Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand.
BMC Genomics. 2012 Aug 31;13:439. doi: 10.1186/1471-2164-13-439.
The tuatara (Sphenodon punctatus) is a species of extraordinary zoological interest, being the only surviving member of an entire order of reptiles which diverged early in amniote evolution. In addition to their unique phylogenetic placement, many aspects of tuatara biology, including temperature-dependent sex determination, cold adaptation and extreme longevity have the potential to inform studies of genome evolution and development. Despite increasing interest in the tuatara genome, genomic resources for the species are still very limited. We aimed to address this by assembling a transcriptome for tuatara from an early-stage embryo, which will provide a resource for genome annotation, molecular marker development and studies of development and adaptation in tuatara.
We obtained 30 million paired-end 50 bp reads from an Illumina Genome Analyzer and assembled them with Velvet and Oases using a range of kmers. After removing redundancy and filtering out low quality transcripts, our transcriptome dataset contained 32911 transcripts, with an N50 of 675 and a mean length of 451 bp. Almost 50% (15965) of these transcripts could be annotated by comparison with the NCBI non-redundant (NR) protein database or the chicken, green anole and zebrafish UniGene sets. A scan of candidate genes and repetitive elements revealed genes involved in immune function, sex differentiation and temperature-sensitivity, as well as over 200 microsatellite markers.
This dataset represents a major increase in genomic resources for the tuatara, increasing the number of annotated gene sequences from just 60 to almost 16,000. This will facilitate future research in sex determination, genome evolution, local adaptation and population genetics of tuatara, as well as inform studies on amniote evolution.
大蜥蜴（Sphenodon punctatus）是一种具有特殊动物学意义的物种，是整个爬行动物目在羊膜动物进化早期分化出来的唯一幸存成员。除了它们独特的系统发育位置外，大蜥蜴生物学的许多方面，包括温度依赖性性别决定、冷适应和极端长寿，都有可能为基因组进化和发育研究提供信息。尽管人们对大蜥蜴基因组的兴趣日益增加，但该物种的基因组资源仍然非常有限。我们的目标是通过从早期胚胎中组装大蜥蜴的转录组来解决这个问题，这将为基因组注释、分子标记开发以及大蜥蜴的发育和适应研究提供资源。
我们从 Illumina Genome Analyzer 获得了 3000 万个配对末端 50bp 读取，并使用 Velvet 和 Oases 利用一系列 kmer 进行组装。在去除冗余和过滤低质量转录本后，我们的转录组数据集包含 32911 个转录本，N50 为 675，平均长度为 451bp。这些转录本中有近 50%（15965 个）可以通过与 NCBI 非冗余（NR）蛋白质数据库或鸡、绿鬣蜥和斑马鱼 UniGene 集进行比较来注释。对候选基因和重复元件的扫描揭示了参与免疫功能、性别分化和温度敏感性的基因，以及超过 200 个微卫星标记。
这个数据集代表了大蜥蜴基因组资源的重大增加，将注释基因序列的数量从仅仅 60 个增加到近 16000 个。这将有助于未来大蜥蜴性别决定、基因组进化、局部适应和种群遗传学的研究，并为羊膜动物进化的研究提供信息。
