Chloroplast Genome Sequencing of Iris Species

Total genomic DNAs of the three Iris species were extracted using the modified cetyltrimethylammonium bromide method [89 (link)]. Three genomic libraries were prepared using the TruSeq DNA Nano Kit (Illumina, San Diego, CA, USA) and sequenced using NextSeq500 platform (Illumina). A total of 3.2–3.4 gigabases (Gb) of paired-end reads (2 × 150 base pairs [bp]) were generated. Trimmed paired-end reads (Phred score ≥ 20) were assembled using the CLC genome assembler (version 4.06 beta; CLC Inc., Rarhus, Denmark) with the default parameters. SOAP de novo gap closer was used to fill in gaps based on alignments of paired-end reads [90 (link)]. Contigs were queried against the non-redundant database of the National Center for Biotechnology Information (NCBI) to identify those representing cp genomes, which were retrieved from the total contigs using Nucmer [91 (link)]. The aligned contigs were ordered using the cp genome sequences of I. koreana (NC_056174), I. minutoaurea (NC_056177), and I. odaesanensis (NC_056178) as references [12 (link)]. Finally, the trimmed paired-end reads were assembled into complete cp genome sequences using BWA software version 0.7.25 [92 (link)] (Figure S1). The newly sequenced chloroplast genomes in the present study were deposited in the NCBI GenBank database.