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

作者：Jinwu He, 中国科学院昆明动物研究所遗传资源与进化国家重点实验室, 云南 昆明 650223, 中国, Ru Zhang, Jie Yang, Zhou Chang, Li-Xin Zhu, Sihan Lu, Feiang Xie, Jun-Lai Mao, Zhiwei Dong, Guichun Liu, Ping Hu, Yan Dong, Wenting Wan, Ruoping Zhao, Tianzhu Xiong, Jorge L. León‐Cortés, C. P. Mao, Wei Zhang, Shuai Zhan, Jun Li, Lei Chen, Wen Wang, Xueyan Li, 西北工业大学生态环境学院, 陕西 西安 710072, 中国, 滁州大学生物与食品工程系, 安徽 滁州 239000, 中国, 浙江海洋大学海洋科学与技术学院, 浙江 舟山 316022, 中国, 哈佛大学生物与进化生物学系, 马萨诸塞州 剑桥 02138, 美国, 南部边境学院野生动物保护生态学, 泛美公路南部/马里亚辅助区, 恰帕斯州 圣克里斯托瓦尔德拉斯卡萨斯 29290, 墨西哥, 北京大学蛋白质与植物基因研究国家重点实验室, 北京 100871, 中国, 中国科学院分子植物科学研究中心昆虫发育与进化生物学重点实验室, 上海 200032, 中国, 中国科学院大学昆明生命科学学院, 云南 昆明 650223, 中国, 中国科学院昆明动物研究所动物进化与遗传交叉卓越创新中心, 云南 昆明 650223, 中国, Ecología para la Conservación de la Fauna Silvestre, El Colegio de la Frontera Sur (ECOSUR), Carretera Panamericana y Periférico Sur s/n Barrio María Auxiliadora, San Cristóbal de Las Casas, Chiapas CP 29290, Mexico · 发表于：动物学研究 · 年份：2022 · DOI：10.24272/j.issn.2095-8137.2021.303 · 被引用次数：13 · 研究领域：Genomics and Phylogenetic Studies、Lepidoptera: Biology and Taxonomy、Genetic diversity and population structure

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, especia...