title: Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP
design: DNA isolation followed a modified version of Georgi et al.62.  An Illumina 300 bp insert TruSeq V2 library was prepared and sequenced by the Center for Genome Research at Oregon State University (http://cgrb.oregonstate.edu/) and sequenced on a HiSeq 2000 (2 x 100 bp sequencing on ⅓ of a lane).  High quality reads were filtered and trimmed using Trimmomatic V0.3456 using: ILLUMINACLIP:2:30:10 and LEADING:25 TRAILING:25 SLIDINGWINDOW:5:25 MINLEN:65.  A linear plastome assembly including just one IR was generated using the Geneious v6.1.6 (Biomatters, Auckland NZ) as the de novo assembler and 3 M read-pairs of data (ca. 100X coverage).  Subsequently, all 30 M read-pairs were mapped to the genome to correct errors and confirm the full genomic sequence.  Independently assembled de novo IR boundary regions were reciprocally mapped to draft IR boundaries to confirm draft boundaries.  These were confirmed using the BLAST-on-BLAST method discussed below (see “dispersed repeats”).  The structural organization of the plastome assembly has since been confirmed by the addition of a 4 kb insert Illumina Nextera mate pair library developed and sequenced (2 x 100bp reads) by the University of Maryland’s Genomic Resource Center.  The annotated plastome sequence has been deposited in GenBank (KT428297).