Franchini Paolo, van der Merwe Mathilde, Roodt-Wilding Rouvay
Molecular Aquatic Research Group, Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
BMC Res Notes. 2011 Mar 11;4:59. doi: 10.1186/1756-0500-4-59.
Worldwide, the genus Haliotis is represented by 56 extant species and several of these are commercially cultured. Among the six abalone species found in South Africa, Haliotis midae is the only aquacultured species. Despite its economic importance, genomic sequence resources for H. midae, and for abalone in general, are still scarce. Next generation sequencing technologies provide a fast and efficient tool to generate large sequence collections that can be used to characterize the transcriptome and identify expressed genes associated with economically important traits like growth and disease resistance.
More than 25 million short reads generated by the Illumina Genome Analyzer were de novo assembled in 22,761 contigs with an average size of 260 bp. With a stringent E-value threshold of 10-10, 3,841 contigs (16.8%) had a BLAST homologous match against the Genbank non-redundant (NR) protein database. Most of these sequences were annotated using the gene ontology (GO) and eukaryotic orthologous groups of proteins (KOG) databases and assigned to various functional categories. According to annotation results, many gene families involved in immune response were identified. Thousands of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were detected. Setting stringent parameters to ensure a high probability of amplification, 420 primer pairs in 181 contigs containing SSR loci were designed.
This data represents the most comprehensive genomic resource for the South African abalone H. midae to date. The amount of assembled sequences demonstrated the utility of the Illumina sequencing technology in the transcriptome characterization of a non-model species. It allowed the development of several markers and the identification of promising candidate genes for future studies on population and functional genomics in H. midae and in other abalone species.
在全球范围内，鲍属有56个现存物种，其中一些已进行商业养殖。在南非发现的六种鲍鱼中，南非鲍是唯一进行水产养殖的物种。尽管其具有重要经济价值，但南非鲍以及一般鲍鱼的基因组序列资源仍然稀缺。新一代测序技术提供了一种快速有效的工具，可生成大量序列集合，用于表征转录组并鉴定与生长和抗病性等经济重要性状相关的表达基因。
Illumina基因组分析仪产生的超过2500万个短读段被从头组装成22761个重叠群，平均大小为260 bp。在严格的E值阈值为10-10的情况下，3841个重叠群（16.8%）与Genbank非冗余（NR）蛋白质数据库有BLAST同源匹配。这些序列大多使用基因本体（GO）和真核生物直系同源蛋白质组（KOG）数据库进行注释，并被分配到各种功能类别。根据注释结果，鉴定出许多参与免疫反应的基因家族。检测到数千个简单序列重复（SSR）和单核苷酸多态性（SNP）。设置严格参数以确保高扩增概率，在181个包含SSR位点的重叠群中设计了420对引物。
这些数据代表了迄今为止南非鲍鱼最全面的基因组资源。组装序列的数量证明了Illumina测序技术在非模式物种转录组表征中的效用。它有助于开发多种标记，并鉴定出有前景的候选基因，用于未来对南非鲍和其他鲍鱼物种的群体和功能基因组学研究。
