Effective Identification and Annotation of Fungal Genomes

In the past few decades,the dangers of mycosis have caused widespread concern.With the development of the sequencing technology,the effective analysis of fungal sequencing data has become a hotspot.With the gradual increase of fungal sequencing data,there is now a lack of sufficient approaches for the identification and functional annotation of fungal chromosomal genomes.To overcome this challenge,this paper firstly deals with the approaches of the identification and annotation of fungal genomes based on short and long reads sequenced by using multiple platforms such as Illumina and Pacbio.Then this paper develops an automated bioinformatics pipeline called PFGI for the identification and annotation task.The experimental evaluation on a real-world dataset ENA(European Nucleotide Archive)shows that PFGI provides a user-friendly way to perform fungal identification and annotation based on the sequencing data analysis,and could provide accurate analyzing results,accurate to the species level(97%sequence identity).

What if esca disease of grapevine were not a fungal disease?

Esca disease,which attacks the wood of grapevine,has become increasingly devastating during the past three decades and represents today a major concern in all wine-producing countries.This disease is attributed to a group of systematically diverse fungi that are considered to be latent pathogens,however,this has not been conclusively established.This study presents the first in-depth comparison between the mycota of healthy and diseased plants taken from the same vineyard to determine which fungi become invasive when foliar symptoms of esca appear.An unprecedented high fungal diversity,158 species,is here reported exclusively from grapevine wood in a single Swiss vineyard plot.An identical mycota inhabits wood of healthy and diseased adult plants and presumed esca pathogens were widespread and occurred in similar frequencies in both plant types.Pioneer esca-associated fungi are not transmitted from adult to nursery plants through the grafting process.Consequently the presumed esca-associated fungal pathogens are most likely saprobes decaying already senescent or dead wood resulting from intensive pruning,frost or other mecanical injuries as grafting.The cause of esca disease therefore remains elusive and requires well executive scientific study.These results question the assumed pathogenicity of fungi in other diseases of plants or animals where identical mycota are retrieved from both diseased and healthy individuals.

Identification of Arbuscular mycorrhizal multiplicity in the saline-sodic soils

This study focused on the Arbuscular mycorrhizal(AM)fungal diversity in the saline-sodic soils based on native spore density and most probable number(MPN)assay.Identification through spore morphology showed existence of five genera in the various crop rhizospheres.The physico-chemical analysis of the native soils revealed that they were saline-sodic with pH ranging from(8.7±0.5)to(9.5±0.6)and habituated five different genera of AM fungi including Glomus,Scutellospora,Acaulospora,Sclerocystis and Gigaspora.Each location revealed presence of varied species of AM fungus namely Acaulospora and Glomus in rhizosphere of maize;Scutellospora and Glomus in tulsi;four isolates of Glomus in onion;Glomus and Sclerocystis in guava;three isolates of Glomus in rice;Glomus in neem and Gigaspora and Glomus in bamboo.The molecular identification through nested PCR analysis showed amplification of 600 bp size in SSU rDNA gene in samples A and C(predominated by Acaulospora and Glomus mosseae respectively).

Can we use environmental DNA as holotypes?

The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community.The idea of using intracellular DNA("mgDNA")from environmental samples as holotypes seems at face value,to be a good idea,considering the expansion of knowledge among these‘dark taxa’or‘dark matter fungi’that it could provide(i.e.sequence based taxa without physical specimens and formal nomenclature).However,the limitations of using mgDNA as holotypes needs careful thought,i.e.can we use a short mgDNA fragment,which may contain a small amount of genetic information,to allow discrimination between species?What is the point and are the potential problems of giving valid scientific names to mgDNA?Numerous mycologists and taxonomists,who have many years of experience working on the taxonomy and phylogeny of different groups of fungi,are concerned about the consequences of providing valid names to mgDNA.There has been much debate,through several publications on the considerable problems of using mgDNA as holotypes.The proponents have tried to debate the virtues of using mgDNA as holotypes.Those against have shown that identification to species using mgDNA does not work in many fungal groups,while those for have shown cases where species can be identified with mgDNA.Different disciplines have different reasons and opinions for using mgDNA as holotypes,however even groups of the same disciplines have dissimilar ideas.In this paper we explore the use of mgDNA as holotypes.We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences.In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa,but relate the issues to fungal taxonomy.In fact we show the value of using sequence data from these approaches,in dealing with the discovery of already named taxa,taxa numbers and ecological roles.We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes.The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed.We provide evidence from case studies on Botryosphaeria,Colletotrichum,Penicillium and Xylaria.The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing.We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species.If this approach adopted,it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes.We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.