Generation of large mitochondrial and nuclear nucleotide sequences and phylogenetic analyses using high-throughput short-read datasets for endangered Placostylinae snails of the southwest Pacific

ABSTRACT

Placostylinae are a sub-family of terrestrial land snails endemic to the southwest Pacific. Some species are harvested for food, and others are critically endangered. Here we assemble and characterise complete mitochondrial genomes, as well as three nuclear markers (partial 45S ribosomal cassettes and the histone genes H3 and H4) of five snail species from three geographical regions (New Zealand, New Caledonia and the Solomon Islands). Mitogenomes of Placostylinae snails ranged between 14,544 bp and 14,711 bp, with minor variation in the position of tRNA tyrosine (Y) and tRNA tryptophane (W). The 45S ribosomal cassette contained intra-genomic nucleotide variation in ITS2. Cassettes containing histone genes H3 and H4 and their non-transcribed spacer region were assembled for three species, with the two genes coded in the same direction. Phylogenetic analysis on this large dataset (mitochondrial genome + nuclear markers) supported geographical clustering of species but could not confidently infer monophyly of the four Placostylus species with respect to Eumecostylus cleryi. Analysis based on shorter cytochrome c oxidase sequences with a wider taxon sampling found species representing the genera Eumecostylus and Placocharis were nested within the phylogenetic diversity of Placostylus. Multi-locus phylogenetic analysis containing mitochondrial and nuclear sequences did not support monophyly of Placostylinae.

KEYWORDS:

• Histone genes
• genetic resources
• mitochondrial genome
• phylogenetics
• Placostylus
• ribosomal cassette

Acknowledgements

We thank Fabrice Brescia and Margaret and Rhys Richards for collection of specimens in New Caledonia and the Solomon Islands; Abraham Breure for his help identifying the Solomon Island species; Eddy Dowle for DNA extractions; and members of the Phoenix group for Evolutionary Ecology and Genetics for helpful discussions (evolves.massey.ac.nz). We also would like to thank the two anonymous reviewers for their useful comments which greatly improved the quality of this manuscript, and the editor and associate editor for their help in the submission process.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

All sequences produced and used in this paper have been uploaded and are available to use in the NCBI GenBank database.

Additional information

Funding

This research was supported by a Massey University PhD scholarship (awarded to MQ) and a grant from the Royal Society of New Zealand Te Apārangi Marsden Fund 12-MAU-008.