Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Abstract

Hypocrealean fungi (Ascomycota) are known for their diversity of lifestyles. Their vital influences on agricultural and natural ecosystems have resulted in a number of sequenced genomes, which provide essential data for genomic analysis. Totally, 45 hypocrealean fungal genomes constructed a phylogeny. The phylogeny showed that plant pathogens in Nectriaceae diverged earliest, followed by animal pathogens in Cordycipitaceae, Ophiocordycipitaceae and Clavicipitaceae with mycoparasites in Hypocreaceae. Insect/nematode pathogens and grass endophytes in Clavicipitaceae diverged at last. Gene families associated with host-derived nutrients are significantly contracted in diverged lineages compared with the ancestral species. Introgression was detected in certain lineages of hypocrealean fungi, and the main functions of the genes located in the introgressed regions are involved in host recognition, transcriptional regulation, stress response and cell growth regulation. These results indicate that contraction of gene families and introgression might be main mechanisms to drive lifestyle differentiation and evolution and host shift of hypocrealean fungi.

Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi

“…These enzymes are important for Metarhizium to degrade and penetrate the chitin- and protein-rich insect cuticles [ 22 ]. Overall, similar to previous observations [ 23 , 24 ], protein family content largely correlates with fungal lifestyles.…”

“…Our results suggested therefore that the tree topological associations would vary in a case-dependent manner but reflect to some extent the links between different protein families. For example, the size distribution of the highly cophylogenetic proteases and CAZy enzymes have been shown with essential roles in determining the adaptation of fungi to different niches including hosts [ 24 , 31 ]. It has been found that the genes/proteins with family size conservation evolved more slowly than those with frequent size changes [ 32 ].…”

Three genomes of Osteoglossidae shed light on ancient teleost evolution

“…Pseudogenes genesis is correlated with the birth of gene families[35]. And expanded or contracted gene families always be related with physiologic function as reported[36, 37]. We detected 1,210, 424 and 829 expanded gene families in A. gigas, H. niloticus and S. formosus genome respectively.…”

Comparative genomics analyses of lifestyle transitions at the origin of an invasive fungal pathogen in the genus Cryphonectria

“…Reductions in CAZymes genes have been observed in biotrophic pathogens and are thought to be an adaptation to reduce the exposure of molecular patterns, which can trigger host defenses (Duplessis et al, 2014;Goulet and Saville, 2017). Moreover, CAZyme loss can occur during host shifts, such as from plant to animal or insect hosts (Zhang et al, 2018). In C.…”