ArticleNucleic acids research2023
DupScan: predicting and visualizing vertebrate genome duplication database.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 8 citations in OpenAlex.
- A comprehensive and accessible database of jawed-vertebrate ohnologs.Science advances · 2026Article
- Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach.Nature protocols · 2024Review
- Seascapes Shaped the Local Adaptation and Population Structure of South China Coast Yellowfin Seabream (Acanthopagrus latus).Marine biotechnology (New York, N.Y.) · 2024Article
- Emergence of the Synucleins.Biology · 2023Article
- The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection.Nucleic acids research · 2023Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Duplicated genes prevail in vertebrates and are important in the acquisition of new genes and novelties. Whole genome duplication (WGD) is one of the sources of duplicated genes. It can provide raw materials for natural selection by increasing the flexibility and complexity of the genome. WGDs are the driving force for the evolution of vertebrates and contribute greatly to their species diversity, especially in fish species with complicated WGD patterns. Here, we constructed the DupScan database (https://dupscan.sysumeg.com/) by integrating 106 chromosomal-level genomes, which can analyze and visualize synteny at both the gene and genome scales, visualize the Ka, Ks, and 4DTV values, and browse genomes. DupScan was used to perform functional adaptation for the intricate WGD investigation based on synteny matching. DupScan supports the analysis of five WGD rounds (R): VGD2 (vertebrate genome duplication 2), Ars3R (Acipenser-ruthenus-specific 3R), Pss3R (Polyodon-spathula-specific 3R), Ts3R (teleost-specific duplication 3R), Ss4R (salmonid-specific 4R), and Cs4R (carp-specific 4R). DupScan serves as one-stop analysis platform for synteny and WGD research in which users can analyze and predict synteny and WGD patterns across 106 species of whole genome sequences. This further aided us in elucidating genome evolutionary patterns across over 60,000 vertebrate species with synteny and WGD events.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.