Centre for Sustainable Tropical Fisheries and Aquaculture & School of Marine and Tropical Biology, James Cook University, Townsville, QLD, 4811, Australia,
Mar Biotechnol (NY). 2013 Dec;15(6):647-58. doi: 10.1007/s10126-013-9514-3. Epub 2013 May 30.
Pearl oysters are not only farmed for their gemstone quality pearls worldwide, but they are also becoming important model organisms for investigating genetic mechanisms of biomineralisation. Despite their economic and scientific significance, limited genomic resources are available for this important group of bivalves, hampering investigations into identifying genes that regulate important pearl quality traits and unique biological characteristics (i.e. biomineralisation). The silver-lipped pearl oyster, Pinctada maxima, is one species where there is interest in understanding genes that regulate commercially important pearl traits, but presently, there is a dearth of genomic information. The objective of this study was to develop and validate a large number of type I genome-wide single nucleotide polymorphisms (SNPs) for P. maxima suitable for high-throughput genotyping. In addition, sequence annotations and Gene Ontology terms were assigned to a large mantle tissue 454 expressed sequence tag assembly (96,794 contigs) and information on known bivalve biomineralisation genes was incorporated into SNP discovery. The SNP discovery effort resulted in the de novo identification of 172,625 SNPs, of which 9,108 were identified as high value [minor allele frequency (MAF)≥ 0.15, read depth ≥ 8]. Validation of 2,782 of these SNPs using Illumina iSelect Infinium genotyping technology returned some of the highest assay conversion (86.6 %) and validation (59.9 %; mean MAF 0.28) rates observed in aquaculture species to date. Genomic resources presented here will be pivotal to future research investigating the biological mechanisms behind biomineralisation and will form a strong foundation for genetic selective breeding programs in the P. maxima pearling industry.
珍珠贝不仅因其宝石品质的珍珠在全球范围内养殖，而且还成为研究生物矿化遗传机制的重要模式生物。尽管它们具有经济和科学意义，但该重要双壳贝类的基因组资源有限，这阻碍了识别调控重要珍珠品质性状和独特生物学特征（即生物矿化）的基因的研究。银唇珍珠贝（Pinctada maxima）是一种人们感兴趣的物种，希望了解调控具有商业价值的珍珠性状的基因，但目前，该物种的基因组信息匮乏。本研究的目的是开发和验证大量适合高通量基因分型的 P. maxima 型 I 全基因组单核苷酸多态性（SNP）。此外，序列注释和基因本体论术语被分配到一个大型套膜组织 454 表达序列标签组装（96794 个丛），并将已知双壳类生物矿化基因的信息纳入 SNP 发现中。SNP 发现工作导致了 172625 个 SNP 的从头鉴定，其中 9108 个被鉴定为高价值[次要等位基因频率（MAF）≥0.15，读取深度≥8]。使用 Illumina iSelect Infinium 基因分型技术对其中的 2782 个 SNP 进行验证，得到了迄今为止在水产养殖物种中观察到的一些最高的检测转换率（86.6%）和验证率（59.9%；平均 MAF 为 0.28）。本文提供的基因组资源对于研究生物矿化背后的生物学机制的未来研究至关重要，并将为 P. maxima 珍珠养殖行业的遗传选择育种计划奠定坚实的基础。
