Sampling Daphnia's expressed genes:: preservation, expansion and invention of crustacean genes with reference to insect genomes
Sampling Daphnia's expressed genes:: preservation, expansion and invention of crustacean genes with reference to insect genomes
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DOI：
10.1186/1471-2164-8-217
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发表时间：
2007-07-06
期刊：
影响因子：
4.4
通讯作者：
Andrews, Justen
中科院分区：
文献类型：
--
作者：
Colbourne, John K.;Eads, Brian D.;Andrews, Justen
背景资料：昆虫基因组的功能和比较研究揭示了基因的互补性，这在一定程度上解释了共同的形态，发育程序和生活史。将昆虫的基因清单与线虫的基因清单进行对比，可以深入了解导致其多样化的基因组变化。然而，线虫与昆虫的关系较弱，因为它们各自属于不同的动物门。一个更好的外群来区分谱系特异性的新奇事物，将包括节肢动物门的其他成员。例如，甲壳类动物的亲密盟友的昆虫（一起形成Pancrustacea）和他们迷人的水生生活方式提供了一个重要的比较，了解适应生活在陆地上与生活在water.Results的遗传基础：本研究报告的第一个表征的cDNA文库和序列的模式甲壳动物蚤状水蚤。我们分析了1，546个EST，其中1，414个代表约787个核基因，通过测量它们与昆虫和线虫蛋白质组的序列相似性。基因的临时注释得到了同伴论文中描述的微阵列研究的表达数据的支持。由于甲壳类动物和昆虫具有共同的生物学特征，因此它们之间预期共有的基因座被确定，包括生殖、调节和细胞过程的基因。我们确定的基因可能是来自泛甲壳纲或失去了线虫。此外，谱系特异性基因家族的扩展被确定，这表明与其生态环境相关的某些生物需求。特别是，多达七个不同的铁蛋白位点被发现在水蚤相比，在大多数昆虫中的三个。最后，相当一部分的采样基因转录本与其他节肢动物没有序列相似性。在发育和繁殖过程中发挥作用的基因在甲壳类动物和昆虫之间相对较好地保守。相比之下，对环境条件有反应的基因（金属胁迫）和无性别偏见的基因包括与昆虫蛋白质组不匹配的基因的最大比例。这项研究沿着相关的微阵列实验是水蚤基因组学联盟协调努力的最初步骤，以建立必要的基因组平台，发现解释属内表型多样性的基因，对甲壳类生物学有了新的认识这项工作将很快包括第一个甲壳类基因组序列。
Background: Functional and comparative studies of insect genomes have shed light on the complement of genes, which in part, account for shared morphologies, developmental programs and life-histories. Contrasting the gene inventories of insects to those of the nematodes provides insight into the genomic changes responsible for their diversification. However, nematodes have weak relationships to insects, as each belongs to separate animal phyla. A better outgroup to distinguish lineage specific novelties would include other members of Arthropoda. For example, crustaceans are close allies to the insects ( together forming Pancrustacea) and their fascinating aquatic lifestyle provides an important comparison for understanding the genetic basis of adaptations to life on land versus life in water.Results: This study reports on the first characterization of cDNA libraries and sequences for the model crustacean Daphnia pulex. We analyzed 1,546 ESTs of which 1,414 represent approximately 787 nuclear genes, by measuring their sequence similarities with insect and nematode proteomes. The provisional annotation of genes is supported by expression data from microarray studies described in companion papers. Loci expected to be shared between crustaceans and insects because of their mutual biological features are identified, including genes for reproduction, regulation and cellular processes. We identify genes that are likely derived within Pancrustacea or lost within the nematodes. Moreover, lineage specific gene family expansions are identified, which suggest certain biological demands associated with their ecological setting. In particular, up to seven distinct ferritin loci are found in Daphnia compared to three in most insects. Finally, a substantial fraction of the sampled gene transcripts shares no sequence similarity with those from other arthropods. Genes functioning during development and reproduction are comparatively well conserved between crustaceans and insects. By contrast, genes that were responsive to environmental conditions (metal stress) and not sex-biased included the greatest proportion of genes with no matches to insect proteomes.Conclusion: This study along with associated microarray experiments are the initial steps in a coordinated effort by the Daphnia Genomics Consortium to build the necessary genomic platform needed to discover genes that account for the phenotypic diversity within the genus and to gain new insights into crustacean biology. This effort will soon include the first crustacean genome sequence.