Insight into the genomes of dominant yeast symbionts of European spruce bark beetle, Ips typographus

Tian Cheng; Tereza Veselská; Barbora Křížková; Karel Švec; Václav Havlíček; Marc Stadler; Miroslav Kolařík

doi:10.3389/fmicb.2023.1108975

Insight into the genomes of dominant yeast symbionts of European spruce bark beetle, Ips typographus

Front Microbiol. 2023 Apr 3:14:1108975. doi: 10.3389/fmicb.2023.1108975. eCollection 2023.

Authors

Tian Cheng^{1

2}, Tereza Veselská¹, Barbora Křížková¹, Karel Švec¹, Václav Havlíček¹, Marc Stadler², Miroslav Kolařík¹

Affiliations

¹ Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Praha, Czechia.
² Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany.

Abstract

Spruce bark beetle Ips typographus can trigger outbreaks on spruce that results in significant losses in the forest industry. It has been suggested that symbiotic microorganisms inhabiting the gut of bark beetles facilitate the colonization of plant tissues as they play a role in the detoxification of plant secondary metabolites, degrade plant cell wall and ameliorate beetle's nutrition. In this study, we sequenced and functionally annotated the genomes of five yeasts Kuraishia molischiana, Cryptococcus sp., Nakazawaea ambrosiae, Ogataea ramenticola, and Wickerhamomyces bisporus isolated from the gut of Ips typographus. Genome analysis identified 5314, 7050, 5722, 5502, and 5784 protein coding genes from K. molischiana, Cryptococcus sp., N. ambrosiae, O. ramenticola, and W. bisporus, respectively. Protein-coding sequences were classified into biological processes, cellular and molecular function based on gene ontology terms enrichment. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation was used to predict gene functions. All analyzed yeast genomes contain full pathways for the synthesis of essential amino acids and vitamin B6, which have nutritional importance to beetle. Furthermore, their genomes contain diverse gene families related to the detoxification processes. The prevalent superfamilies are aldo-keto reductase, ATP-binding cassette and the major facilitator transporters. The phylogenetic relationships of detoxification-related enzymes aldo-keto reductase, and cytochrome P450 monooxygenase, and ATP-binding cassette are presented. Genome annotations also revealed presence of genes active in lignocellulose degradation. In vitro analyses did not confirm enzymatic endolytic degradation of lignocellulose; however, all species can utilize and pectin and produce a large spectrum of exolytic enzymes attacking cellulose, chitin, and lipids.

Keywords: Scolytinae; detoxification; gut microbiome; nutrition; plant cell wall; spruce; symbiosis; yeast.

Grants and funding

This research was funded by the Czech Science Foundation (GACR), Grant Number 19-09072S and Charles University Grant Agency (GAUK project no. 380021). TC was supported from ESF project “International mobility of researchers of the Institute of Microbiology of the CAS, v.v.i. No. 2” registration number CZ.02.2.69/0.0/0.0/18_053/0017705. The authors benefited from the H2020-RISE project Mycobiomics–Joining forces to exploit the mycobiota of Asia, Africa and Europe for beneficial metabolites and potential biocontrol agents, using -OMICS techniques (No. 101008129).