Colorful Siamese Fighting Fish
Siamese Fighting Fish is easy to reproduce and breed, and provides a useful resource for exploring the genetic basis of vertebrate behavior and morphology due to its high intraspecies variability and extensive characterization of phenotypes. It also shows a classic example of how direct and indirect choices of humans shape a domesticated species.
Recently, Professor Hong Yijiang's team of School of Life Sciences, Nanchang University, reported the efficient chromosomal genome assembly of female Bifidobacterium , and resequencing data of 727 domesticated individuals and 59 wild individuals from six other species in the Siamese fighting fish complex. The researchers studied evolutionary relationships and origins among breeds and used association mapping to identify the genetic basis of many different traits, including SD, fin morphology, coloration, body shape and aggressiveness, and other behaviors.
Genomic Assembly, Annotation and Comparative Analysis of Siamese Fighting Fish
Researchers used a multifaceted sequencing and assembly workflow to generate high-quality chromosomal assembly of beta fish, including PacBio reads, Illumina reads, Hi-C reads, 10x genomic reads and BioNano optical mapping. The final assembled genome was 451.29 million base pairs , with continuum and scaffold N50 reaching 4.07 and 19.63 Mb, respectively. A total of 93.6% of the scaffolds were placed on 21 chromosomes, which is consistent with the previously reported karyotypes.
This component contains 119 Mb repeats and 25,104 annotated structural genes, of which 22,788 (90.77%) are functionally annotated. Analysis of the core eukaryotic gene map method confirmed that 239 of 248 (96.4%) complete core eukaryotic genes were found, and the benchmark universal single-copy ortholog evaluation showed that 2522 of 2586 (97.5%) single-copy homologous genes were annotated, indicating high integrity of genomic and gene annotation.
researchers used to construct a phylogenetic from 465 single-copy homologs shared by Siamese fighting fish and 13 other hard bones, and showed that Siamese fighting fish differentiated with other flora about 109.6 million years ago. High-quality genome assembly coupled with comprehensive genome annotation is an important supplement and improvement to the existing reference genome resources for Siamese fighting fish research.
(A) Phylogenetic of bone fish (B) Tandem-wide genome single nucleotide polymorphism (C) PCA of Siamese fighting fish. (D) Mixed analysis of Bifidobacterium.
Diversification of beta fish during domestication
Researchers collected 14 breeds of Siamese fighting fish, which vary in tail type, color, gender and body shape and performed whole-genome resequencing of 727 individuals, resulting in ~2.7 Tb sequencing data.
In order to clarify the population history of the Siamese Fighting Complex and the origin of domesticated Siamese Fighting Complex, the researchers further sequenced 59 individuals from six wild species from the Siamese Fighting Complex and co-analysed 20 randomly selected individuals of each species. The maximum likelihood phylogenesis from the tandem sequence, representing the mean genomic coalescing tree, suggesting that domesticated species form a single-line population relative to other wild species. Furthermore, in principal component analysis, they consistently form a tight cluster, unlike other wild individuals.
These observations are consistent with the hypothesis that all current breeds of Siamese fighting fish were domesticated from the same group of wild double Fischemia . Betasia Molinta Individual In the tree, a single-line branch forms in the cluster of individuals. Several branches of betfish breeds fall as outgroups of other domesticated breeds in the phylogenetic tree, which is consistent with the breeding record, that is, the fighter breeds represent early domestication forms, and the earliest domesticated beta fish were actually selected for combat.
However, these observations can also be attributed to the penetration of wild species into betfish, face-tail and crown-tail varieties, as extensive gene flow signals are observed in different fish populations.Population structures, such as phylogenetic, PCA, and admixture analysis, show that varieties defined by color and morphology are often clustered together.
Although researchers note that this conclusion may be affected by the sampling strategy used here. The half-moon Prakat breed is a short-fin type, unlike the combat type and wild Siamese fighting fish, with a round tail shape and body shape, and is also clustered according to appearance, mainly related to color. The red, yellow, orange, turquoise green, royal blue, steel blue varieties group had a large number of population-specific genetic drifts, which were significant in structural analysis and genome-wide phylogenetic, indicating that these groups experienced strong bottleneck effects in their domestication history.
mixed analysis showed that there was a large amount of gene flow between wild and domesticated species of Siamese fighting fish. These results show a general heterogeneity of gene flow between domesticated species and wild species, even in individuals of the same breed. The high heterogeneity of inter-individual mixtures suggests that gene flow is not only common in wild and domesticated breeds, but has only recently emerged, possibly due to artificial influence. There are at least two wild species, Beta Mahachai and Bifidobacter , which contributed to the genome composition of domesticated Siamese fighting fish. It may thus also contribute to phenotypic variation in these varieties. The regulatory variant in
dmrt1 mediated male heterogameloids of Bifidobacterium
To map the loci, the researchers used the mixed linear model to map all 727 individuals, including 590 males and 137 females. The first three main components of the affinity matrix and PCA were used as covariates to minimize the effects of population stratification.
researchers found a very important map location at positions 27.75 to 27.81 Mb on chromosome 9. The signal is repeated consistently with the mapping of different breeds, supporting the common genetic basis of SD in all of these breeds, which is also consistent with previous studies. Of the 537 individuals with lead variant heterozygous genotypes, 533 individuals were phenotypic males and 130 of the 137 AA homozygous individuals were females, which strongly supported the hypothesis of heterogamite (XY/XX) for Siamese fighting fish males.
A) GWAS analysis of SD B) Distribution map on related peak areas. C) Expression levels of ovarian and testicular genes. D) Manhattan diagram of phenotype F) Color pattern phenotype
The most strongly associated variant cluster consists of dmrt1 and kank1kkank1. kank1 plays a role in cell skeleton formation by regulating actin polymerization, which makes it unlikely to become SD. By contrast, dmrt1 is a well-known gene that contributes to SD in fish, birds and reptiles.
In addition, mRNA sequencing shows that dmrt1 is highly expressed in the testes, but is almost undetectable in the ovaries. dmrt1 in Siamese fighter fish is evolutionarily close to 未分文 dmy gene, which is the first gender-determining gene identified in hard bone. The presence of males with homogammate female genotypes may indicate that environmental factors, such as temperature, may also play a role in SD like many other fish.
Other wild species, including Bifidobacterium , Xiya Moritalis , Bifidobacterium Mahachai , Mahachai , s Malagina Bifidobacterium, html l3 guitar Bifidobacterium and Bifidobacterium , may have different SD mechanisms, as both female and male individuals are homozygous at the leading single nucleotide polymorphism (SNP), and the whole genome association study (GWAS) with these individuals did not restore the signal at dmrt1333333dmrt133333 loci.
color and color pattern of beta fish
study shows that the difference between the steel blue breed Siamese fighting fish and other breeds is the lack of red blood cells in the lower layer of the scales. GWA analysis encoded steel blue, royal blue and turquoise green as 1, 2 and 3 identified a single locus at a rate of 8.96 to 9.19 Mb on chromosome 24, and GWAS with other coding schemes were always mapped to the same location. Genotype analysis of
SNP peaks showed that turquoise green and steel blue are homozygous for different alleles, and 27 of the 28 royal blue individuals were heterozygous , which is highly consistent with the co-dominant genetic pattern. This site contains 13 protein-encoded genes, including mthfd1l. mthfd1l participates in the synthesis of tetrahydrofolate . tetrahydrofolate is engaged in the de novo assembly of purine . Purine is the key component in the production of iridescent balls, producing iridescent colors, including blue and green.
Therefore, mthfd1l is a promising candidate that requires in-depth functional research. The copper breed Siamese fighter has a characteristic metal appearance on the scales. Reproductive records show that it is derived by introducing a “metal gene” into the genetic background of the steel blue varieties.
performed GWAS and identified two most important peaks. The strongest one overlaps the loci below the Royal Blue, Steel Blue and Turquoise Green Changes, and the other is located at 10.37 Mb of chromosome 5. All peak variants are present in the srgap3 gene, a cytoskeleton regulator. Genotype analysis of the lead SNP at this site showed that steel blue is a homozygous of the T allele, while copper individuals carry one or two copies of the alternative allele (C), consistent with known genetic patterns.
Therefore, the researchers believe that the relevant regions are strong candidates for the hypothetical Mendel metal gene. In hard bone, the red cell mass and the yellow mass produce red and yellow pigments, respectively, and the orange color can be imparted by a pteridine component or a mixture of red and yellow pigments. Case control GWAS compared orange varieties with red and yellow varieties. A major site was identified at the location of 5.83 Mb of chromosome 8, containing 93 variants, all located in the rnf213 gene, and participated in angiogenesis and non-canonical Wnt signaling pathway in vascular development.
Red and yellow varieties are homozygous with T allele deletion, while TA allele insertion frequency is higher in orange varieties. Mosaic colored patterns are a spectacular phenotype in Siamese fighting fish, with a variety of commercial names including koi, candy, galaxies, lemons and marble. Although mosaic color patterns have also been observed in koi and pineapple fish, the potential molecular basis has not been studied.
Here, the researchers performed GWAS, performing case control designs between solid and mosaic colors. Nine related sites were identified on eight chromosomes, suggesting the polygenic basis of this phenotype. The two strongest signals were found in two adjacent peaks on chromosome 11. At the most important sites, the slc39a7, chs3, chs8 and col11a23, and col11a2, and tubular involved in intracellular pigment mobilization. In addition, adjacent trajectories also contain pigmentation-related genes, including breech , eppk1, slc17a5 and slc52a2.
It is worth noting that in the association peak, there are eight copies of plec, which is the central gene in the analysis of a gene co-expression network for the "pink-dark green" color change in cave fish. The eyes of Siamese fighting fish also show great diversity , with at least six color categories including black, white, tan, yellow, light blue and brown, which can be visually recognized. However, GWA mapping for each group did not show strongly related sites, possibly indicating the complex genetic structure or environmental cues behind eye color changes.The functional gain of
kcnj15 causes overgrowth of fins
The most significant morphological difference between Siamese fighting fish is the fins, especially the caudal fins. Veil Tail and Half Moon show significant growth in the dorsal fin, anal fin and caudal fin compared to combat type. Hybrids show that all albinofin varieties share a common genetic basis, with the albinofin phenotype being better than the short fin phenotype.
In order to map potential genetic variation, GWAS was performed to compare long-fin and short-fin individuals. A very significant site was identified at 9.60 Mb of chromosome 14. There are three lead variants in the complete link: a synonymous mutation, an internal rotation located in smg8, and a 3'untranslated region (3'UTR) located in kcnj15.
All three variants perfectly distinguish between long and short fins in domesticated individuals. Smg8 protein acts as a regulator of kinase activity, is involved in meaningless mediated mRNA decay, and is unlikely to be a candidate for the albino phenotype. In contrast, kcnj15 encodes the potassium channel, which is a better candidate, because several genes encoding the potassium channel, including kcnk5b, kcnh2a, kcnj13 and kcc4a, have been identified as causing various longfin phenotypes in zebrafish .
In addition, when comparing the expression profiles of two candidate genes in the caudal fin between long-fin and short-fin individuals by RNA sequencing (RNA-seq), it was found that the expression level of smg8 was similar between different fish groups, while kcnj15 expressed high in the long-fin variety, showing significant differences, and its transcripts were almost undetectable in the short-fin variety.
A) morphology diagram of long fins and short fins. B) Genome-wide signal map. C) Caudal fin gene profile. D) Bifidobacterium SNP. E to G) Manhattan diagram, H) GWAS diagram.
Most wild species, including splendid bifidobacter bacillus, bi, bifidobacter , Bifidobacter and Bifidobacter , are considered short fins, and all of these individuals are always fixed at the G allele at the SNP of kcnj15, and transcripts are rarely detected. In the Bifidobacterium smaragdina and Bifidobacterium guitar populations, this variant is still isolated. In heterozygous Bifidobacterium smaragina individuals, predicted transcripts can be detected, but the expression level is low, which may be due to the recent invasion of long-tail varieties in captivity breeding. Given that the lead variant is located on the 3'UTR and there is a strong association between the variant allele and the expression level of kcnj15, it is speculated that this variant may affect the mRNA stability of kcnj15.
Face tail, crown tail and half-month phenotype
There are many additional phenotype variations in the longfin variety, and the face tail, crown tail and half-month varieties are some of the most unique varieties. The facetail was the first longfin breed recorded, and the tailfin ray was later selected to fully spread 180° to produce a half-moon breed. The difference between the crown tail varieties and the half-month varieties is that the webbing tissue is reduced between the fins.
GWAS versus veil tail and half month identified a 300 kb region of 13.48 to 13.79 Mb on chromosome 16, which may be related to the fin diffusion phenotype. In this site, four genes (znf407, zadh2, tshz1 and znf516) encode zinc finger protein and are widely involved in transcription regulation and cellular function. GWAS comparison of half-month and crown tails showed significant signals of 12.21 to 12.27 Mb on chromosome in 2, which may be related to the webbing phenotype.
Inside the site, a cluster of significantly related variants located in the intergenic region between a0zsk3 (neocystoxin subunit α) and cep70 (centrosomal protein 70), which has no function directly related to the phenotype, which may indicate the regulatory effect of potential causal variation. Comparing the coronal tail and face tail varieties, it was found that one locus (8.25 to 8.40 Mb) on chromosome 22 spanned eight genes , including frmd6, which is involved in actin structural tissue and has expression loss associated with epithelial to mesenchymal transition characteristics, making it a strong candidate gene to explain the morphological phenotype differences between coronal tail and face tail varieties.
"Ducumbent" phenotype
The pectoral fin of the boned animal is homologous to the pre-attachment of amphibian , reptiles and mammals. A breed, Dumbo, characterized by its paired pectoral fins overgrowth, with more and slender fin rays. GWAS using Dumbo as case and Non-Dumb as controls identified two strong signals, located on chromosomes 11 and 19, respectively.
Based on gene expression analysis, the causal gene may be kcnh8. However, this gene is located outside the relevant loci on chromosome 11 identified in our study. Furthermore, when comparing the Dumboy and Non-Minius breeds, no differential expression of kcnh8 was detected in the pectoral fin tissue. The main SNPs in the
study are located in a region containing eight gene clusters from the hoxah gene family, which is essential for the formation of fin bones and fingers in hard bones. For signals on chromosome 19, one of the SNPs is located on the 3′UTR of fbxl15, a gene involved in dorsal/ventral pattern formation and bone bass maintenance, making it a powerful candidate gene.
Giant phenotype
body type shows polygenic inheritance in many organisms, including humans. In Siamese fighting fish, giant mutants show significant body enlargement, such as total length, standard length, weight increase. Control GWAS used body length measurements to compare sizes with normal-sized varieties and GWAS, and a common important site was found at the 2.03 to 2.26 Mb position of chromosome 8, which explained 8.1% to 9.0% of phenotype variance .
carefully examined genes in the locus and the researchers found no genes encoding global body development regulators, which was expected, as the huge changes were observed to cause enlargement of many organs. Despite this, researchers highlighted mrps34 and spsb3, which are related to human height in the GWAS directory.
A to D) Body measurements of five groups of Siamese fighting fish. E) Giant and control GWAS. F) Siamese fighting fish standard body length GWAS
aggressive
aggressive behavior is a complex phenotype involving genetics , endocrine, neurophysiology and metabolism. In one-on-one battles, the male winner of Siamese fighting fish has been selected by the breeder to improve combat performance, resulting in more aggressive, longer combat durations and more active combat breeds.
used the combat type as a control and identified 36 association peaks distributed on 21 chromosomes. S36 to S39, indicating the multigene basis for behavioral differences between combat-type and other breeds. The strongest correlation signal was found on chromosome 4, and the SNP was located near the two esyt2 copies of . It has been shown to promote neural transmission of Dructofly and synaptic growth, promising to become a candidate gene for the invading phenotype.
researchers also emphasized six other nervous system -related genes marked by association peaks, including apbb2 encoding β-amyloid A4 precursor protein binds family B member 2 proteins, and is associated with neurodegeneration and Alzheimer's disease ; pank23 Encoding pantothenate kinase and is associated with neurodegeneration and Parkinson's syndrome ; crhr2 encoding corticotropin-releasing hormone receptor 2, mediating anxiety in mice; ece2 encoding endothelin converting enzyme-2, regulating human neurogenesis and neuronal migration ; gpr139 Encoding orphan G protein-coupled receptors, which are the core participants in opioid regulation of brain circuits, ; and grm33 is associated with bipolar disorder and schizophrenia . Further research into these associations may provide mechanics insights into the neural basis behind aggressive behavior.
A) Fighting type and control group GWAS. B) Quantitative aggressive approach. C to J) Phenotype diagram of combat versus non-control group. K, L) GWAS analysis diagram.
To study the behaviors related to combat, 10 different behaviors displayed during simulation combat were analyzed, including proximity, air breathing, gill flares, fin flares, twitching, mouth opening, pacing and regression, and correlation mapping was performed to identify the genetic structure of each behavior. GWAS used for behavior during combat identified a closely related SNP. It is located near two copies of gfra2 and plays a key role in controlling neuronal survival and differentiation.
It is worth noting that the correlation signal indicates the shared genetic basis of these two related behaviors during combat in GWAS. Aggression is quantified by synthesizing all 10 behaviors in the attack index, according to which warrior type shows a strong 143% aggressiveness. GWAS identified a group of related variants on chromosome 8 on the invasion index, located on or near the atp5g2 gene, which is a subunit of mitochondrial adenosine triphosphate synthase. Another signal on chromosome 9 marks the unc-13 homologous B gene , which is related to the risk of human schizophrenia and partial epilepsy.
Summary
Nanchang University Professor Hong Yijiang's team shows that beta fish is an excellent model for understanding the genetic basis of many different characteristics in vertebrates, including coloring and patterning, skeletal development of fins/limbs, and behavioral characteristics such as aggression. As a prone animal, beta fish has great potential as an biomedical research model and can be used as a supplement to existing vertebrate models such as zebrafish and mice.
To ensure that you can receive every article, please add attention!
Welcome to recommend me to your family and friends~
If you like this article, please like, forward and post your comment~~
