De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance.

BACKGROUND: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. RESULTS: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. CONCLUSIONS: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

Mid1 affects ion transport, cell wall integrity, and host penetration of the entomopathogenic fungus Metarhizium acridum.

Calcium signaling plays important roles in stress tolerance and virulence in fungi. Mid1, an accessory protein of Cch1 calcium channel, has been discussed in baker's yeast and some filamentous fungi. However, functions of the Mid1 gene in entomopathogenic fungi are not clear. In this study, the Mid1 gene was functionally characterized by deleting it in the entomopathogenic fungus Metarhizium acridum. The growth of the ΔMaMid1 mutant was similar as the wild type on normal growth medium, but inhibited by exogenous Ca2+, Fe2+, Mg2+, Mn2+, Li+, and calcium chelator ethylene glycol tetraacetic acid (EGTA). Cation transportation-related genes were upregulated and intracellular calcium concentration was decreased in ΔMaMid1. Deletion of the MaMid1 gene impaired the tolerance to cell wall-disrupting agents but had no impact on heat or ultraviolet irradiation tolerance compared with the wild type. Bioassays showed that ΔMaMid1 had decreased virulence, with defects in the ability to penetrate the host cuticle. Compared with the wild type, appressorium formation on locust wings and fungal growth in the insect hemocoel were significantly decreased in the ΔMaMid1 mutant in a bioassay through topical inoculation. The phenotypes of ΔMaMid1 were fully restored in a complementation strain. Taken together, our study demonstrates that the MaMid1 affects intracellular ion homeostasis and contributes to virulence by affecting the initial penetration process in M. acridum.

The Rab GTPase activating protein Gyp2 contributes to UV stress tolerance in Metarhizium acridum.

GTPase activation protein (GAP) for Rab GTPases can accelerate GTP hydrolysis to alter the activity of Rab GTPases. To explore the function of GAP in entomopathogenic fungi, we constructed a deletion mutant of Gyp2 gene, a member of the Gyp (GAP for Ypt/Rab proteins) family in the locust-specific fungal pathogen, Metarhizium acridum. Results showed that the ∆MaGyp2 mutant had dramatically decreased tolerance to ultraviolet irradiation compared to wild type strain. Quantitative real-time PCR revealed that UV irradiation repair related genes Uve1 and WC1 were downregulated in ∆MaGyp2 mutant. Seven of other ten Gyp family members had significantly increased transcription in ∆MaGyp2 mutant compared with wild type, which may partly rescue the deficiency of MaGyp2.

An insect chemosensory protein facilitates locust avoidance to fungal pathogens via recognition of fungal volatiles.

Locusts (Locusta migratoria) are one of the most destructive insect pests worldwide. Entomopathogenic fungi can infect and kill locusts, with Metarhizium acridum having evolved as a specialized acridid pathogen. However, locusts have evolved countermeasures to limit or avoid microbial pathogens, although the underlying molecular mechanisms behind these defenses remain obscure. Here, we demonstrate that L. migratoria exhibit avoidance behaviors towards M. acridum contaminated food via recognition of fungal volatiles, with locust perception of the volatile mediated by the LmigCSP60 chemosensory protein. RNAi-knockdown of LmigCSP60 lowered locust M. acridum avoidance behavior and increased infection and mortality. The fungal volatile, 2-phenylethanol (PEA), was identified to participate in locust behavioral avoidance. RNAi-knockdown of LmigCSP60 reduced antennal electrophysiological responses to PEA and impaired locust avoidance to the compound. Purified LmigCSP60 was able to bind a set of fungal volatiles including PEA. Furthermore, reduction of PEA emission by M. acridum via construction of a targeted gene knockout mutant of the alcohol dehydrogenase gene (ΔMaAdh strain) that contributes to PEA production reduced locust avoidance behavior towards the pathogen. These findings identify an olfactory circuit used by locusts to detect and avoid potential microbial pathogens before they are capable of initiating infection and highlight behavioral and olfactory adaptations affecting the co-evolution of host-pathogen interactions.

An odorant binding protein is involved in counteracting detection-avoidance and Toll-pathway innate immunity.

INTRODUCTION: Odorant-binding proteins (OBPs) are a class of small molecular weight soluble proteins that exist as expanded gene families in all insects, acting as ligand carriers mediating olfaction and other physiological processes. During fungal infection, a subset of insect OBPs were shown to be differentially expressed. OBJECTIVES: We tested whether the altered expression of insect OBPs during pathogenic infection plays a role in behavioral or immune interactions between insect hosts and their pathogens. METHODS: A wide range of techniques including RNAi-directed knockdown, heterologous protein expression, electrophysiological/behavioral analyses, transcriptomics, gut microbiome analyses, coupled with tandem mass spectrometry ion monitoring, were used to characterize the function of a locust OBP in host behavioral and immune responses. RESULTS: The entomopathogenic fungus Metarhizium anisopliae produces the volatile compound phenylethyl alcohol (PEA) that causes behavioral avoidance in locusts. This is mediated by the locust odorant binding protein 11 (LmOBP11). Expression of LmOBP11 is induced by M. anisopliae infection and PEA treatment. LmOBP11 participates in insect detection of the fungal-produced PEA and avoidance of PEA-contaminated food, but the upregulation of LmOBP11 upon M. anisopliae infection negatively affects the insect immune responses to ultimately benefit successful mycosis by the pathogen. RNAi knockdown of LmOBP11 increases the production of antimicrobial peptides and enhances locust resistance to M. anisopliae infection, while reducing host antennal electrophysiological responses to PEA and locust avoidance of PEA treated food. Also, transcriptomic and gut microbiome analyses reveal microbiome dysbiosis and changes in host genes involved in behavior and immunity. These results are consistent with the elevated expression of LmOBP11 leading to enhanced volatile detection and suppression of immune responses. CONCLUSION: These findings suggest a crosstalk between olfaction and immunity, indicating manipulation of host OBPs as a novel target exploited by fungal pathogens to alter immune activation and thus promote the successful infection of the host.