Fungal Genome Sequencing Service-Third-Gen Long-Read Assembly | Verygenome

Fungal De Novo Sequencing

Fungal genome de novo sequencing assembles the fungal genome without a reference, then annotates and analyzes it downstream. Combining the long reads of third-generation sequencing with the throughput of second-generation sequencing ensures high-quality assemblies. As research trends toward refinement, a high-quality fungal genome map provides the genomic basis for downstream work—sequencing and assembling the full genome to study its structure and function.

Principle Introduction

The core is technology complementarity plus fungus-specific assembly. Fungal genomes are large and complex; joint short/long-read assembly achieves advanced (near-finished) assemblies, predicting key genes/proteins and mechanisms. Workflow: sample/DNA prep, multi-platform library construction and sequencing, assembly, quality validation and functional annotation.

Literature

Published in Fungal Diversity, "Deciphering the evolutionary and taxonomic complexity of Diaporthales (Sordariomycetes, Ascomycota) through integrated phylogenomic and divergence time estimation" performed genome de novo sequencing on 113 Diaporthales fungi (pathogens, endophytes, saprobes), revising taxonomy, discovering 55 new species and revealing 181.5 million years of evolution. The team collected >10,000 specimens and isolated 800+ strains across China over eight years, integrating morphology, ecology, multi-gene and genome phylogenies, molecular clocks and metabolic pathway annotation to elucidate phylogenetic history, divergence timing and metabolic traits of this important Ascomycota group.

Deliverables

Sequencing data

short-read, long-read, mitochondrial data with notes.

Assembly

core files, nuclear and mitochondrial genome sequences, QC reports.

Visualization

nuclear scaffold length distribution; mitochondrial circular map (gene positions).

Annotation

gene structure, functional and non-coding RNA annotation.

Report

basic module (QC, assembly validation); advanced module (comparative genomics, phylogenetics, secondary metabolite cluster prediction).

FAQ

Why focus on both nuclear and mitochondrial genomes?

The nuclear genome holds core functional genes; the mitochondrial genome, fast-evolving and low-recombining, is an ideal taxonomic/phylogenetic marker and links to environmental adaptation, and its easy assembly (10–100 kb) validates nuclear assembly quality.

DNA sample prep tips?

Use vegetative hyphae at asexual stage, avoid complex-structure periods; if possible, germinate a single spore into mass hyphae for uniform prep.

Core advantage of long reads (Nanopore)?

Fungal genomes have many repeats and secondary-metabolite clusters; short reads (<300 bp) fragment assemblies, while 100 kb+ Nanopore reads span repeats for gap-free scaffolds, avoid PCR bias (better high-GC capture) and detect DNA methylation.

Primary vs. advanced assembly?

Primary assesses genome size, GC, repeats, heterozygosity and contamination with a 50X short-read library (data-volume only, no assembly metrics); advanced uses joint short/long-read libraries.

Microbiomics