RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation and diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians.

中文翻译：

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凯氏两栖动物的多组织转录组突显了脊椎动物基因家族的不完全知识。

RNA测序（RNA-seq）已成为揭示生物适应和多样性的基因组基础的最强大工具之一。尽管具有挑战性，但RNA-seq对于非模型性，分泌性物种的研究特别有前途，这些物种无法在自然界中轻易观察到，因此仍需进行相对较少的研究。在这些动物中，尽管是古老的两栖动物谱系非常明显，但它们却是最不为人所知的脊椎动物。在这里，我们表征了五种caecilians的多组织转录组，它们代表了整个订单中的广泛多样性。我们确定了不同组织特异性的凯撒功能基因的脊椎动物同源元素，揭示了许多未分类的基因家族，尤其是皮肤。我们为那些未知的候选基因家族注释了几个蛋白质结构域，以研究其功能。我们还对五个凯撒科物种和脊椎动物其他主要谱系中的1,955个候选直系同源基因的植物基因组数据集进行了超级树分析，推断出的树与当前脊椎动物进化论和系统学观点相符。我们的研究提供了对脊椎动物蛋白质编码基因的进化的见识，并为进一步研究特定的生物学和适应性的凯撒两栖动物的分子元素提供了基础。推断的树与脊椎动物进化论和系统学的当前观点一致。我们的研究提供了对脊椎动物蛋白质编码基因的进化的见识，并为进一步研究特定的生物学和适应性的凯撒两栖动物的分子元素提供了基础。推断的树与脊椎动物进化论和系统学的当前观点一致。我们的研究提供了对脊椎动物蛋白质编码基因的进化的见识，并为进一步研究特定的生物学和适应性的凯撒两栖动物的分子元素提供了基础。