Vicia faba cv. Hedin3 enzymatic methylation sequencing

Faba bean (Vicia faba L.) is one of the first domesticated plants at the dawn of agriculture. The giga-size chromosomes (in total ~13 Gb) bloated by repetitive sequences had hampered its study and crop improvement. Heavy-level invariable DNA methylation might have reduced removal rate of repetitive sequences and, together with an insertion-biased DNA double-strand break repair, contributed to genome enlargement without a recent whole-genome duplication. We generated a genome-wide DNA methylation map from leaf tissue with a single base resolution. V. faba cv. Hedin3 genomic DNA was sheared to 350-400 bp . The sheared DNA was subjected to a large insert NEBnext Enzymatic Methyl-seq library preparation. Four libraries were constructed with different sequencing indexes. Index PCR was performed with five PCR cycles to include indexes and amplify the libraries. The final libraries were quantified by qPCR, pooled at equimolar concentration, and sequenced for 500 cycles (2 x 250 bp paired-end reads) on an SP-flow cell of the Novaseq6000 system (Illumina, Inc., San Diego, USA).