Genome sequencing and assembly
Total genomic DNA was further fractionated into 10-50 kb fragments with
BluePippin to construct libraries following the Nanopore library
construction protocol. The libraries were sequenced at the Nextomics
Biosciences Company (Wuhan, China) using the GridION X5 sequencer
platform (Oxford Nanopore Technologies, UK). Quality-controlled reads
were used for de novo assembly using Nextdenovo v. 2.3.051
(https://github.com/Nextomics/NextDenovo). We corrected sequencing
errors with NextCorrect, assembled with NextGraph, and polished with
NextPolish v. 1.2.424 (Hu et al., 2020). At this stage, the short and
long reads were used three times for genome correction. Finally,
purge_haplotigs (Roach et al., 2018) was used to remove allelic
haplotigs, resulting in the final genome assembly. Benchmarking
Universal Single-Copy Orthologs (BUSCO) v. 2.026 (Simão et al., 2015),
with 1,350 genes from Embryophyta odb10, was used to evaluate the
completeness and accuracy of the assembled genome.