| Trichoderma Pers.is widely distributed in a variety of habitats.Due to their ability to produce various industrial enzymes and antibiotics,and antagonism ability to plant pathogens,it is widely used in industrial production and agricultre.The diversified inhabits and nutrition styles provide an opportunity to studying this effect on Trichoderma differentiation.Comparative genomics was used to study the gene differences among closely related species,laying foundation for further exploring environmental factors infecting Trichoderma species differentiation.In this study,the diversity of Trichoderma in rocky desertification soils which had not been studied previously was investigated.Whole genomes of Trichoderma species from three different inhabits,i.e.T.reesei from decaying wood,T.parareesei from soil and T.aquaticum from aquatic plant were compared to explore genes variation during absorbing different substrances.The main results are as follows:1.Trichoderma diversity in rocky desertification soilsA total of 381 soil samples were collected from Miandian town,Jianshui county,Yunnan province,and 76 Trichoderma strains were isolated.Combined morphological characteristics and ITS,TEF1,RPB2 sequence,11 new species were identified: T.achlamydosporum,T.amoenum,T.inaequilaterale,T.obovatum,T.pluripenicillatum,T.propepolypori,T.pseudoasiaticum,T.simile,T.subazureum,T.subuliforme,T.supraverticillatum;and 10 known species were identified: T.atroviride,T.gamsii,T.hamatum,T.harzianum,T.koningii,T.koningiopsis,T.longibrachiatum,T.spirale,T.virens,T.velutinum.Belong to Atroviride,Hamatum,Harzianum,Koningii,Longibrachiatum,Virens,Spirale,Viridescens Clades.The morphological characteristics and phylogenetic analysis of the new species and their relatives were compared.T.supraverticillatum does not belong to any known clade.2.Genomes comparison of T.aquaticum and two closely related species(1)7116 single-copy orthologous genes were found in T.aquaticum,T.parareesei and T.reesei,and 75 unique genes were particular in T.aquaticum,of which only 16 were annotated in non-redundant protein sequence database.KEGG annotation of this three species suggest that T.aquaticum has 38 unique KO4 genes,which are involved in21 unique KO3 metabolic pathways,including various amino acid metabolism pathways,protein kinase,cell growth,PI3K-Akt signaling pathway,etc.,which play an important role in protein phosphorylation,treatment of nervous system diseases and spore growth;the result of repeat sequence annotation show that the obvious difference among this three species was simple repeats sequence: T.aquaticum has 596803 bp,T.parareesei has 544978 bp,T.reesei has 619343 bp.(2)Mycoparasitic species have a large number of mycoparasitism-related genes,including carbohydrate-active enzymes(CAZymes),secondary metabolism-related genes and protease genes.Annotated results showed that T.aquaticum has 366 CAZymes in total,T.reesei has 362 CAZymes,T.parareesei has 363 CAZymes.These mainly include GH18 chitinase,?-1,3/1,6-glucanase,cellulohydrolase,hemicellulohydrolase.T.aquaticum encodes 24 nonribosomal peptide synthetase(NRPS)and polyketide synthase(PKS)genes,same as T.reesei,while 21 in T.parareesei.In T.aquaticum,there are 291 genes encoding nutrition-related protease,T.parareesei has 311 genes,T.reesei has 299 genes.In short,there are 681nutrition-related genes in T.aquaticum,which is similar to that of T.parareesei(695),T.reesei(685),and is more than those in T.longibrachiatum(664),but significantly less than those in T.atroviride(887)and T.virens(942),suggesting that T.aquaticum may have lost nutrition-related genes during evolution.(3)The calculation results of selection pressure of homologous nutrition-related genes showed that,there are 57 CAZymes homologous genes in T.aquaticum,T.reesei,T.atroviride and T.virens,and 39 of them had lower selection pressures in T.aquaticum-T.reesei than that in T.atrovirid-T.virens.The selection pressure of 99 homologous genes was calculated in the protease,and 47 of them were lower in T.aquaticum-T.reesei than that in T.atrovirid-T.virens.And the Ka/Ks values of all calculated genes were lower than 1.Therefore,we speculated that the living environment of aquatic plants had influenced the parasitic capacity of T.aquaticum,and its nutrition style was saprophytic and parasitic.In addition,we also filtered out 15 positive selection genes of T.aquaticum and functionally annotated them,of which only two genes were annotated in KEGG: alpha-L-fucosidase 2 and N-acetylglucosamine-6-phosphate deacetylase.Among the 15 positive selection genes of T.aquaticum,we found 73 mutation sites,which were different from T.reesei and T.parareesei.However,whether the mutation of these sites will cause changes in protein structure and function remains to be explored. |
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