NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

Abstract

Summary Large-scale comparative genomic studies have provided important insights into species evolution and diversity, but also lead to a great challenge to visualize. Quick catching or presenting key information hidden in the vast amount of genomic data and relationships among multiple genomes requires an efficient visualization tool. However, current tools for such visualization remain inflexible in layout and/or require advanced computation skills, especially for visualization of genome-based synteny. Here, we developed an easy-to-use and flexible layout tool, NGenomeSyn (multiple (N) Genome Synteny), for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats. Availability and implementation NGenomeSyn is freely available at GitHub (https://github.com/hewm2008/NGenomeSyn) and Zenodo (https://doi.org/10.5281/zenodo.7645148). Supplementary information Supplementary data are available at Bioinformatics online.

CpG Island Definition and Methylation Mapping of the T2T-YAO Genome

“…Therefore, the difference between the two genomes is approximately 4.7%–5.8%. Second, using NGenomeSyn [23], we created a collinearity map of the two genomes and observed that the two sequences are very similar both in identity and chromosome length ( Figure 2) in general [24]. The divergent sequences between the two genomes are mainly concentrated in specific regions of each chromosome (Figure 2B).…”

“…Secondly, Figure 2A describes the mapping of similar sequences between Chinese T2T-YAO-hp and T2T-CHM13 genomes by using NGenomeSyn [20] to make a collinearity map. We observed that most of the T2T-CHM13 sequences are very similar to the sequences of the corresponding chromosomes of T2T-YAO, which is consistent with the expected chromosome correspondence.…”

Genomic evidence for hybridization and introgression between blue peafowl and green peafowl and selection for white plumage

“…We also performed collinearity analysis using MCscanx 67 with default parameters. The NGenomeSyn 68 (v.1.4.1) was used for synteny visualization.…”

Comparative genomics and transcriptomics reveal differences in effector complement and expression between races ofFusarium oxysporumf.sp.lactucae

“…Pairwise alignments were performed using Minimap2 v2.17-r941 (Li, 2018) and prior to visualisation, core genome alignments smaller than 100 kb and accessory genome alignments smaller than 10 kb were discarded. The results were visualised using NGenomeSyn v1.41 (He et al, 2023).…”

“…that were associated with a mimp. The lack of any DNA or protein sequence similarity between effectors in F. oxysporum emphasises the importance of understanding effector protein structure (Yu et al, 2023) and highlighted some short-comings of the mimp-based effector discovery pipeline employed here. Mimp-associated candidate effectors from each F. oxysporum genome were clustered at 65% identity using CD-HIT which designates the longest sequence within each cluster as the representative sequence, which is then submitted to EffectorP for identification.…”