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[…] Genomic PE and MP libraries were quality-checked using FastQC v0.11.2 () and trimmed accordingly with Trimmomatic v0.33 () to remove remnant adapter sequences (ad hoc) and the low-quality 5' read ends (sliding window = 4 and requiring a minimum Phred quality = 30). A minimum length equal to the original read length was required. During the quality-trimming process, libraries of unpaired forward reads were kept as single-end reads (SE). After trimming, the read survival rate for each DNA library was as follows: Pirum, PE 30.2%, MP 91.2%; Abeoforma, PE 75.5%, MP 31.0%; Chromosphaera, PE 81.1%, MP 89.9%; and Corallochytrium, PE 94.7%, MP 73.1%.Genome assemblies were performed using Spades v3.6.2 () with the BayesHammer error correction algorithm (). For each organism, PE data were analyzed using Kmergenie () to determine the optimal k-mer length for the assembly process, which was used in the Spades assembly in combination with smaller and larger values, including the maximum possible odd length below the maximum read length after trimming. The optimized assemble parameters for each genome were as follows: Pirum, max. read length = 125, k = 55,123; Abeoforma, max. read length = 100, k = 47,91; Chromosphaera, max. read length = 125, k = 91,121; Corallochytrium, max. read length = 100, k = 41,63,91. In the cases of Corallochytrium and Chromosphaera genomes, Spades was run in careful mode, taking into account PE, SE and MP data in the same run. In the cases of the highly repetitive Abeoforma and Pirum genomes, an initial Spades assembly of PE and SE libraries was combined with MP libraries using the Platanus v1.2.1 scaffolding module (). Each assembly was later processed using the GapCloser module from SOAPdenovo assembler with PE data, in order to extend the scaffolded contigs by shortening N stretches (). Genome assembly statistics (genome size, N50, L75) were calculated using Quast v2.3 (), and completeness was assessed using the BUSCO v1.1 () database of universal eukaryotic genes, based on the predicted transcripts. […]

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