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.