Sequencing

Paired-end sequencing is performed on an Illumina MiniSeq platform (San Diego, CA) using a 1.2 pM loading concentration, supplemented with a 33.3% PhiX Control v3 (Illumina, San Diego, CA; Cat. No. FC-110-3001) spike-in.

Depending on the total number of samples in the sequencing pool, we use either a MiniSeq Mid Output Kit (300-cycles) or a MiniSeq High Output Reagent Kit (300-cycles) (Illumina, San Diego, CA; Cat. Nos. FC-420-1004 and FC-420-1003) to make sure we get sufficient read depth per sample.

Note

A 2×150 bp (300 cycle) sequencing run guarantees sufficient overlap for assembly. A 2×75 bp (150 cycle) run enables assembly of trnL reads from all but one food plant in the reference: the water chestnut Eleocharis dulcis, which has an unusually long 154 bp trnL-P6 sequence (7 standard deviations outside the mean reference sequence length).