An integrated transcriptome-wide analysis of cave and surface dwelling Astyanax mexicanus.
An integrated transcriptome-wide analysis of cave and surface dwelling Astyanax mexicanus.
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DOI：
10.1371/journal.pone.0055659
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Stahl BA
中科院分区：
文献类型：
--
作者：
Gross JB;Furterer A;Carlson BM;Stahl BA
地球仪上的许多生物已经成功地适应了地下环境。研究洞穴适应性的一个强有力的系统是淡水特征鱼，墨西哥丽脂鲤。先前在该系统中的研究已经为许多退化性状的进化建立了遗传基础，最显着的是视力和色素沉着减少。然而，由于遗传和基因组资源有限，这些形态学变化背后的精确遗传改变的鉴定一直被推迟。为了解决这一问题，我们使用Roche/454焦磷酸测序技术对洞穴和地表栖息的Astyanax变体进行了转录组分析。通过这种方法，我们获得了576，197个Pachón洞穴鱼类特异性读数和438，978个表面鱼类特异性读数。使用这个数据集，我们分别组装了洞穴鱼和水面鱼的转录组，以及一个整合的转录组，该转录组结合了来自两种形态型的1，499，568个读数。整合组装是最成功的方法，产生了22，596个高质量的连续序列，包括21，363，556 bp的总转录组长度。通过穷举blast搜索获得序列同一性，揭示了由高度多样的基因本体论（GO）术语表示的成人转录组。我们的数据集促进了形态型之间序列多态性的快速鉴定。这些数据，沿着从斑马鱼基因组收集的位置信息，揭示了Astyanax和Danio之间的几个同线区域。我们证明了这个位置信息的效用，通过一个表面x Pachón洞穴F2家系白化的QTL分析，使用65个多态性标记，从我们的集成组件。我们还将我们的数据集用于RNA-seq研究，揭示了许多负责表面鱼类视觉系统维护的基因，这些基因的表达在成年Pachón洞穴鱼中未检测到。相反，在洞穴鱼类中表达的几个代谢相关基因在水面鱼类中没有检测到。这一资源将使强大的遗传和基因组分析在未来，将更好地澄清遗传的遗传变化，管理适应洞穴环境。
Numerous organisms around the globe have successfully adapted to subterranean environments. A powerful system in which to study cave adaptation is the freshwater characin fish, Astyanax mexicanus. Prior studies in this system have established a genetic basis for the evolution of numerous regressive traits, most notably vision and pigmentation reduction. However, identification of the precise genetic alterations that underlie these morphological changes has been delayed by limited genetic and genomic resources. To address this, we performed a transcriptome analysis of cave and surface dwelling Astyanax morphs using Roche/454 pyrosequencing technology. Through this approach, we obtained 576,197 Pachón cavefish-specific reads and 438,978 surface fish-specific reads. Using this dataset, we assembled transcriptomes of cave and surface fish separately, as well as an integrated transcriptome that combined 1,499,568 reads from both morphotypes. The integrated assembly was the most successful approach, yielding 22,596 high quality contiguous sequences comprising a total transcriptome length of 21,363,556 bp. Sequence identities were obtained through exhaustive blast searches, revealing an adult transcriptome represented by highly diverse Gene Ontology (GO) terms. Our dataset facilitated rapid identification of sequence polymorphisms between morphotypes. These data, along with positional information collected from the Danio rerio genome, revealed several syntenic regions between Astyanax and Danio. We demonstrated the utility of this positional information through a QTL analysis of albinism in a surface x Pachón cave F2 pedigree, using 65 polymorphic markers identified from our integrated assembly. We also adapted our dataset for an RNA-seq study, revealing many genes responsible for visual system maintenance in surface fish, whose expression was not detected in adult Pachón cavefish. Conversely, several metabolism-related genes expressed in cavefish were not detected in surface fish. This resource will enable powerful genetic and genomic analyses in the future that will better clarify the heritable genetic changes governing adaptation to the cave environment.
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影响因子：
3.7
作者：
Bai X;Mamidala P;Rajarapu SP;Jones SC;Mittapalli O
通讯作者：
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