Mycena genomes resolve the evolution of fungal bioluminescence

作者：Huei-Mien Ke, Hsin-Han Lee, C. Lin, Yu-Ching Liu, Min R. Lu, J. Hsieh, Chiung-Chih Chang, Pei-Hsuan Wu, Meiyeh J Lu, Jeng-yi Li, Gaus Shang, Rita Jui-Hsien Lu, L. Nagy, Pao-Yang Chen, H. Kao, Isheng. J. Tsai · 发表于：Proceedings of the National Academy of Sciences of the United States of America · 年份：2020 · DOI：10.1073/pnas.2010761117 · 被引用次数：49 · 研究领域：Biology、Medicine

Significance We present the genomes of five new bonnet mushroom Mycena species, formerly the last fungal bioluminescent lineage lacking reference genomes. These genome-scale datasets allowed us to construct an evolutionary model pinpointing all possible changes in the luciferase cluster across all fungi and additional genes involved in bioluminescence. We show that luciferase clusters were differentially lost in different fungal lineages and in particular a substantial loss was observed in the mycenoid lineage. This can be attributed to genome regions of Mycena that underwent different evolutionary dynamics. Our findings offer insights into the evolution of how a gene cluster emerged 160 million years ago and was frequently lost or maintained due to differences in genome plasticity. Mushroom-forming fungi in the order Agaricales represent an independent origin of bioluminescence in the tree of life; yet the diversity, evolutionary history, and timing of the origin of fungal luciferases remain elusive. We sequenced the genomes and transcriptomes of five bonnet mushroom species (Mycena spp.), a diverse lineage comprising the majority of bioluminescent fungi. Two species with haploid genome assemblies ∼150 Mb are among the largest in Agaricales, and we found that a variety of repeats between Mycena species were differentially mediated by DNA methylation. We show that bioluminescence evolved in the last common ancestor of mycenoid and the marasmioid clade of Agaricales and was ma...