2.1 Sampling, library construction, and sequencing
Fresh Asian Clam (Corbicula fluminea ) samples were collected from
Hongze Lake, Jiangsu, China. Healthy, disease-free, and tender
individuals of C. fluminea were selected for genome sequencing.
After shelling and removing the intestines by hand, the remaining body
tissues were immediately transferred into liquid nitrogen and sequenced
by Biomarker Technologies Corporation, Beijing. High-quality genomic DNA
was extracted from the Asian Clam using a DNeasyRBlood & Tissue Kit
(Qiagen, Hilden, Germany). The DNA quality was measured with Qubit 3.0
(Invitrogen, Carlsbad, CA, USA) and was checked using 1% agarose gel
electrophoresis.
Illumina libraries were constructed according to the manufacturer’s
standard PCR-free protocol (Illumina) and sequenced on an Illumina HiSeq
X Ten platform (Illumina, Inc., San Diego, CA, USA) using the paired-end
150 (PE150) strategy. Approximately 30 μg of genomic DNA was used to
construct PacBio libraries by shearing into ~20 kb
targeted size fragments with BluePippin (Sage Science, Beverly, MA,
USA). Then, the qualified libraries were prepared for single-molecule
real-time (SMRT) genome sequencing using S/P2-C2 sequencing chemistry on
the PacBio Sequel II platform (PacBio, Pacific Biosciences, USA). The
Hi-C libraries were cross-linked in situ using formaldehyde with a final
concentration of 2% and homogenized with tissue lysis by the
restriction enzyme Hind III. The libraries for Hi-C with insert
sizes of 300–700 bp were sequenced on an Illumina HiSeq X Ten platform
(Illumina, SanDiego, CA, USA). All processes were performed at Biomarker
Technologies Corporation following the standard protocols.