Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx.
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx.
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DOI：
10.1186/1471-2164-10-219
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发表时间：
2009-05-12
期刊：
影响因子：
4.4
通讯作者：
Matz MV
中科院分区：
文献类型：
--
作者：
Meyer E;Aglyamova GV;Wang S;Buchanan-Carter J;Abrego D;Colbourne JK;Willis BL;Matz MV
需要新的方法来对新兴模式生物进行基因组规模的分析，这些模式生物举例说明了重要的生物学问题，但缺乏完全测序的基因组。例如，迫切需要了解珊瑚适应气候变化的潜力，但很少有分子资源可用于研究造礁珊瑚的这些过程。为了促进珊瑚和其他非模型系统的基因组学研究，我们描述了使用454进行转录组测序的方法，以及从输出中组装有用的基因目录的策略。我们应用这些方法对珊瑚千孔鹿角（Acropora millepora）的planulae幼虫的转录组进行了测序。在单次454测序运行中产生的60多万个reads被组装成约40,000个contigs，平均测序覆盖率为5倍。基于与已知蛋白质的序列相似性，这些分析确定了在热应力和沉降诱导等一系列条件下表达的约11,000种不同基因。组装的序列用基因名称、保守结构域和基因本体术语进行注释。使用这些注释的目标搜索确定了与基本代谢途径和保守信号通路相关的大多数基因，以及与压力相关过程相关的新候选基因。与海葵Nematostella vectensis的基因组比较，发现了约8,500对同源基因和约100个候选珊瑚特异性基因。在珊瑚序列中检测到超过30,000个snp，其中一部分通过重新测序得到了验证。本文描述的转录组深度测序方法应该广泛适用于生成新兴模式生物的基因和遗传标记目录。我们的数据提供了目前可用于造礁珊瑚的最全面的序列资源，并包括广泛收集的潜在遗传标记，用于关联和种群连通性研究。对这种被广泛研究的珊瑚的幼虫转录组进行表征，将有助于研究珊瑚应激反应的生物学过程以及对全球气候变化的进化适应。
New methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand the potential for corals to adapt to climate change, but few molecular resources are available for studying these processes in reef-building corals. To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as well as strategies for assembling a useful catalog of genes from the output. We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora. More than 600,000 reads produced in a single 454 sequencing run were assembled into ~40,000 contigs with five-fold average sequencing coverage. Based on sequence similarity with known proteins, these analyses identified ~11,000 different genes expressed in a range of conditions including thermal stress and settlement induction. Assembled sequences were annotated with gene names, conserved domains, and Gene Ontology terms. Targeted searches using these annotations identified the majority of genes associated with essential metabolic pathways and conserved signaling pathways, as well as novel candidate genes for stress-related processes. Comparisons with the genome of the anemone Nematostella vectensis revealed ~8,500 pairs of orthologs and ~100 candidate coral-specific genes. More than 30,000 SNPs were detected in the coral sequences, and a subset of these validated by re-sequencing. The methods described here for deep sequencing of the transcriptome should be widely applicable to generate catalogs of genes and genetic markers in emerging model organisms. Our data provide the most comprehensive sequence resource currently available for reef-building corals, and include an extensive collection of potential genetic markers for association and population connectivity studies. The characterization of the larval transcriptome for this widely-studied coral will enable research into the biological processes underlying stress responses in corals and evolutionary adaptation to global climate change.
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影响因子：
3.5
作者：
Heyward, AJ;Negri, AP
通讯作者：
Negri, AP
通过454转录组测序发现SNP。
影响因子：
7.2
作者：
Barbazuk, W Brad;Emrich, Scott J;Chen, Hsin D;Li, Li;Schnable, Patrick S
通讯作者：
Schnable, Patrick S
影响因子：
14.9
作者：
Karp PD;Ouzounis CA;Moore-Kochlacs C;Goldovsky L;Kaipa P;Ahrén D;Tsoka S;Darzentas N;Kunin V;López-Bigas N
通讯作者：
López-Bigas N
影响因子：
3.5
作者：
Iwao, K;Fujisawa, T;Hatta, M
通讯作者：
Hatta, M
测序的Medicago truncatula使用454个生命科学技术表达了测序标签。
影响因子：
4.4
作者：
Cheung, Foo;Haas, Brian J;Goldberg, Susanne M D;May, Gregory D;Xiao, Yongli;Town, Christopher D
通讯作者：
Town, Christopher D