WGS of Q. suber:mate pair using 2000bp inserts
Long-insert mate pair libraries were constructed using the BGI '2-10Kb Mate-Pair Library Construction Protocol':  20?g(2~6k library)/30?g(10k library) DNA is fragmented by Covaris. Following DNA fragmentation, the fragments are end-repaired with biotin dNTPs mix, and incubate at 20? for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen), target fragments are selected by running a 0.6% agarose gel. Then add Ligation Mix and incubate at 16? over night. The DNA fragments are circularized, and non-circularized DNA is removed by digestion. Circular DNA is fragmented (Covaris) and biotinylated fragments (corresponding to the ends of the original DNA ligated together) are purified by Dynabeads M-280 streptation (Invitrogen). Then add End-repaired Mix and , and incubate at 20? for 30 min. Purify the end-repaired DNA with streptavidin beads? then add A-Tailing Mix, incubate at 37? for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20? for 15 min. Purify the Adapter-ligated DNA. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the 400-600bp PCR products are selected by running a 2% agarose gel. Purify the gel with QIAquick Gel Extraction kit (QIAGEN).