| Phosphorus is a basic component of nucleic acid and phospholipid as well as an essential element for organisms.Phosphorus participates in biochemical and metabolic processes such as photosynthesis,nucleotide synthesis,and cell membrane remodeling and protein modification.However,phosphorus is easy to be adsorbed by soil particles,resulting in a low availability of phosphorus for plants.To cope with low phosphorus availability,plants have evolved various adaptive mechanisms,such as forming symbiotic mycorrhizal associations with fungi.Mycorrhizae can release phosphatases in rhizosphere soil to mobilize soil organic phosphorus,thus improve plant phosphorus acquisition.In forest and agricultural ecosystems,apart from ectomycorrhizal and arbuscular mycorrhizal fungi that can form reciprocal symbioses with plants,where also exist a large number of non-mycorrhizal fungi,such as saprophytic fungi.In addition to acquire carbon or nitrogen from dead materials,saprophytic fungi also obtain inorganic nutrients including phosphorus from their habitats to meet their own growth and development.In contrast,besides their own phosphorus requirement,mycorrhizal fungi also need to supply phosphorus to their host plant in exchange for carbon.Therefore,there are significant differences in phosphorus requirements between these two types of fungi.Will mycorrhizal fungi evolve more active and stronger phosphatase genes or gene families to activate organic phosphorus in soil?To explore whether secretory phosphatase genes have adaptive evolution in mycorrhizal fungi,using bioinformatics assays this study identified and analyzed four secretory phosphatase genes or gene family from 100 fungal genomes downloaded from an American public database(Joint Genome Institute,https://mycocosm.jgi.doe.gov/mycocosm/home).These four secretory phosphatases and their gene or gene family are as follows:(1)alkaline phosphatase gene(ALKG);(2)purple acid phosphatase gene(PAPG);(3)yeast acid phosphatase gene(YAPG)and(4)another kind of acid phosphatase gene family(APGF),not includes genes from(2)and(3).To get a better understanding of these fungal secretory phosphatase genes on soil phosphorus activation and availability for the potential understory cultivation of the precious native truffles in China,we further used the sequencing scheme of second-generation and third-generation nanopore sequencing to sequence the whole genes of three native truffles(Tuber jinshajiangense,T.huidongenseand T.Shii).After obtaining the high-quality truffle genome,we then analyzed the genomic information of these three native truffles and identified the copy number of these secretory phosphatase genes in the whole truffle fungi.The research results based on the fungal genome on the public database are as follows:1.There were no significant differences in the copy number of secretory phosphatase genes between mycorrhizal fungi and non-mycorrhizal fungi,but the number of secretory phosphatase genes seemed to be related to the evolutionary lineage of fungi.Purple acid phosphatase gene was missing in all Glomerales and Boletales fungi,and the secretory phosphatase genes in Pezizomycetes fungi was dramatically less than that in Dothideomycetes and Leotiomycetes.2.The secretory phosphatase genes did not show extreme mutation at the amino acid level between mycorrhizal and saprophytic fungi,and there were no significant differences in the amino acid frequency of a certain locus.The cluster patterns of the four types of secretory phosphatase genes in the phylogenetic tree followed the evolutionary pedigree of fungi: the secretory phosphatase genes of fungi from the same pedigree were basically clustered together.3.The amino acid sequences of secretory phosphatase genes of these four types of fungi had different rules of domain and motif composition.However,there was no evidence in showing a significant difference between domain and motif sequences of mycorrhizal and non-mycorrhizal fungi.4.This study applied the a BSERL model to detect whether genes were under the pressure of natural selection during the process of evolution.The results showed that13 of 234 fungal YAPG homologous genes,13 of 232 fungal APGF homologous genes,9 of 98 fungal PAPG homologous genes and only one of 44 fungal ALKG homologous genes were under selection pressure.These genes considered to be under selection pressure came from 30 different types of fungi,most of them were plant symbiotic fungi,including 4 arbuscular mycorrhizal fungi,3 rhododendron mycorrhizal fungi and 14 ectomycorrhizal fungi.However,the number of genes selected was small,and there was no obvious evidence that different nutritional patterns or modes had led to the adaptive evolution of secretory phosphatase genes in their genomes.In order to further verify the phenomenon if the number of secretory phosphatase genes in the genome of Pezizomycetes could be less than that of Dothideomycetes and Leotiomycetes,this study then sequenced the whole genes of three native truffles in China and identified their secretory phosphatase genes.The main results are as follows:1.Tuber huidongense,T.jinshajiangense and T.Shii assembled 19,20 and 47 scaffolds,and the values of scaffolds N50 were 7138266,5545914 and 4708604 bp,respectively.The number of scaffolds of truffle genome published in the above-mentioned database ranged from 164 to 3244,and scaffolds N50 were between0.12-2.15 Mbp.Numbers of the scaffolds of truffle genome assembled and sequenced in this study were far less than,while scaffolds N50 were far greater than those in other truffle genomes.A BUSCO-software integrity evaluation showed that the coverage of these three truffle genomes was higher than 96% from the fungi＿db10database analysis,indicating that this study had obtained high-quality truffle genomes.2.There were numerous repetitive sequences in the genomes of Tuber huidongense,T.jinshajiangense and T.Shii,among them their TE accounted for46.10%,39.86% and 42.26%,respectively.Combined with a homology prediction,Ab initio prediction and RNA-seq annotation,9942,10262 and 9792 genes were annotated in these three truffle genomes,respectively.There were no significant differences in the gene structure of the three truffles,and so did in the average single gene length,average c DNA length,average CDs length,average number of single gene exons and average single exon length.3.The collinearity analysis of coding genes showed a good collinearity of coding genes between the genomes of Tuber jinshajiangense and T.Shii.In contrast,Tuber huidongense had a poor collinearity with the genome coding genes of the above two truffles.The phylogeny showed that T.jinshajiangense and T.Shii had a close phylogenetic relationship,while T.huidongense had a faraway phylogenetic relationship with the other two truffles.4.A total of 4 ALKG,4 YAPG,7 APGF and 0 PAPG genes were identified from a total of 15 truffle genomes,indicating a total loss of PAPG gene in these 15 truffle genomes.The copy number of the PAPG genes in the truffle genome was less than that from the fungi of Dothideomycetes and Leotiomycetes.In conclusion,we have not found that alkaline phosphatase gene(ALKG),acid phosphatase gene family(APGF),purple acid phosphatase gene(PAPG)and yeast acid phosphatase gene(YAPG)have a broad-spectrum adaptive evolution in mycorrhizal fungi,while the evolution of all the tested four secretory phosphatase genes is relatively conservative during their differentiation process by following along with the fungal nutritional mode. |
