Sample collection and sequencing
A female and a male Chinese bahaba, approximately one year old, were obtained from Guangdong Beluga Whale Marine Biotechnology Co., Ltd. (Guangdong, China). The sex was confirmed through paraffin sectioning and hematoxylin and eosin (HE) staining of the gonadal tissue, following the methods outlined by Chen et al (Chen et al., 2007). Multiple tissues, including heart, intestine, kidney, liver, muscle, skin, spleen, stomach, and swim bladder, were promptly frozen in liquid nitrogen and stored at -80°C.
DNA extraction, library preparation, and sequencing were performed on the female sample to obtain PacBio HiFi reads and ONT ultra-long reads, following the standard protocols provided by Pacific Biosciences (PacBio, Menlo Park, CA) and Oxford Nanopore Technologies (ONT). The Hi-C library was prepared using the female muscle tissue, which was first fixed with formaldehyde, followed by DNA digestion with MboI and repair of the 5’ overhangs of the digested DNA with a biotinylated residue, according to the protocol described by Li (C. Li, 2018). A paired-end library with an insert size of approximately 300 bp was constructed for Hi-C sequencing and sequenced on the BGISEQ-500 platform.
For transcriptome sequencing, RNA was extracted from all nine tissues using TRIzol reagent (Invitrogen, USA). The RNA libraries were then prepared using the MGIEasy RNA Library Prep Set (MGI, China) and sequenced on the BGISEQ-500 platform.