2.1 | Samples
All specimens of Sichuan B. schroederi population were collected from the giant panda (Ailuropoda melanoleuca ) with naturally acquired infections from the China Conservation and Research Center for Giant Panda during the period August 2018 to July 2019. Samples of Qinling B. schroederi population were obtained from the intestines of a wild giant panda that died shortly after being found in the Foping National Nature Reserve (Qinling Mountains) in 2018. The captive and wild individuals differed by geography and the different pressure of deworming history. Roundworms were washed extensively in sterile physiological saline (37 oC), sexes separated, snap-frozen and transported on dry ice and then stored at -80oC until use. Several specimens were stored in RNA preservation solution for transcriptome sequencing. All experimental designs and nematodes handling were approved by the Institutional Animal Care and Use Committee of Northeast Forestry University.
2.2 |Library construction, sequencing and assembly
PacBio libraries were generated with a SMRTbell Template Prep Kit 1.0 (Pacific Biosciences, USA) and the SMRTbell Damage Repair Kit (Pacific Biosciences, USA) and were sequenced with one SMRT cell on the PacBio SMRTplatform. In addition, a 100‐bp paired‐end library was constructed and sequenced on a BGISEQ platform to assess the complexity of genome and to polish PacBio data (for details, see supplementary text).
The B. schroederi genome was assembled using a “correct-then-assemble” strategy. First, NextDenovo (v2.0-beta.1;https://github.com/Nextomics/NextDenovo) was used to correct and assemble a draft genome. The Arrow (v0.3.2) algorithm was then used to carry out a second round of correction for this assembly (Archibald, 2017). NextPolish (v1.0.5) (J. Hu, Fan, Sun, & Liu, 2019) was further used for genome polishing by using the WGS data. To finally ligate the scaffolds to chromosomes, Hi-C technology (Lieberman-Aiden et al., 2009) was used to capture the chromosome conformations. 105Gb (~400 X) Hi-C sequencing data were generated from a single Hi-C library which was constructed as previously described. We next used Juicer (v1.5.7) to analyze the Hi‐C data sets, and a three‐dimensional de novo assembly (3D‐DNA v180322) pipeline (Dudchenko et al., 2017) to scaffold spotted B. schroederi genome to chromosome-length scaffolds (for details, see supplementary text). We used the diamond (v0.9.10) software to blast the genome against the NCBI NR database, then deleted the scaffolds that blasted to bacteria (such as Escherichia coli ,Lactococcus lactis ) and generated the final genome file. Finally, we used the Purge_Dups pipeline (Guan et al., 2020) to remove haplotig sequences from the genome. The completeness of the genome was evaluated using sets of Benchmarking Universal Single-Copy Orthologs (BUSCO v3.0.1) with genome mode and lineage data from nematode odb9 and eukaryote odb9, respectively (Simão, Waterhouse, Panagiotis, Kriventseva, & Zdobnov, 2015).