High-quality reference genomes of swallowtail butterflies provide insights into their coloration evolution.

Swallowtail butterflies (Papilionidae) are a historically significant butterfly group due to their colorful wing patterns, extensive morphological diversity, and phylogenetically important position as a sister group to all other butterflies and have been widely studied regarding ecological adaption, phylogeny, genetics, and evolution. Notably, they contain a unique class of pigments, i.e., papiliochromes, which contribute to their color diversity and various biological functions such as predator avoidance and mate preference. To date, however, the genomic and genetic basis of their color diversity and papiliochrome origin in a phylogenetic and evolutionary context remain largely unknown. Here, we obtained high-quality reference genomes of 11 swallowtail butterfly species covering all tribes of Papilioninae and Parnassiinae using long-read sequencing technology. Combined with previously published butterfly genomes, we obtained robust phylogenetic relationships among tribes, overcoming the challenges of incomplete lineage sorting (ILS) and gene flow. Comprehensive genomic analyses indicated that the evolution of Papilionidae-specific conserved non-exonic elements (PSCNEs) and transcription factor binding sites (TFBSs) of patterning and transporter/cofactor genes, together with the rapid evolution of transporters/cofactors, likely promoted the origin and evolution of papiliochromes. These findings not only provide novel insights into the genomic basis of color diversity, especially papiliochrome origin in swallowtail butterflies, but also provide important data resources for exploring the evolution, ecology, and conservation of butterflies. 凤蝶（凤蝶科）具有多彩的翅膀图案、丰富的形态多样性、重要的系统发育地位（是所有其他蝴蝶的姐妹类群）等，是历史上备受关注的蝴蝶类群。这一类群在生态适应、系统发育、遗传学和进化等领域都被广泛研究。值得注意的是，它们含有一类独特的色素类型，即凤蝶色素，这有助于颜色多样性的形成和各种生物学功能的发挥，如躲避捕食者和择偶。然而，到目前为止，系统发育和遗传的背景下，它们颜色多样性和凤蝶色素起源的基因组和遗传基础仍未可知。该研究使用长读长测序技术，解析了11种凤蝶的高质量参考基因组。结合之前发表的蝴蝶基因组，克服了不完全谱系分选和基因流等挑战，构建了族水平稳定的系统发育树。系统的基因组分析表明，模式基因和转运体/辅助因子等编码基因的凤蝶科特异的保守非外显子元件和转录因子结合位点的进化，以及转运体/辅因子的快速进化，可能促进了凤蝶色素的起源与进化。这些结果不仅为了解颜色多样性的基因组基础尤其是凤蝶色素的起源提供了新见解，而且为探索蝴蝶的进化、生态学和保护提供了重要的数据资源。.