3.3.2. Nakazawaea atacamensis whole genome sequencing
Based on the genome sequencing and assembly of the N. atacamensisATA-11A-BT isolate, we assessed the genome complexity and quality of the novel species. Illumina sequencing yielded approximately 7.2 x 105 filtered reads, providing a sequence coverage depth of 8.8X. Seven genome assemblers were compared, and the best assembly was obtained using SPAdes/Shovill (Table S3 ). The resulting genomic draft of N. atacamensis had a 12.4 Mbp length, with an estimated GC content of 36.7%. The N. atacamensis assembly consisted of 115 contigs, with 42 contigs exceeding 501 bp, accounting for 99% of the assembled sequences. The largest contig had a length of 2,070.2 Kbp, and the N50 value of the assembly was 729,094 bp, indicating the contiguity of the assembly. The details of the sequencing results and assembled contigs can be found inTable S3 .
Next, we utilize the available genomes from the Nakazawaea genus to generate a phylogenetic tree. The genus Nakazawaea currently contains four publicly available genomes: N. ishiwadae , N. holstii , N. peltata and N. ambrosiae . The phylogenetic tree placed N. atacamensis together with N. peltata(Figure 3 ), which differs from the D1/D2 phylogeny. Differences can arise since the D1/D2 marker represents a single-locus DNA marker, thus potentially inheriting limitations associated with its use, such as missing information between sister taxa as to compared to whole-genome data (Kauserud, 2023). In general, the level of phylogenetic resolution allowed by single genes is insufficient, while the utilization of whole genome concatenated orthologous genes represents a better approximation to resolve the phylogenetic relationship between species (Brown et al. , 2001, Yokono et al. , 2018)