Fungi provide essential services for forest ecosystems like breakdown of complex organic matter and nutrient cycling. However, wood is a major building material and energy supply for humans, therefore forests are heavily managed. In Central European commercial forests, only a minor part of wood is actually “allowed” to undergo natural decomposition. Protected areas include the remains of larger deadwood bodies, and thus the unique organisms associated with it. Among the latter are rare wood-associated fungi (i.e. endangered and “red-list” species), the ecology of which is often cryptic.
As a key step, we isolated the following rare deadwood-associated fungal species from the Bavarian Forest National Park: Antrodiella citrinella, Bondarzewia mesenterica, Dentipellis fragilis, Fomitopsis rosea, Hericium alpestre, Phellinidium pouzarii and Phlebia centrifuga, and sequenced, assembled and annotated their genomes. We have addressed two questions, i) can genomic traits, i.e. genes associated with lignocellulose decomposition, identify the lifestyle of a fungus, and ii) are we able to use the genomic resources to find good marker regions with high copy numbers for a fungal molecular survey in wood samples (without the help of fruiting bodies)?
Results/Conclusions
i) The assembly sizes of the fungal genomes ranged between 28.6 and 36.9 Mb. 8,473 to 11,718 genes were predicted, among them 368 to 479 belonging to enzymes active on carbohydrates or lignin. Except F. rosea, all fungi analyzed contain genes encoding manganese peroxidases (4-11 copies) that are responsible for incipient lignin decomposition and indicative for white-rot fungi. Additional support for this ecotype has come from the finding of several cellobiohydrolase genes and carbohydrate binding modules of family 1 (associated to cellulose) in these six fungi, which are missing in F. rosea that is a brown-rot fungus.
ii) A copy number analysis revealed 24 to 163 copies of the ribosomal cistron compared to single copy genes. Furthermore, copy numbers of mitochondria were estimated with 17 to 173 copies. Mitochondrial marker genes like cox1, cox2, rrnS and rrnL were frequently identified. Mitochondria counts can vary depending on the physiological status of the fungus whereas the ribosomal gene copy number is inherited. Nevertheless, the copy numbers were generally high and in the next step, these markers will have to be evaluated in field trials.
Genome sequencing of endangered species with cryptic lifestyles is a useful tool to develop markers and it provides first insights into the eco-physiology of respective organisms, which eventually, is critical for a successful conservation strategy.