In genomes we trust: assessing genomic reliability within the family Nectriaceae
Villani, A.; Ghionna, V.; Susca, A.; Menicucci, A.; Prodi, A.; Faino, L.; Moretti, A.; Baroncelli, R.
Show abstract
The Nectriaceae includes major plant and human pathogens, yet the genomic foundation underpinning its taxonomy remains uneven and largely unassessed. We analysed 1,530 genome sequence assemblies to quantify metadata completeness, geographic and taxonomic bias, and assembly quality across the family. One-third of the assemblies lacked essential metadata, sequencing was heavily skewed toward a few agriculturally important lineages, and sampling of many genera was limited or nonexistent. BUSCO and QUAST metrics revealed striking heterogeneity in assembly quality, with widespread fragmentation and a substantial subset of genomes falling outside the expected quality thresholds. From orthologous protein sequences of 763 single-copy genes in 576 high-quality genomes, we reconstructed a phylogenomic backbone for the Nectriaceae and quantified gene- and site-level concordance. While major clades broadly match current concepts, extensive gene-tree discordance and a polyphyletic Nisikadoi complex highlight unresolved evolutionary and taxonomic boundaries. Our study delivers the first integrated, family-wide evaluation of Nectriaceae genomic resources and outlines a framework for quality standards, curated metadata, and stable phylogenomic inference to support future taxonomic and comparative work.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires 94%
- Conserving a threatened North American walnut: a chromosome-scale reference genome for butternut (Juglans cinerea) 94%
- The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes 94%
Similar papers in this journal
- A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology 94%
- Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome. 93%
- Adaptative and ancient co-evolution of integrons with Xanthomonas genomes 93%
Similar papers in this journal
- Convergent losses of arbuscular mycorrhizal symbiosis in carnivorous plants 94%
- Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia 94%
- Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation 93%
Similar papers in this journal
- In-depth phylogenomic analysis of arbuscular mycorrhizal fungi based on a comprehensive set of de novo genome assemblies 97%
- The plot thickens: haploid and triploid-like thalli, hybridization, and biased mating type ratios in Letharia 95%
- Dispensable genome and segmental duplications drive the genome plasticity in Fusarium solani 95%
Similar papers in this journal
- Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces 95%
- Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus 95%
- Abundant secreted hydrolytic enzymes and secondary metabolite gene clusters in genomes of the Botryosphaeriaceae reflect their role as important plant pathogens 95%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.