Whole-genome resequencing infers genomic basis of giant phenotype in Siamese fighting fish ( Betta splendens).
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ABSTRACT:
SUBMITTER: Wang L
PROVIDER: S-EPMC8743251 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Metformin, the medicine most commonly prescribed for treatment of Type II diabetes, is among the most abundant pharmaceuticals being introduced into the environment. Pharmaceuticals are increasingly found in wastewater and surface waters around the world, often due to incomplete metabolism in humans and subsequent excretion in human waste. Risk analyses and exposure studies have raised concerns about potential negative impacts of pharmaceuticals at current environmental levels. Results of the present study indicate that metformin at concentrations in the range of what has been documented in freshwater systems and waste-water effluent (40 μg/L) affects aggressive behavior in adult male Betta splendens. Subjects exhibited less aggression toward a male dummy stimulus after four weeks exposure to metformin-treated water when compared to behavior measured immediately prior to their exposure, and in comparison to a separate cohort of un-exposed control fish. This effect persisted after 20 weeks exposure as well. Subjects exposed to metformin at a concentration twice that currently observed in nature (80 μg/L) exhibited an even more substantial reduction in aggressive behaviors compared to controls and pre-exposure measurements than those observed in the low-dose treatment group. Such changes in behavior have the potential to affect male fitness and possibly impact the health of natural populations of aquatic organisms exposed to the drug.
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Project description:In Southeast Asia, males of the Siamese fighting fish Betta splendens have been selected across centuries for paired-staged fights. During the selection process, matched for size males fight in a small tank until the contest is resolved. Breeders discard losing batches and reproduce winner batches with the aim of increasing fight performance. We assessed the results of this long-term selection process by comparing under standard laboratory conditions male and female aggressive behaviour of one strain selected for staged fights ("fighters") and one strain of wild-types. The aggressive response of adult fish was tested against their mirror image or a size-matched conspecific. Fighter males were more aggressive than wild-type males for all measured behaviours. Differences were not only quantitative but the pattern of fight display was also divergent. Fighter males had an overall higher swimming activity, performing frequent fast strikes in the direction of the intruder and displaying from a distance. Wild-type males were less active and exhibited aggressive displays mostly in close proximity to the stimuli. Females of the fighter strain, which are not used for fights, were also more aggressive than wild-type females. Aggressive behaviours were correlated across male and female fighter siblings, suggesting common genetic and physiological mechanisms to male and female aggression in this species. The study further shows that results were largely independent of the stimulus type, with the mirror test inducing similar and less variable responses than the live conspecific presentation. These results suggest that selection for male winners co-selected for high-frequency and metabolic demanding aggressive display in males and also enhanced female aggression, opening a wide range of testable hypothesis about the ultimate and proximate mechanisms of male and female aggression in B. splendens.
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Project description:Siamese fighting fish Betta splendens are notorious for their aggressiveness and accordingly have been widely used to study aggression. However, the lack of a reference genome has, to date, limited the understanding of the genetic basis of aggression in this species. Here, we present the first reference genome assembly of the Siamese fighting fish. Frist, we sequenced and de novo assembled a 465.24-Mb genome for the B. splendens variety Giant, with a weighted average (N50) scaffold size of 949.03 Kb and an N50 contig size of 19.01 Kb, covering 99.93% of the estimated genome size. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 75.24 Gb reads using the BGISEQ-500 platform. We anchored approximately 93% of the scaffold sequences into 21 chromosomes and evaluated the quality of our assembly using the high-contact frequency heat map and Benchmarking Universal Single-Copy Orthologs. We also performed comparative chromosome analyses between Oryzias latipes and B. splendens, revealing a chromosome conservation evolution in B. splendens. We predicted 23,981 genes assisted by RNA-sequencing data generated from brain, liver, muscle, and heart tissues of Giant and annotated 15% repetitive sequences in the genome. Additionally, we resequenced five other B. splendens varieties and detected ∼3.4 M single-nucleotide variations and 27,305 insertions and deletions. We provide the first chromosome-level genome for the Siamese fighting fish. The genome will lay a valuable foundation for future research on aggression in B. splendens.
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Project description:Here, we announce the complete genome of a previously undescribed papillomavirus from a betta fish, Betta splendens. The genome is 5,671 bp with a GC content of 38.2%. Variants were detected in public databases. This genome is most similar to papillomaviruses that infect sea bass (52.9 % nucleotide identity).
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Project description:Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university master's course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using the Hi-C data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master's course. The use of ∼35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.
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Project description:Betta pi is the largest species of mouthbrooding fighting fish, while B. splendens is a globally ornamental bubble nesting fish. Complete mitochondrial genomes (mitogenomes) of wild individuals of B. pi and B. splendens were determined. The mitogenome sequences were 16,521 and 16,980 base pair in length, containing 37 genes with gene order identical to most teleost mitogenomes. Overall A?+?T content was 57.72% for B. pi and 61.92% for B. splendens. Phylogenetic analysis showed that B. pi and B. splendens were highly supported monophyletic clades. Our results will facilitate further genetic studies, including mitochondrial variations and population structure of fighting fishes.
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Project description:Conspecific male animals fight for resources such as food and mating opportunities but typically stop fighting after assessing their relative fighting abilities to avoid serious injuries. Physiologically, how the fighting behavior is controlled remains unknown. Using the fighting fish Betta splendens, we studied behavioral and brain-transcriptomic changes during the fight between the two opponents. At the behavioral level, surface-breathing, and biting/striking occurred only during intervals between mouth-locking. Eventually, the behaviors of the two opponents became synchronized, with each pair showing a unique behavioral pattern. At the physiological level, we examined the expression patterns of 23,306 brain transcripts using RNA-sequencing data from brains of fighting pairs after a 20-min (D20) and a 60-min (D60) fight. The two opponents in each D60 fighting pair showed a strong gene expression correlation, whereas those in D20 fighting pairs showed a weak correlation. Moreover, each fighting pair in the D60 group showed pair-specific gene expression patterns in a grade of membership analysis (GoM) and were grouped as a pair in the heatmap clustering. The observed pair-specific individualization in brain-transcriptomic synchronization (PIBS) suggested that this synchronization provides a physiological basis for the behavioral synchronization. An analysis using the synchronized genes in fighting pairs of the D60 group found genes enriched for ion transport, synaptic function, and learning and memory. Brain-transcriptomic synchronization could be a general phenomenon and may provide a new cornerstone with which to investigate coordinating and sustaining social interactions between two interacting partners of vertebrates.
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Project description:The Betta fish displays a remarkable variety of phenotypes selected during domestication. However, the genetic basis underlying these traits remains largely unexplored. Here, we report a high-quality genome assembly and resequencing of 727 individuals representing diverse morphotypes of the Betta fish. We show that current breeds have a complex domestication history with extensive introgression with wild species. Using a genome-wide association study, we identify the genetic basis of multiple traits, including coloration patterns, the "Dumbo" phenotype with pectoral fin outgrowth, extraordinary enlargement of body size that we map to a major locus on chromosome 8, the sex determination locus that we map to dmrt1, and the long-fin phenotype that maps to the locus containing kcnj15. We also identify a polygenic signal related to aggression, involving multiple neural system-related genes such as esyt2, apbb2, and pank2. Our study provides a resource for developing the Betta fish as a genetic model for morphological and behavioral research in vertebrates.
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Project description:Betta splendens isolate:Giant Genome sequencing and assembly
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Project description:Siamese fighting (betta) fish are among the most popular and morphologically diverse pet fish, but the genetic bases of their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced 98 individuals across five closely related species. We find evidence of bidirectional hybridization between domesticated ornamental betta and other wild Betta species. We discover dmrt1 as the main sex determination gene in ornamental betta and that it has lower penetrance in wild B. splendens. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body or on the shape of individual fins and that most are unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication and launch betta as a powerful new system for evolutionary genetics.
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