Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs.
Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs.
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作者：
Guðbrandsson J;Franzdóttir SR;Kristjánsson BK;Ahi EP;Maier VH;Kapralova KH;Snorrason SS;Jónsson ZO;Pálsson A
密切相关的分类群或种群之间的表型差异可以通过遗传变异产生，也可以由环境诱导，导致发育过程中基因转录的改变。对密切相关物种或物种内可变种群的比较发育研究有助于阐明与进化差异和物种形成相关的分子机制。对北极沙鱼(Salvelinus Alpinus)和相关鲑鱼的研究表明，种群之间的表型差异很大，在北极沙鱼中，记录到了许多湖泊内广泛变化的情况(资源多态)。一个例子是∼10000年前的Thingvalavatn湖中的四种北极炭形态，它们在许多形态和生活史特征上都不同。我们开始研究这种多态的分子和发育根源，通过研究在一个普通的花园中饲养的三个变种的胚胎中的基因表达。我们进行了RNA测序，从头开始的转录组组装，并在早期发育的重要时间框架内，即关键营养结构形成之前，比较了不同形态之间的基因表达。不出所料，发育时间是主要的解释变量。由于数据受到某种形式的RNA降解的影响，即使所有样本都通过了质量控制测试，3‘-偏差的估计是第二个最常见的解释变量。重要的是，形态既是一个自变量，也是一个与发育时间相互作用的变量，影响了许多转录本的表达。具有形态效应的转录本在表达水平上分离了这三种形态，其中两种底栖形态更相似。然而，基因本体论分析并未显示组之间转录本的明显功能丰富。定量聚合酶链式反应证实了多种基因在不同亚型之间的差异表达，包括调控基因，如AT-Rich相互作用结构域4A(Arid4a)和翻译蛋白(Tsn)。这些数据与这样一种情景相一致，即在这些共域北极字符形态的早期发育过程中，遗传差异导致了多个基因和系统的差异表达。
Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, leading to altered transcription of genes during development. Comparative developmental studies of closely related species or variable populations within species can help to elucidate the molecular mechanisms related to evolutionary divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10,000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during an important timeframe in early development, i.e., preceding the formation of key trophic structures. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by some form of RNA-degradation even though all samples passed quality control testing, an estimate of 3′-bias was the second most common explanatory variable. Importantly, morph, both as an independent variable and as interaction with developmental time, affected the expression of numerous transcripts. Transcripts with morph effect, separated the three morphs at the expression level, with the two benthic morphs being more similar. However, Gene Ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as AT-Rich Interaction Domain 4A (arid4a) and translin (tsn). The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.
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影响因子：
16.6
作者：
Berthelot, Camille;Brunet, Frederic;Chalopin, Domitille;Juanchich, Amelie;Bernard, Maria;Noel, Benjamin;Bento, Pascal;Da Silva, Corinne;Labadie, Karine;Alberti, Adriana;Aury, Jean-Marc;Louis, Alexandra;Dehais, Patrice;Bardou, Philippe;Montfort, Jerome;Klopp, Christophe;Cabau, Cedric;Gaspin, Christine;Thorgaard, Gary H.;Boussaha, Mekki;Quillet, Edwige;Guyomard, Rene;Galiana, Delphine;Bobe, Julien;Volff, Jean-Nicolas;Genet, Carine;Wincker, Patrick;Jaillon, Olivier;Roest Crollius, Hugues;Guiguen, Yann
通讯作者：
Guiguen, Yann
影响因子：
4.4
作者：
Danzmann RG;Kocmarek AL;Norman JD;Rexroad CE 3rd;Palti Y
通讯作者：
Palti Y
影响因子：
3.7
作者：
Ahi EP;Guðbrandsson J;Kapralova KH;Franzdóttir SR;Snorrason SS;Maier VH;Jónsson ZO
通讯作者：
Jónsson ZO
SalmondB：Salmo Salar和Oncorhynchus Mykiss的生物信息学资源。
DOI：
10.1093/database/bar050
发表时间：
2011
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Di Génova A;Aravena A;Zapata L;González M;Maass A;Iturra P
通讯作者：
Iturra P
影响因子：
7
作者：
Coolon JD;McManus CJ;Stevenson KR;Graveley BR;Wittkopp PJ
通讯作者：
Wittkopp PJ