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).