Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Mol Ecol Resour
2026 Feb 01;262:e70097. doi: 10.1111/1755-0998.70097.
Show Gene links
Show Anatomy links
QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics.
Chen G, Du H, Cao Z, Wu Y, Zhang C, Zhou Y, Ao J, Sun Y, Yuan Z.
???displayArticle.abstract???
The rapid growth of genome sequencing has outpaced the development of efficient annotation tools, especially for species lacking transcriptome data. To address this challenge, we present QuickProt, a fast, accurate and user-friendly homology-based protein annotation tool. QuickProt constructs a non-redundant gene model by aligning homologous proteins from closely related species, offering an accurate and cost-effective solution suitable for large-scale comparative genomic studies. Benchmarking against BRAKER2 and GALBA across reference genomes demonstrated that QuickProt offers high specificity and dramatically improved runtime, while maintaining competitive annotation accuracy. To demonstrate its utility, we applied QuickProt to diverse genomes, including a non-model teleost (Epinephelus bruneus), two tetraploid Xenopus species and 11 Rutaceae plants. Across these datasets, QuickProt supported robust phylogenetic reconstruction, identification of conserved orthologs and detection of biologically functional genes, pathways, and chromosomal evolution mechanisms, regardless of genome ploidy. Notably, it revealed a potential horizontal gene transfer event between groupers and Vibrio, and uncovered conserved modules involved in volatile oil biosynthesis and oil gland development in citrus. With its scalability and minimal computational demands, QuickProt provides a powerful platform for genome annotation and evolutionary inference. As the number of sequenced genomes continues to expand, QuickProt is a useful tool for accelerating comparative genomics and functional exploration across the tree of life.
FIGURE 1. Schema of the QuickProt algorithm. (A) This step uses Miniprot to align protein sequences to the genome. (B) This step delineates coding regions and assembles them into pseudo‐transcripts. (C) This step predicts gene structures within the pseudo‐transcripts, splits overlapping genes based on their positional information and filters out low‐quality genes according to their length and prediction scores.
FIGURE 2. Performance and annotation overview of QuickProt in teleost genomes. (A) Density distribution of protein‐coding gene length. (B) Comparison of processing time for QuickProt, BRAKER2 and GALBA using 24 threads on Ubuntu 22.04. (C). Venn diagram showing the overlap of the annotation categories of
E. bruneus
protein‐coding genes annotated by QuickProt. (D) Distribution of best‐hit species from NR database annotation using QuickProt predicted protein coding genes from
E. bruneus
. (E) BUSCO evaluation showing the genome completeness.
FIGURE 3. Benchmarking of QuickProt against BRAKER2 and GALBA across four model organisms. (A–D) Sensitivity and specificity of gene prediction at the base level in four reference genomes. (E) Comparison of F1‐score for gene prediction across four genomes. (F) Running time of BRAKER2, GALBA and QuickProt in each genome, demonstrating computational efficiency.
FIGURE 4. Comparative genomics and protein domain analysis in groupers. (A) The phylogenetic tree of groupers with
C. striata
as the outgroup. (B) Number of orthologous genes identified between groupers and C. striata. (C) Genome synteny between E. moara and
E. bruneus
. (D) Domain structure of reverse transcriptase domain‐containing proteins in
E. bruneus
.
FIGURE 5. Evolutionary analysis of reverse transcriptase domain‐containing proteins. (A) Alignment of proteins in the clade inferred to be derived from horizontal gene transfer (HGT). (B) Phylogenetic tree of the reverse transcriptase domain‐containing proteins across species.
FIGURE 6. Comparative analysis of relative synonymous codon usage (RSCU). (A) RSCU pattern in
P. leopardus
. (B) RSCU in
V. parahaemolyticus
. (C) RSCU in
E. bruneus
. (D) RSCU in the HGT derived clade.
FIGURE 7. Comparative genomics analysis in Xenopus. (A) Phylogenetic tree based on protein‐coding genes of Xenopus. The suffixes ‘L’ and ‘S’ used after the species names denote large and small subgenomes, respectively. (B) Synteny analysis in Xenopus species.
FIGURE 8. Comparative genomics and functional enrichment in the Rutaceae family. (A) Phylogenetic tree and estimated divergence time among Rutaceae species (Species names in red are annotated by QuickProt). (B) Number of orthologous gene groups shared within the Rutaceae species. (C) KEGG enrichment of the core genes across the Rutaceae family.
