Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis

Guiling Sun,Yuxing Xu,Jing Li,Jinfeng Qi,Ian T Baldwin,Jianqiang Wu,Lei Wang,Wei Chang,Ting Sun,Yan Qin,Hui Liu,Christian Hettenhausen,Guojing Shen,Zhenhua Guo,Jingxiong Zhang

doi:10.1038/s41467-018-04721-8

Abstract

Dodders (Cuscuta spp., Convolvulaceae) are root- and leafless parasitic plants. The physiology, ecology, and evolution of these obligate parasites are poorly understood. A high-quality reference genome of Cuscuta australis was assembled. Our analyses reveal that Cuscuta experienced accelerated molecular evolution, and Cuscuta and the convolvulaceous morning glory (Ipomoea) shared a common whole-genome triplication event before their divergence. C. australis genome harbors 19,671 protein-coding genes, and importantly, 11.7% of the conserved orthologs in autotrophic plants are lost in C. australis. Many of these gene loss events likely result from its parasitic lifestyle and the massive changes of its body plan. Moreover, comparison of the gene expression patterns in Cuscuta prehaustoria/haustoria and various tissues of closely related autotrophic plants suggests that Cuscuta haustorium formation requires mostly genes normally involved in root development. The C. australis genome provides important resources for studying the evolution of parasitism, regressive evolution, and evo-devo in plant parasites.

Highlights

Dodders (Cuscuta spp., Convolvulaceae) are root- and leafless parasitic plants
Our analyses reveal that the genome of C. australis experienced massive gene losses, including important genes involved in leaf and root development, flowering-time control, as well as defense against pathogens and insects
Comparison of Cuscuta haustorium/prehaustorium gene expression patterns with the tissues from closely related autotrophic plants suggests that Cuscuta haustorium formation likely requires genes that are normally involved in root development

Summary

Introduction

Dodders (Cuscuta spp., Convolvulaceae) are root- and leafless parasitic plants. The physiology, ecology, and evolution of these obligate parasites are poorly understood. C. australis genome harbors 19,671 protein-coding genes, and importantly, 11.7% of the conserved orthologs in autotrophic plants are lost in C. australis Many of these gene loss events likely result from its parasitic lifestyle and the massive changes of its body plan. Dodders obtain water and nutrients, but secondary metabolites, mRNAs, and proteins from their host plants[3,4,5] These features make Cuscuta an important model to elucidate plant–parasite interactions and the evolution of plant parasites. Our analyses reveal that the genome of C. australis experienced massive gene losses, including important genes involved in leaf and root development, flowering-time control, as well as defense against pathogens and insects. Comparison of Cuscuta haustorium/prehaustorium gene expression patterns with the tissues from closely related autotrophic plants suggests that Cuscuta haustorium formation likely requires genes that are normally involved in root development

Methods

Results

Conclusion