Visualizing genomic evolution in Caenorhabditis through WormSynteny.
C. Elegans
Caenorhabditis
Comparative genomics
Genomic alignment
Genomic evolution
Nematode
Progressive cactus
Synteny
WormSynteny
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
28 Oct 2024
28 Oct 2024
Historique:
received:
03
09
2024
accepted:
17
10
2024
medline:
29
10
2024
pubmed:
29
10
2024
entrez:
29
10
2024
Statut:
epublish
Résumé
Understanding the syntenic relationships among genomes is crucial to elucidate the genomic mechanisms that drive the evolution of species. The nematode Caenorhabditis is a good model for studying genomic evolution due to the well-established biology of Caenorhabditis elegans and the availability of > 50 genomes in the genus. However, effective alignment of more than ten species in Caenorhabditis has not been conducted before, and there is currently no tool to visualize the synteny of more than two species. In this study, we used Progressive Cactus, a recently developed multigenome aligner, to align the genomes of eleven Caenorhabditis species. Through the progressive alignment, we reconstructed nine ancestral genomes, analyzed the mutational types that cause genomic rearrangement during speciation, and found that insertion and duplication are the major driving forces for genome expansion. Dioecious species appear to expand their genomes more than androdioecious species. We then built an online interactive app called WormSynteny to visualize the syntenic relationship among the eleven species. Users can search the alignment dataset using C. elegans query sequences, construct synteny plots at different genomic scales, and use a set of options to control alignment output and plot presentation. We showcased the use of WormSynteny to visualize the syntenic conservation of one-to-one orthologues among species, tandem and dispersed gene duplication in C. elegans, and the evolution of exon and intron structures. Importantly, the integration of orthogroup information with synteny linkage in WormSynteny allows the easy visualization of conserved genomic blocks and disruptive rearrangement. In conclusion, WormSynteny provides immediate access to the syntenic relationships among the most widely used Caenorhabditis species and can facilitate numerous comparative genomics studies. This pilot study with eleven species also serves as a proof-of-concept to a more comprehensive larger-scale analysis using hundreds of nematode genomes, which is expected to reveal mechanisms that drive genomic evolution in the Nematoda phylum. Finally, the WormSynteny software provides a generalizable solution for visualizing the output of Progressive Cactus with interactive graphics, which would be useful for a broad community of genome researchers.
Identifiants
pubmed: 39468698
doi: 10.1186/s12864-024-10919-6
pii: 10.1186/s12864-024-10919-6
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1009Subventions
Organisme : National Natural Science Foundation of China
ID : Excellent Young Scientists Fund for Hong Kong and Macau, 32122002
Organisme : Research Grants Council, University Grants Committee
ID : GRF 17107021, GRF 17106322, GRF 17105523, and CRF C7026-20G
Organisme : Health Bureau
ID : HMRF 09201426
Informations de copyright
© 2024. The Author(s).
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