The silver-lipped pearl oyster, Pinctada maxima, is an iconic bivalve farmed in tropical Australia and South-east Asia to produce high valued South Sea pearls. Here, we present the first high-quality, chromosome-level reference genome of P. maxima. The final genome assembly has a total size of 1.27 Gb, with a scaffold N50 length of 209.20 Mb. Using high-throughput chromosome conformation capture (Hi-C) technology, we have anchored 80.99% of the assembly to 14 chromosomes. The BUSCO analysis revealed a high level of accuracy and completeness, identifying 87.9% (n = 4,658) of conserved metazoan genes, which exceeds the average completeness of 79.2% reported for other mollusc genomes sequenced and annotated to date. The assembly includes 62.79% repeat elements (809 Mb), and gene annotation predicted 25,752 protein-coding genes. This genomic resource offers a powerful tool for unraveling the molecular mechanisms underlying pearl formation and facilitating continued research into the evolutionary biology of pearl oysters worldwide.

A single Pinctada maxima individual from the Roko Pearls farm (Roko Island Cape York, Queensland, Australia) was collected. The individual was air-shipped alive to James Cook University (July 2019) for dissection. To limit exogenous contamination, 800 mg of tissue was cut from the interior adductor muscle and diced on a petri dish. Tissue was lysed overnight at 50 °C in a blend of 9.5 ml of Qiagen buffer, 19 μL RNase A buffer and 1ml proteinase K. Lysates were centrifuged at 500g for 10 min at 4 °C. Lysates were then loaded onto Qiagen Genomic-tip 100/G DNA extraction columns and washed with the QC buffer as specified in the manufacturer’s protocol. Samples were eluted in 5 ml of QF buffer and precipitated by adding 3.5 ml of isopropanol. Samples were then centrifuged at 8,000 g for 30 min at 4 °C. Supernatant was then removed and pellets were washed with 70% ethanol at -20 °C and centrifuged again at 8,000 g for 30 min at 4 °C. Pellets were then air-dried for 10 minutes on ice. Quality and quantity were assessed using a Nanodrop spectrophotometer and a 0.8% agarose gel. Extracted DNA was kept at 4 °C until it was received by the sequencing facilities. Long-read PacBio libraries were prepared using a PacBio sheared gDNA kit and sequenced on eight runs of PacBio Sequel II at the Genome Quebec sequencing platform (Canada). Short-read Illumina libraries, Chromium 10X and DNA-seq, were prepared using TrueSeq DNA nano kit and sequenced on a full chip of Illumina NovaSeq 6000 150bp paired-end (PE) at the Australian Genome Research Facilities (Melbourne, Australia). Overall, library sequencing resulted in a total of 6M (mean size 7.5 Kb; ranges from 50 to 114 Kb; 45X coverage) PacBio reads and 431M Illumina reads (Table 1). In parallel, gill tissue, from the same individual, was sent on dry ice to the NextGen platform (Plateforme Génomique IHPE Ifremer facilities Montpellier, France) for Dovetail Hi-C library preparation. Libraries were prepared using the Omni-C kit (Dovetail Genomic, DNAse enzyme) and were sequenced in two runs on the Illumina 6000 NovaSeq (1/3 full chip).