Comparative Genomics of Three Aspergillus Strains Reveals Insights into Endophytic Lifestyle and Endophyte-Induced Plant Growth Promotion

Abstract

Aspergillus includes both plant pathogenic and beneficial fungi. Although endophytes beneficial to plants have high potential for plant growth promotion and improving stress tolerance, studies on endophytic lifestyles and endophyte-plant interactions are still limited. Here, three endophytes belonging to Aspergillus, AS31, AS33, and AS42, were isolated. They could successfully colonize rice roots and significantly improved rice growth. The genomes of strains AS31, AS33, and AS42 were sequenced and compared with other Aspergillus species covering both pathogens and endophytes. The genomes of AS31, AS33, and AS42 were 36.8, 34.8, and 35.3 Mb, respectively. The endophytic genomes had more genes encoding carbohydrate-active enzymes (CAZymes) and small secreted proteins (SSPs) and secondary metabolism gene clusters involved in indole metabolism than the pathogens. In addition, these endophytes were able to improve Pi (phosphorus) accumulation and transport in rice by inducing the expression of Pi transport genes in rice. Specifically, inoculation with endophytes significantly increased Pi contents in roots at the early stage, while the Pi contents in inoculated shoots were significantly increased at the late stage. Our results not only provide important insights into endophyte-plant interactions but also provide strain and genome resources, paving the way for the agricultural application of Aspergillus endophytes.

Genomic insights into Aspergillus sydowii 29R-4-F02: unraveling adaptive mechanisms in subseafloor coal-bearing sediment environments

“…In addition, we assembled the mitochondrial genome of strain 29R-4-F02, which has a length of 26,185 bp and contains 13 genes, including 7 NADH–ubiquinone oxidoreductase genes, 3 cytochrome c oxidase genes, 1 cytochrome b gene, 1 ribosomal protein gene, and 1 ATP synthase gene, with a GC content of 23.67%. The size and number of genes in the mitochondrial genome of strain 29R-4-F02 are similar to those of other Aspergillus species, with genome sizes ranging from 27,817 to 77,649 bp and gene numbers ranging from 14 to 21 ( Zhao et al, 2012 ; Takahashi et al, 2021 ; Jing et al, 2022 ).…”

“…Some strains of A. sydowii isolated from marine ecosystems can cause an epizootic infection of sea fan corals ( Kim and Harvell, 2004 ; Hayashi et al, 2016 ), while others can produce a series of secondary metabolites with novel structure and bioactivities ( Wang et al, 2019 ; Niu et al, 2020 ), and degrade the refractory substances such as xylan ( Brandt et al, 2020 ), lignocellulose ( Cong et al, 2017 ), and waste engine oil ( Kumar et al, 2021 ). Given the wide distribution and important application value of A. sydowii , five strains of this species have been sequenced, assembled and annotated ( de Vries et al, 2017 ; Brandt et al, 2021 ; Kumar et al, 2021 ; Jing et al, 2022 ), of which strain CBS593.65 had been fully studied. Of the sequenced strains, AS31, AS42, Fsh102, CBS593.65, and BOBA1 were isolated from terrestrial land and deep sea, respectively.…”

Computational Tools and Phytopathogenic Fungi Secretome: Unraveling the Protein Arsenal

“…By properly using the available tools, it is possible to unravel the entire protein arsenal secreted by fungi, from the gene to the functional attribution of the proteins, contributing to a better understanding of the enzymatic profile of these organisms. Table 1 shows some examples of software that have been used in fungal secretome analysis [39,40].…”

Transcriptomic analysis and carbohydrate metabolism-related enzyme expression across different pH values in Rhizopus delemar

“…These PGP abilities are governed by the organism’s genetic makeup. Notably, three PGP Aspergillus strains closely related to A. puulaauensis and A. sydowii in Ascomycota were found to carry more carbohydrate-active enzyme (CAZymes) genes, small secreted protein (SSPs) genes, and gene clusters encoding indole metabolism compared to pathogenic Aspergillus strains ( Jing et al, 2022 ). To our knowledge, little attention has been given to exploring the PGP properties and related genes in zygomycetes.…”

“…Changes in pH lead to changes in the activities of glucosidase, cellulase and other CAZymes ( Lou et al, 2013 ) that play key roles in the synthesis or decomposition of complex carbohydrates by degrading, modifying, and generating glycosidic bonds ( Cantarel et al, 2009 ; Davies and Williams, 2016 ). In addition, CAZymes may contribute to PGP ability ( Jing et al, 2022 ). To the best of our knowledge, there are no studies on the effect of pH on R. delemar CAZymes.…”