British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB30ET, UK.
BMC Genomics. 2010 Jun 8;11:362. doi: 10.1186/1471-2164-11-362.
The Antarctic clam, Laternula elliptica, is an infaunal stenothermal bivalve mollusc with a circumpolar distribution. It plays a significant role in bentho-pelagic coupling and hence has been proposed as a sentinel species for climate change monitoring. Previous studies have shown that this mollusc displays a high level of plasticity with regard to shell deposition and damage repair against a background of genetic homogeneity. The Southern Ocean has amongst the lowest present-day CaCO3 saturation rate of any ocean region, and is predicted to be among the first to become undersaturated under current ocean acidification scenarios. Hence, this species presents as an ideal candidate for studies into the processes of calcium regulation and shell deposition in our changing ocean environments.
454 sequencing of L. elliptica mantle tissue generated 18,290 contigs with an average size of 535 bp (ranging between 142 bp-5.591 kb). BLAST sequence similarity searching assigned putative function to 17% of the data set, with a significant proportion of these transcripts being involved in binding and potentially of a secretory nature, as defined by GO molecular function and biological process classifications. These results indicated that the mantle is a transcriptionally active tissue which is actively proliferating. All transcripts were screened against an in-house database of genes shown to be involved in extracellular matrix formation and calcium homeostasis in metazoans. Putative identifications were made for a number of classical shell deposition genes, such as tyrosinase, carbonic anhydrase and metalloprotease 1, along with novel members of the family 2 G-Protein Coupled Receptors (GPCRs). A membrane transport protein (SEC61) was also characterised and this demonstrated the utility of the clam sequence data as a resource for examining cold adapted amino acid substitutions. The sequence data contained 46,235 microsatellites and 13,084 Single Nucleotide Polymorphisms(SNPs/INDELS), providing a resource for population and also gene function studies.
This is the first 454 data from an Antarctic marine invertebrate. Sequencing of mantle tissue from this non-model species has considerably increased resources for the investigation of the processes of shell deposition and repair in molluscs in a changing environment. A number of promising candidate genes were identified for functional analyses, which will be the subject of further investigation in this species and also used in model-hopping experiments in more tractable and economically important model aquaculture species, such as Crassostrea gigas and Mytilus edulis.
南极蛤（Laternula elliptica）是一种底栖狭温双壳贝类软体动物，分布范围广泛。它在底栖和上层海洋耦合中起着重要作用，因此被提议作为气候变化监测的哨兵物种。先前的研究表明，这种软体动物在贝壳沉积和损伤修复方面具有高度的可塑性，同时保持着遗传同质性。南大洋是现今碳酸钙饱和度最低的海洋区域之一，预计在当前海洋酸化情景下将成为最早不饱和的海洋之一。因此，这种物种是研究我们变化的海洋环境中钙调节和贝壳沉积过程的理想候选物种。
对南极蛤套膜组织进行的 454 测序生成了 18290 个 Contigs，平均大小为 535bp（范围在 142bp-5.591kb 之间）。BLAST 序列相似性搜索将数据集的 17%赋予了可能的功能，其中很大一部分转录本参与结合，并且根据 GO 分子功能和生物学过程分类，具有潜在的分泌性质。这些结果表明套膜是一个转录活跃的组织，正在积极增殖。所有转录本都与一个内部数据库进行了筛选，该数据库包含参与后生动物细胞外基质形成和钙稳态的基因。鉴定了一些经典的贝壳沉积基因，如酪氨酸酶、碳酸酐酶和金属蛋白酶 1，以及家族 2 G-蛋白偶联受体（GPCRs）的新成员。还鉴定了一种膜转运蛋白（SEC61），这证明了蛤序列数据作为研究冷适应氨基酸取代的资源的效用。该序列数据包含 46235 个微卫星和 13084 个单核苷酸多态性（SNP/INDEL），为种群和基因功能研究提供了资源。
这是来自南极海洋无脊椎动物的第一个 454 数据。对这种非模式物种套膜组织的测序大大增加了研究环境变化中贝壳沉积和修复过程的资源。鉴定了一些有前途的候选基因进行功能分析，这将是该物种进一步研究的主题，并将用于更易于处理和经济上更重要的养殖物种（如太平洋牡蛎和贻贝）的模型跳跃实验。
