Methods
Tissues from single, wild-collected individuals with permits and ethical approval were used for this study. DNA extraction was performed using the Qiagen DNEasy genomic extraction kit using the standard process. Paired-end sequencing libraries were constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150bp format. The resulting fastq files were trimmed of adapter/primer sequences and low-quality regions with Trimmomatic v0.33 (Bolger et al. 2014). The trimmed sequence was assembled by SPAdes v3.15.4 (Bankevich et al. 2012) followed by a finishing step using Zanfona (Kieras et al. 2021).
Because a substantial proportion of the genome consists of repetitive sequences, Illumina assemblies will typically be considerably smaller than the expected genome size. This occurs because short sequencing reads often cannot be reliably assembled across long or highly similar repeat regions. As a result, multiple copies of a repeat may be collapsed into a single representative sequence during assembly, rather than being assembled as separate copies. Consequently, although the repeat sequences are represented in the assembly, their total contribution to the assembled genome length will be substantially underestimated.
Results and Data Availability
Funding
Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa.