Forcina, G., Camacho–Sanchez, M., Cornellas, A., Leonard, J. A., 2022. Complete mitogenomes reveal limited genetic variability in the garden dormouse Eliomys quercinus of the Iberian Peninsula. Animal Biodiversity and Conservation
Adapter trimming and minimal quality filtering on the 3' end were performed with cutadapt 2.10 using script1. A reference mitogenome for Eliomys quercinus was created with NOVOPlasty3.7 using script2. The four samples were pooled. NOVOPlasty is able to assemble de-novo mitogenomes using a seed sequence. I used a cytochrome b GQ453669 from E. quercinus. NOVOPlasty was able to reconstruct a single contig with the expected size of the mitogenome.
Individual samples of Eliomys were mapped to the reference mitogenome using BWA mem 0.7.12-r1039. SAMtools 1.3 (using htslib 1.3), was used to discard reads with quality mapping below 40 and remove PCR duplicates, with script3.
Mitogenomes were annotated with MITOS2 webserver. MITOS provided better annotations compared to MitoZ. The annotations have been manually curated after comparing them with the NCBI staff-curated mitochondrial genomes of two close species: Muscardinus avellanarius - NC_050264 and Glis glis - NC_001892.1.
All cytochrome b sequences from E. quercinus available in GenBank were retrieved with the rentrez R package using script5. They were combined with assembled cytb sequences using script6 and written to a fasta.
Using script7, cytb sequences were aligned using mafft v7.453. The resulting MSA was trimmed using trimAl v1.4.rev15 build 2013-12-17 to remove sequences and positions in the MSA to maximize the amount of information. The MSA was converted to nexus using AMAS. Final haplotype networks were reconstructed with PopArt, using the TCS algorithm. The msa NEXUS file is available in output/cyb-network.nex.
A maximum likelihood tree was reconstructed with 1st and 2nd codon positions of protein-coding genes from all mitogenomes of Gliridae available in GenBank. Initial trees with Sciuridae included lots of saturated positions. I tried then a ML tree with only dormice and Glis glis as sister to all of them, as in Upham et al. 2019. The final tree was produced following these steps and this DNA alignment.
Mitogenomes were deposited in GenBank under the BioProject PRJNA727082: Genetic resources for small mammals.
| sample | species | BioSample | accession no. | SRA |
|---|---|---|---|---|
| EBD 2003.101.123M | Eliomys quercinus | SAMN19006130 | MZ130252 | SRR14415825 |
| EBD 2011.020.017M | Eliomys quercinus | SAMN19006131 | MZ130253 | SRR14415824 |
| EBD 2013.075.014M | Eliomys quercinus | SAMN19006132 | MZ130255 | SRR14415823 |
| EBD 2012.022.013M | Eliomys quercinus | SAMN19006133 | MZ130254 | SRR14415822 |