Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain.
Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK.
DNA Res. 2019 Feb 1;26(1):13-20. doi: 10.1093/dnares/dsy034.
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.
RNA 测序（RNA-seq）已成为揭示生物适应性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 对于研究那些难以在自然界中观察到的、因此相对研究较少的非模式、隐秘物种特别有前景。在这些动物中，蚓螈（蚓螈目）可能是最不为人知的脊椎动物群体之一，尽管它们是一种古老而显著独特的两栖动物谱系。在这里，我们对蚓螈目五个物种的多组织转录组进行了特征描述，这些物种代表了该目中广泛的多样性。我们鉴定了蚓螈功能基因的脊椎动物同源元素，这些元素具有不同的组织特异性，揭示了大量未分类的基因家族，特别是皮肤中的基因家族。我们对这些未知候选基因家族的几个蛋白结构域进行了注释，以研究它们的功能。我们还对五个蚓螈物种和其他主要脊椎动物谱系的 1955 个候选直系同源基因的系统基因组数据集进行了超级树分析，推断出的树与脊椎动物进化和系统发生的当前观点一致。我们的研究提供了对脊椎动物蛋白编码基因进化的深入了解，并为未来研究蚓螈两栖动物独特生物学和适应性的分子基础奠定了基础。
