Systemic paralogy and function of retinal determination network homologs in arachnids.
Systemic paralogy and function of retinal determination network homologs in arachnids.
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DOI：
10.1186/s12864-020-07149-x
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发表时间：
2020-11-23
期刊：
影响因子：
4.4
通讯作者：
Sharma PP
中科院分区：
文献类型：
--
作者：
Gainett G;Ballesteros JA;Kanzler CR;Zehms JT;Zern JM;Aharon S;Gavish-Regev E;Sharma PP
蛛形纲动物是洞穴生态系统的重要组成部分，并展示了许多穴居动物的例子，如失明，脱色和细长的附属物。人们对蛛形纲动物的眼睛是如何遗传的知之甚少，更不用说穴居蛛形纲动物眼睛减少和丧失的机制了。此外，重复的视网膜决定基因网络（RDGN）同源物在蜘蛛复杂的功能推断外推单拷贝同源物在泛甲壳动物模型。本研究调查了以色列洞穴鞭蛛的一对姐妹种--伊阿尼沙蛛Charinus ioanniticus和伊阿尼沙蛛C. Israelensis（Arachnopulmonata，Amblypygi），其中一种具有退化的眼睛。我们产生了两个Amblypygi物种的胚胎转录组，并发现几个RDGN同系物表现出重复。我们发现，重复的RDGN同源物是系统性的arachnopulmonates（蜘蛛目，承担书肺），而不是一个蜘蛛特有的现象。差异基因表达（DGE）分析比较了RDGN基因在两个物种的田间采集的胚胎中的表达，确定了参与鞭蜘蛛眼睛形成和减少的候选RDGN基因。为了将表达模式的生物信息学推断与功能实验结合起来，我们询问了在蜘蛛Parasteatoda tepidariorum中使用RNAi从DGE中鉴定的三个候选RDGN基因的功能。我们提供的功能证据表明，这些旁系同源物之一，正弦oculis/Six 1 A（soA），是必要的所有蛛形纲动物的眼睛类型的发展。我们的工作建立了一个基础，调查洞穴蜘蛛的troglomorphic适应的遗传学，并链接差异基因表达的节肢动物的眼睛表型首次以外的Pancrustacea。我们的研究结果支持保守的至少一个RDGN组件在节肢动物，并提供了一个框架，以确定基因复制的作用，在产生蛛形纲动物的眼睛多样性。
Arachnids are important components of cave ecosystems and display many examples of troglomorphisms, such as blindness, depigmentation, and elongate appendages. Little is known about how the eyes of arachnids are specified genetically, let alone the mechanisms for eye reduction and loss in troglomorphic arachnids. Additionally, duplication of Retinal Determination Gene Network (RDGN) homologs in spiders has convoluted functional inferences extrapolated from single-copy homologs in pancrustacean models. We investigated a sister species pair of Israeli cave whip spiders, Charinus ioanniticus and C. israelensis (Arachnopulmonata, Amblypygi), of which one species has reduced eyes. We generated embryonic transcriptomes for both Amblypygi species, and discovered that several RDGN homologs exhibit duplications. We show that duplication of RDGN homologs is systemic across arachnopulmonates (arachnid orders that bear book lungs), rather than being a spider-specific phenomenon. A differential gene expression (DGE) analysis comparing the expression of RDGN genes in field-collected embryos of both species identified candidate RDGN genes involved in the formation and reduction of eyes in whip spiders. To ground bioinformatic inference of expression patterns with functional experiments, we interrogated the function of three candidate RDGN genes identified from DGE using RNAi in the spider Parasteatoda tepidariorum. We provide functional evidence that one of these paralogs, sine oculis/Six1 A (soA), is necessary for the development of all arachnid eye types. Our work establishes a foundation to investigate the genetics of troglomorphic adaptations in cave arachnids, and links differential gene expression to an arthropod eye phenotype for the first time outside of Pancrustacea. Our results support the conservation of at least one RDGN component across Arthropoda and provide a framework for identifying the role of gene duplications in generating arachnid eye diversity.
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影响因子：
3.4
作者：
Eriksson BJ;Fredman D;Steiner G;Schmid A
通讯作者：
Schmid A
影响因子：
14.9
作者：
Finn RD;Clements J;Arndt W;Miller BL;Wheeler TJ;Schreiber F;Bateman A;Eddy SR
通讯作者：
Eddy SR
影响因子：
3.3
作者：
Battelle BA;Ryan JF;Kempler KE;Saraf SR;Marten CE;Warren WC;Minx PJ;Montague MJ;Green PJ;Schmidt SA;Fulton L;Patel NH;Protas ME;Wilson RK;Porter ML
通讯作者：
Porter ML
影响因子：
4.1
作者：
Barnett AA;Thomas RH
通讯作者：
Thomas RH
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T