The pangenome of the fungal pathogenNeonectria neomacrospora
Authors: Nielsen Knud Nor , Sirén Kimmo , Petersen Bent , Sicheritz-Pontén Thomas , Gilbert M. Thomas P. , Korneliussen Thorfinn Sand , Hansen Ole Kim 
Published: March 2021

ABSTRACTThe fungal plant pathogenNeonectria neomacrospora(C. Booth & Samuels) Mantiri & Samuels (Ascomycota, Hypocreales) is a bark parasite causing twig blight, canker, and in severe cases, dieback in fir (Abiesspp.). Although often described as a mild pathogen, foresty and phytosanitary agencies have expressed their concern for potential economic impact. Two epidemics caused by this species are known: one from eastern Canada and one current within Northern Europe. We present key genome features ofN. neomacrospora, to facilitate the research into the biology of this pathogen.We present the first genome assembly ofN. neomacrosporaas well as the first pangenome within this genus. The reference genome forN. neomacrosporais a long-read sequenced Danish isolate, while the pangenome is pieced together using additional 60 short-read sequenced strains covering the known geographical distribution of the species, including Europe, North America, and China.The gapless reference genome consist of twelve chromosomes sequenced telomere to telomere to a total length of 37.1 Mb. The mitochondrial genome was assembled and circularised with a length of 22 Kb.The gapless nuclear genome contains a total of 11,291 annotated genes, where 642 only have a hypothetical function, and a 4.3 % repeat content. Two minor chromosomes are enriched in transposable elements, AT content, and effector candidates. Chromosome 12 segregates within the population, indicating an accessory nature. The pangenome compile 15,101 genes, 34% more genes than present in the single isolate reference genome ofN. neomacrospora. These genes organise into 13,069 homologous clusters, of which 8,316 clusters are present in all analysed strains, 985 are private to single strains.The British Columbian population branched out before the other populations and are characterized by comparatively larger genomes. The increased genome size can be explained by an expansion of repetitive elements.The comparative analysis finds a higher number of genes with a signal peptide withinN. neomacrosporaand species within the genus compared to the closely related genera. A species-specific pattern is observed in the carbohydrate-active enzyme repertoire, with a reduced number of polysaccharide lyases, compared to other species within the genus. The CAZymes battery responsible for plant cell wall degradation is similar to that observed in necrotrophic and hemibiotrophic plant pathogenic fungi.The genome size ofN. neomacrosporais close to the median size for Ascomycota but is the smallest genome within theNeonectriagenus. Comparative analysis revealed significant intraspecies genome size differences between populations explained by a difference in repeat content. Isolates with the smallest genomes formed a monophyletic group consisting of all strains from Europe and Quebec. Based on the field observations, we assume thatN. neomacrosporais a hemibiotroph. Our analysis revealed a secretome consistent with a hemibiotrophic lifestyle.