Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits

Zhang, Suyu; Song, Yue; Liu, Meiru; Yuan, Zengbao; Zhang, Mengqi; Zhang, He; Seim, Inge; Fan, Guangyi; Liu, Shanshan; Liu, Xin

doi:10.1093/dnares/dsad018

Cited by 2 publications

(1 citation statement)

References 77 publications

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“…This observation becomes particularly interesting when considering the behavior of coral reef fish eggs. After two days of incubation, coral reef fish eggs floated away with the current, and they might have returned to their birth reef by smell when they became capable of swimming [106]. These analyses demonstrated that the gene families of the parrotfish had undergone expansion and contraction during their evolutionary process, significantly influenced by environmental factors.…”

Section: Enrichment Of Expansion and Contraction Gene Familiesmentioning

confidence: 93%

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

Liang,

Xian,

Pan

et al. 2024

Genes

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Scarus forsteni, a whitespot parrotfish from the Scaridae family, is a herbivorous fish inhabiting coral reef ecosystems. The deterioration of coral reefs has highly affected the habitats of the parrotfish. The decline in genetic diversity of parrotfish emphasizes the critical importance of conserving their genetic variability to ensure the resilience and sustainability of marine ecosystems for future generations. In this study, a genome of S. forsteni was assembled de novo through using Illumina and Nanopore sequencing. The 1.71-Gb genome of S. forsteni, was assembled into 544 contigs (assembly level: contig). It exhibited an N50 length of 17.97 Mb and a GC content percentage of 39.32%. Our BUSCO analysis revealed that the complete protein of the S. forsteni genome had 98.10% integrity. Combined with structure annotation data, 34,140 (74.81%) genes were functionally annotated out of 45,638 predicted protein-coding genes. Upon comparing the genome size and TE content of teleost fishes, a roughly linear relationship was observed between these two parameters. However, TE content is not a decisive factor in determining the genome size of S. forsteni. Population history analysis results indicate that S. forsteni experienced two major population expansions, both of which occurred before the last interglacial period. In addition, through a comparative genomic analysis of the evolutionary relationship of other species, it was found that S. forsteni had the closest relationship with Cheilinus undulatus, another member of the Labridae family. Our expansion and contraction analysis of the gene family showed that the expansion genes were mainly associated with immune diseases, organismal systems, and cellular processes. At the same time, cell transcription and translation, sex hormone regulation, and other related pathways were also more prominent in the positive selection genes. The genomic sequence of S. forsteni offers valuable resources for future investigations on the conservation, evolution, and behavior of fish species.

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Section: Enrichment Of Expansion and Contraction Gene Familiesmentioning

confidence: 93%

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

Liang,

Xian,

Pan

et al. 2024

Genes

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Fish Genomics and Its Application in Disease‐Resistance Breeding

Huang,

Li,

et al. 2024

Reviews in Aquaculture

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Global aquaculture production has been rising for several decades, with up to 76% of the total production from fish. However, the problem of fish diseases is becoming more and more prominent in today's context of pursuing sustainable aquaculture. Since the first fish genome assembly reported in 2002, genomic approaches have been successfully implemented in fish breeding to enhance disease resistance and reduce economic losses caused by diverse fish diseases. Here, we present a review of the current progress in fish genomics and its application in disease‐resistance breeding. First, assembly data for all publicly available fish genomes were curated and statistical analysis of these data were performed. Subsequently, genomics‐assisted breeding approaches (including quantitative trait loci mapping, genome‐wide association study, marker‐assisted selection, genomic selection, gene transfer, and genome editing) that have been applied in practical disease–resistance breeding programs are outlined. In addition, candidate genetic markers that could possibly be utilized in breeding were summarized. Finally, remaining challenges and further directions were discussed. In summary, this review provides insight into fish genomics and genomics‐assisted breeding of disease‐resistant fish varieties.

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Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits

Cited by 2 publications

References 77 publications

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

Fish Genomics and Its Application in Disease‐Resistance Breeding

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