Nuclear Target Sequencing Protocol

For nuclear target sequencing, a total of 500 ng was fragmented to 400-bp fragments with a Bioruptor^® ultrasonicator (Diagenode, Liège, Belgium). Library preparations were performed following de La Harpe et al. (2019) (link) and using a KAPA LTP library preparation kit (Roche, Basel, Switzerland) for sample cleaning, end-repair, and A-tailing steps, and the protocol of Meyer and Kircher (2010) (link) for adaptor ligation and adaptor fill-in reactions steps. Four μl of the ligated fragment solution were amplified for eight cycles using KAPA HiFi DNA Polymerase (Roche, Basel, Switzerland) and the set of 60 dual index primers described in Loiseau et al. (2019) (link). Libraries were quantified with a Qubit^® Fluorometer v2.2 before pooling in equimolar ratio. Target capture was performed using the custom kit PopcornPalm developed by de La Harpe et al. (2019) (link), and targeting 4,051 palm genes. Target capture was conducted on pools of 50 or 51 samples, following myBait^® Custom Target Capture Kits protocol v3.0 (Arbor Biosciences, Ann Arbor, MI, United States), with 18 h of incubation time at 65°C and 12 cycles of post-capture PCR reactions. The pooled target capture reactions were quantified with Qubit^® Fluorometer v 2.2, before sequencing with an Illumina HiSeq 3000 sequencer (Illumina, San Diego, CA, United States) in paired-end 2 × 150-bp mode.