Sequencing of Agave americana chloroplast genome
Chloroplasts were isolated from the Agave americana leaf tissue using a Chloroplast Isolation Kit (Sigma, Cat CP-ISO). Then DNA was extracted from the enriched chloroplasts using the DNeasy DNA extraction kit (QIAGEN, Cat No. 69104). Paired-end (PE) sequencing libraries with an average insert size of 500bp were constructed from the chloroplast DNA using the Illumina TruSeq DNA Sample Prep kit v2 and sequenced on a Miseq instrument using the Miseq V3 2x300 kit. The PE reads (2x300bp) were trimmed using Trimmomatic (Bolger et al., 2014) with MINLEN = 100 and SLIDINGWINDOW=4:20.