Ngs qc tool kit v2

Total genomic DNA was extracted from 100 mg fin tissues using a Genomic DNA Isolation Kit (QiaGene) according to the manufacturer's instructions. Complete mitochondrial genome sequencing was performed on the Illumina MiSeq platform (Illumina Inc). The Illumina raw sequence reads were edited using the NGS QC Tool Kit v2.3.3 (Patel & Jain, 2012), with a cutoff value of 50 and 20, respectively, for percentage of read length and PHRED quality score. High‐quality reads were assembled into contigs using the de novo assembler SPAdes 3.9.0 (Bankevich et al., 2012), utilizing a k‐mer set of 93, 95, 97, 103, 105, 107, and 115. The de novo contigs were then assembled into complete mitochondrial genomes by further connection using SOAPdenovo (Luo et al., 2012). The harvested mitogenome sequences of S. fasciolata (16,560 bp) and S. incerta (16,561 bp) were deposited in GenBank (KY404236 and MK361215).

The B. colvilei (GJ2, GJ3) and B. sessilifolia (GJ9, GJ10, GJ11) plant samples were collected from Goruwale, Mechi, Nepal and Yadong, Tibet, China, B. sessilifolia plant samples were collected from the Gaoligong mountain, Yunnan, China, and the Gaoligong Mountain, Myanmar. Table S2 gives details of the collections. Total genomic DNA was extracted from 100 mg fresh leaves using a modified CTAB method [50 (link)]. The complete cp genome sequencing was performed on the Illumina MiSeq 2000 (Illumina Inc, San Diego, CA, USA), at the Laboratory of Molecular Biology of Germplasm Bank of Wild Species in Southwest China, following the method of Yang [51 (link)]. The Illumina raw sequence reads were edited using the NGS QC Tool Kit v2.3.3 [52 (link)], with a cut-off value of 80 and 30 respectively for percentage of read length and PHRED quality score respectively. High-quality reads were assembled into contigs using the de novo assembler SPAdes 3.9.0 [53 (link)], using a k-mer set of 93, 105, 117, 121. The de novo contigs were assembled into complete chloroplast genomes by further connection using NOVOPlasty version 2.6.2 [54 (link)].