Long reads Syagrus oleracea by Nanopore
Genomic DNA from leaves of Syagrus oleracea (1636'29.5"S 4916'17.4"W), stored at -80C (LGBio/UFG), was extracted using two methods for sequencing on the PromethION 2 Solo platform (Oxford Nanopore). The first extraction followed the 2% CTAB protocol (Doyle & Doyle, 1987), yielding fragments of ~54 kb (Qubit/TapeStation). The library was prepared with the SQK-LSK114 kit (1,500 ng input) and sequenced on Flow Cell R10.4.1 (FLO-PRO114M), with washing and reloading at 44h. Basecalling (MinKNOW v24.06.8, Dorado v7.4.13 SUP mode) produced an N50 of 4.58 kb. To optimize fragment size, the second extraction used a high molecular weight (HMW) protocol adapted from Kang et al. (2023), involving nuclei isolation, lysis in Carlson buffer, extraction with CIA, and precipitation. The DNA (161 ng/L) was mechanically sheared (26G syringe, 40 cycles) and purified with the Short Fragment Eliminator kit. The second library (SQK-LSK114, 1,000 ng input) was sequenced on a new Flow Cell R10.4.1 for 72h. Basecalling (MinKNOW v25.05.14, Dorado v7.9.8 SUP mode, Q  10) resulted in an N50 of 25.59 kb.