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. 2024 May 7;22(5):e3002405.
doi: 10.1371/journal.pbio.3002405. eCollection 2024 May.

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments

Sanjida H Rangwala  1 , Dmitry V Rudnev  1 , Victor V Ananiev  1 , Dong-Ha Oh  1 , Andrea Asztalos  1 , Barrett Benica  1 , Evgeny A Borodin  1 , Nathan Bouk  1 , Vladislav I Evgeniev  1 , Vamsi K Kodali  1 , Vadim Lotov  1 , Eyal Mozes  1 , Marina V Omelchenko  1 , Sofya Savkina  1 , Ekaterina Sukharnikov  1 , Joël Virothaisakun  1 , Terence D Murphy  1 , Kim D Pruitt  1 , Valerie A Schneider  1
Affiliations

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments

Sanjida H Rangwala et al. PLoS Biol. .

Abstract

We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by National Center for Biotechnology Information (NCBI) using assembly alignment algorithms developed by us and others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed where available. CGV currently provides approximately 800 alignments from over 350 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Overview of CGV.
(A) CGV selection menu. (B) Taxonomic distribution of species represented by alignments in CGV. Numbers in the pie charts are current as of February 5, 2024 (C) CGV ideogram view of whole-genome assembly alignment. Buttons in the lower right provide download access for complete whole-genome alignment data or an SVG image of the current alignment view. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/browse/GCF_015227675.2/GCF_000001635.27/27835/10116 (D) CGV zoomed to a chromosome-by-chromosome view, with an information panel shown. This panel can be viewed by clicking to select an alignment segment. (i) Flip orientation; (ii) zoom in/out; (iii) pan left/right; (iv) view assembly in GDV; (v) information panel. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/browse/GCF_015227675.2/GCF_000001635.27/27835/10116#NC_051343.1:44657546-50471623/NC_000075.7:41365809-52285446/size=10000. (E) CGV search interface and sample search results. (F) Adjust Your View configure options for the ideogram view. Webpage source: National Library of Medicine. CGV, Comparative Genome Viewer; GDV, Genome Data Viewer.
Fig 2
Fig 2. CGV dotplot view of Xenopus laevis and Xenopus tropicalis alignment.
(A) Full genome dotplot. (B) Dotplot of chromosome 8 of Xenopus tropicalis vs. chromosome 8S of Xenopus laevis. These views can be recreated at https://ncbi.nlm.nih.gov/genome/cgv/plot/GCF_000004195.4/GCF_017654675.1/38475/8355. CGV, Comparative Genome Viewer.
Fig 3
Fig 3. CGV shows conservation of linkage groups in the absence of conservation of gene order.
(A) CGV ideogram view of alignment between Drosophila albomicans and Drosophila melanogaster genomes. Alignments are restricted to a single chromosome or chromosome region. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/browse/GCF_009650485.2/GCF_000001215.4/40865/7291. (B) CGV dotplot view of alignment between Drosophila albomicans and Drosophila melanogaster demonstrates that sequence order is “scrambled” within linkage groups, as demonstrated by a scatter pattern indicating many short rearranged alignments. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/plot/GCF_009650485.2/GCF_000001215.4/40865/7291. (C) CGV dotplot view of alignment between starfish species Luida sarsii and Asteria rubens with similar scatter pattern to Drosophila alignments. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/plot/GCA_949987565.1/GCF_902459465.1/41045/2723838. (D) CGV ideogram view of alignment between chromosome 1 of Luida sarsii and chromosome 1 of Asteria rubens. These chromosomes align to each other across their length, but the alignment is broken into multiple short segments which are extensively rearranged. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/browse/GCA_949987565.1/GCF_902459465.1/41045/2723838#OX465101.1/NC_047062.1/size=1,firstpass=0. (E) CGV dotplot view of alignment between starfish species Luida sarsii and Patiria pectinifera with similar scatter pattern to Drosophila alignments. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/plot/GCA_949987565.1/GCA_029964075.1/41165/7594. (F) CGV dotplot view of alignment between starfish species Plazaster borealis and Pisaster ochraceus. Alignments show less scatter and more of a diagonal slope, indicating more conservation of sequence order between these 2 species’ genomes. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/plot/GCA_021014325.1/GCA_010994315.2/41175/466999. CGV, Comparative Genome Viewer.
Fig 4
Fig 4. CGV can help uncover gene duplications and rearrangements in closely related genomes.
(A) Gene search of a T2T/HPRC-generated alignment between 2 human assemblies in CGV finds an alpha-amylase gene cluster on chromosome 1 containing 10 copies in the T2T-CHM113v2.0 assembly and 4 copies in the GRCh38.p14 assembly. (B) CGV view showing that T2T-CHM13v2.0 contains an insertion relative to GRCh38.p14, which appears as an unaligned region on chromosome 1. This insertion contains additional alpha-amylase gene copies. An information panel (tooltip) indicates one of these additional family members. These tooltips appear when the user hovers their cursor over the gene annotation or gene label. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/browse/GCF_009914755.1/GCF_000001405.40/23025/9606#NC_060925.1:103415704-103764412/NC_000001.11:103566852-103915505/size=1000,firstpass=0. (C) CGV view showing that chromosome 2 of Canis lupus familiaris (dog) UMICH_Zoey_3.1 aligns to chromosomes 2, 15, 23, and 25 of Dog10K_Boxer_Tasha. The view can be recreated at https://ncbi.nlm.nih.gov/genome/cgv/browse/GCF_005444595.1/GCF_000002285.5/17685/9615#NC_049262.1:6542815-78714085//size=10000. (D) UMICH_Zoey_3.1 assembly chromosome 2 alignment to Dog10K_Boxer_Tasha chromosome 25 contains the MALRD1 gene, which is annotated as LOC608668 in the Tasha assembly (boxed in red). Gene synteny is not conserved outside of the region of this gene. Webpage source: National Library of Medicine. CGV, Comparative Genome Viewer.
Fig 5
Fig 5. Genome and CDS coverage of assembly-assembly alignments relative to Mash distance.
Percentages of total target genome or CDS nucleotides covered by ungapped alignments are plotted against the Mash distance between the pair of genomes. (A) Alignments between the human GRCh38.p14 assembly and other vertebrates. (B) Alignments of fall army worm (FAW, Spodoptera frugiperda, a major insect agricultural pest) and related insects. At lower Mash distances, the whole-genome alignments cover most of the genome and CDS. At Mash distances greater than 0.25 or 0.3, the alignment covers less than 20% of the genome overall, and between 30% and 60% of the CDS. Refer to S1 Data for the data used to populate these graphs. CDS, coding sequence.
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This work was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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