DOI: 10.5061/dryad.280gb5n1j
title: Chromosome-level genome assembly and annotation of the emblematic silver-lipped pearl oyster, Pinctada maxima Jameson, 1901

description: 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.
description: A single <em>Pinctada maxima</em> 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).
description: # Chromosome-level genome assembly and annotation of the emblematic
 silver-lipped pearl oyster, Pinctada maxima Jameson, 1901
 [https://doi.org/10.5061/dryad.280gb5n1j](https://doi.org/10.5061/dryad.280gb5n1j) ## Description of the data and file structure The enclosed data are :  * p.maxima.chr.bed: the genome in .bed format * p.maxima.gff3: the genome in .gff3 format * p.maxima.scaff.chr.fasta in .fasta format * pmaxima-main.zip : all the scripts used to generate the genome assembly (on Zenodo)