ArticleGigaScience2019
Chromosome-level assembly of the mustache toad genome using third-generation DNA sequencing and Hi-C analysis.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 32 citations in OpenAlex.
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- Chromosome-level genome assembly of a high-altitude-adapted frog (Rana kukunoris) from the Tibetan plateau provides insight into amphibian genome evolution and adaptation.Frontiers in zoology · 2023Article
- Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana.G3 (Bethesda, Md.) · 2022Article
- Evolutionary analyses of visual opsin genes in frogs and toads: Diversity, duplication, and positive selection.Ecology and evolution · 2022Article
- A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridizing fire-bellied toads (Bombina bombina and Bombina variegata).G3 (Bethesda, Md.) · 2021Article
- A single QTL with large effect is associated with female functional virginity in an asexual parasitoid wasp.Molecular ecology · 2021Article
- Erythrocytes 3D genome organization in vertebrates.Scientific reports · 2021Article
- Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.Genomics, proteomics & bioinformatics · 2021Article
- Perspectives on studying molecular adaptations of amphibians in the genomic era.Zoological research · 2020Review
- A draft genome assembly of the eastern banjo frogGigaByte (Hong Kong, China) · 2020Article
- Chromosome-level assembly of the mustache toad genome using third-generation DNA sequencing and Hi-C analysis.GigaScience · 2019Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe mustache toad, Vibrissaphora ailaonica, is endemic to China and belongs to the Megophryidae family. Like other mustache toad species, V. ailaonica males temporarily develop keratinized nuptial spines on their upper jaw during each breeding season, which fall off at the end of the breeding season. This feature is likely result of the reversal of sexual dimorphism in body size, with males being larger than females. A high-quality reference genome for the mustache toad would be invaluable to investigate the genetic mechanism underlying these repeatedly developing keratinized spines.
findingsTo construct the mustache toad genome, we generated 225 Gb of short reads and 277 Gb of long reads using Illumina and Pacific Biosciences (PacBio) sequencing technologies, respectively. Sequencing data were assembled into a 3.53-Gb genome assembly, with a contig N50 length of 821 kb. We also used high-throughput chromosome conformation capture (Hi-C) technology to identify contacts between contigs, then assembled contigs into scaffolds and assembled a genome with 13 chromosomes and a scaffold N50 length of 412.42 Mb. Based on the 26,227 protein-coding genes annotated in the genome, we analyzed phylogenetic relationships between the mustache toad and other chordate species. The mustache toad has a relatively higher evolutionary rate and separated from a common ancestor of the marine toad, bullfrog, and Tibetan frog 206.1 million years ago. Furthermore, we identified 201 expanded gene families in the mustache toad, which were mainly enriched in immune pathway, keratin filament, and metabolic processes.
conclusionsUsing Illumina, PacBio, and Hi-C technologies, we constructed the first high-quality chromosome-level mustache toad genome. This work not only offers a valuable reference genome for functional studies of mustache toad traits but also provides important chromosomal information for wider genome comparisons.
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