Comparative genomic analyses reveal the features for adaptation to nematodes in fungi

Ruizhen Wang; Leiming Dong; Ran He; Qinghua Wang; Yuequ Chen; Liangjian Qu; Yong-An Zhang

doi:10.1093/dnares/dsx053

Comparative genomic analyses reveal the features for adaptation to nematodes in fungi

DNA Res. 2018 Jan 5;25(3):245-256. doi: 10.1093/dnares/dsx053. Online ahead of print.

Authors

Ruizhen Wang^{1

2}, Leiming Dong³, Ran He^{1

2}, Qinghua Wang¹, Yuequ Chen^{1

4}, Liangjian Qu¹, Yong-An Zhang¹

Affiliations

¹ The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.
² Institute of Botany, Beijing Botanical Garden, Beijing 100093, China.
³ State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
⁴ Forestry Resources Protection Institute, Jilin Provincial Academy of Forestry Sciences, Changchun 130031, China.

Abstract

Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche. A number of gene families involved in pathogenicity were expanded, and some pathogenic orthologous genes underwent positive selection. NP fungi with diverse morphological features exhibit similarities of evolutionary convergence in attacking nematodes, but their genetic makeup and microscopic mechanism are different. Endoparasitic NP fungi showed similarity in large number of transporters and secondary metabolite coding genes. Noteworthy, expanded families of transporters and endo-beta-glucanase implied great genetic potential of Ev in quickly perturbing nematode metabolism and parasitic behavior. These results facilitate our understanding of NP fungal genomic features for adaptation to nematodes and lay a solid theoretical foundation for further research and application.

Keywords: Esteya vermicola; adaptation and evolution; comparative genome; genome feature; nematophagous fungi.