Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559, Hannover, Germany.
Department of Zoology, University of Cambridge, Downing St, Cambridge, CB2 3EJ, England.
BMC Genomics. 2020 Apr 15;21(1):301. doi: 10.1186/s12864-020-6719-5.
Animal coloration is usually an adaptive attribute, under strong local selection pressures and often diversified among species or populations. The strawberry poison frog (Oophaga pumilio) shows an impressive array of color morphs across its distribution in Central America. Here we quantify gene expression and genetic variation to identify candidate genes involved in generating divergence in coloration between populations of red, green and blue O. pumilio from the Bocas del Toro archipelago in Panama.
We generated a high quality non-redundant reference transcriptome by mapping the products of genome-guided and de novo transcriptome assemblies onto a re-scaffolded draft genome of O. pumilio. We then measured gene expression in individuals of the three color phenotypes and identified color-associated candidate genes by comparing differential expression results against a list of a priori gene sets for five different functional categories of coloration - pteridine synthesis, carotenoid synthesis, melanin synthesis, iridophore pathways (structural coloration), and chromatophore development. We found 68 candidate coloration loci with significant expression differences among the color phenotypes. Notable upregulated examples include pteridine synthesis genes spr, xdh and pts (in red and green frogs); carotenoid metabolism genes bco2 (in blue frogs), scarb1 (in red frogs), and guanine metabolism gene psat1 (in blue frogs). We detected significantly higher expression of the pteridine synthesis gene set in red and green frogs versus blue frogs. In addition to gene expression differences, we identified 370 outlier SNPs on 162 annotated genes showing signatures of diversifying selection, including eight pigmentation-associated genes.
Gene expression in the skin of the three populations of frogs with differing coloration is highly divergent. The strong signal of differential expression in pteridine genes is consistent with a major role of these genes in generating the coloration differences among the three morphs. However, the finding of differentially expressed genes across pathways and functional categories suggests that multiple mechanisms are responsible for the coloration differences, likely involving both pigmentary and structural coloration. In addition to regulatory differences, we found potential evidence of differential selection acting at the protein sequence level in several color-associated loci, which could contribute to the color polymorphism.
动物的颜色通常是一种适应性特征，在强烈的局部选择压力下，通常在物种或种群之间多样化。草莓毒蛙（Oophaga pumilio）在中美洲的分布范围内表现出令人印象深刻的颜色形态。在这里，我们量化基因表达和遗传变异，以确定参与产生巴拿马博卡斯德尔托罗群岛红、绿和蓝 O. pumilio 种群之间颜色分化的候选基因。
我们通过将基因组指导和从头转录组组装的产物映射到 O. pumilio 重新组装的草图基因组上，生成了高质量的非冗余参考转录组。然后，我们测量了三种颜色表型个体的基因表达，并通过将差异表达结果与五个不同颜色功能类别的先验基因集进行比较，确定了与颜色相关的候选基因 - 蝶呤合成、类胡萝卜素合成、黑色素合成、虹彩途径（结构颜色）和色素细胞发育。我们发现了 68 个候选颜色基因座，它们在颜色表型之间的表达差异具有统计学意义。值得注意的上调例子包括蝶呤合成基因 spr、xdh 和 pts（在红、绿青蛙中）；类胡萝卜素代谢基因 bco2（在蓝青蛙中）、scarb1（在红青蛙中）和鸟嘌呤代谢基因 psat1（在蓝青蛙中）。我们发现红、绿青蛙中的蝶呤合成基因集表达显著高于蓝青蛙。除了基因表达差异外，我们还在 162 个注释基因上检测到 370 个外显子 SNP，这些基因显示出多样化选择的特征，包括 8 个色素相关基因。
具有不同颜色的三个青蛙种群的皮肤基因表达高度分化。蝶呤基因差异表达的强烈信号与这些基因在产生三种形态的颜色差异中的主要作用一致。然而，跨途径和功能类别发现差异表达的基因表明，多种机制负责颜色差异，可能涉及色素和结构颜色。除了调控差异外，我们还在几个与颜色相关的基因座中发现了蛋白质序列水平上差异选择的潜在证据，这可能有助于颜色多态性。
