next-RAD of Coffea arabica: Bourbon chiroso variety
Genomic DNA was first fragmented with Nextera DNA Flex reagent (Illumina, Inc), which also ligates short adapter sequences to the ends of the fragments. The Nextera reaction was scaled for fragmenting 50 ng of genomic DNA, although 75 ng of genomic DNA was used for input to compensate for the amount of degraded DNA in the samples and to increase fragment sizes. Fragmented DNA was then amplified for 27 cycles at 74 degrees, with one of the primers matching the adapter and extending 10 nucleotides into the genomic DNA with the selective sequence GTGTAGAGCC. Thus, only fragments starting with a sequence that can be hybridized by the selective sequence of the primer will be efficiently amplified. The nextRAD libraries were sequenced on a HiSeq 4000 with one lane of 159 bp reads (University of Oregon)