylus dichotomus Japanese rhinoceros beetle.

ABSTRACT: The draft whole-genome sequence of the Japanese rhinoceros beetle, Trypoxylus dichotomus was obtained using long-read PacBio sequence technology. The final assembled genome consisted of 739 Mbp in 2,347 contigs, with 24.5× mean coverage and a G+C content of 35.99%.

SUBMITTER: Ogata N

PROVIDER: S-EPMC8553429 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Whole-Genome Sequence of the <i>Trypoxylus dichotomus</i> Japanese rhinoceros beetle.

Ogata Norichika N

microPublication biology 20211011

The draft whole-genome sequence of the Japanese rhinoceros beetle, <i>Trypoxylus dichotomus</i> was obtained using long-read PacBio sequence technology. The final assembled genome consisted of 739 Mbp in 2,347 contigs, with 24.5× mean coverage and a G+C content of 35.99%. ...[more]

PMID: 34723147

Similar Datasets

Project description:The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional Chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability, and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific-locus amplified fragment sequencing (SLAF-seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping. Phylogenetic analysis of SNPs indicated the presence of three distinct genetic groups, suggesting that the various subspecies could be treated as three groups of populations. PCA and ADMIXTURE analysis also identified three genetic clusters (North, South, West), which corresponded to their locations, suggesting that geographic factors were important in maintaining within population homogeneity and between population divergence. Analyses of SNP data confirmed the monophyly of certain subspecies on islands, while other subspecies (e.g., T. d. septentrionalis) were found to be polyphyletic and nested in more than one lineage. AMOVA demonstrated high level of differentiation among populations/groups. Also, pairwise F ST values revealed high differentiation, particularly between South and West, as well as between North and South. Despite the differentiation, measurable gene flow was inferred between genetic clusters but at varying rates and directions. Our study demonstrated that SLAF-seq derived markers outperformed 16S and COII sequences and provided improved resolution of the genetic differentiation of rhinoceros beetle populations from a large part of the species' range.

Dataset Information

Whole-Genome Sequence of the Trypoxylus dichotomus Japanese rhinoceros beetle.

Publications

Whole-Genome Sequence of the <i>Trypoxylus dichotomus</i> Japanese rhinoceros beetle.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets