Unveiling the underwater threat: Exploring cadmium's adverse effects on tilapia.

Prolonged exposure to environmentally relevant amounts of cadmium (Cd) in aquatic environments, even at small doses (0.1 and 1 µg/L), might endanger the health of underwater creatures. This research delved into the impacts of a four-month cadmium exposure on Mozambique tilapia (Oreochromis mossambicus), aiming to uncover the mechanisms behind it. Through close examination, we found that the 4-momth cadmium exposure led to harmful effects on the fish's gills, muscles, brain, and intestines. This exposure also triggered changes in gene expressions in the brain and liver, affected the respiratory system and weakened liver's ability to detoxify and defend against potential infections. Looking deeper into the fish's gut, we noticed alterations in energy-related genes and disruptions in immune pathways, making it more susceptible to illnesses. The exposure to cadmium also had an impact on the fish's gut and water-dwelling microorganisms, reducing diversity and encouraging harmful microbial communities. Interestingly, some gut microbes seemed to assist in breaking down and detoxifying cadmium, which could potentially protect the fish. Taken together, prolonged low-level cadmium exposure impaired gill, muscle, and brain function, suppressed immunity, disrupted intestines, and altered microbial balance, leading to hindered growth. These insights illuminate cadmium's impact on fish, addressing vital environmental concerns.

Silencing Asian Seabass gab3 Inhibits Nervous Necrosis Virus Replication.

The nervous necrosis virus (NNV) causes the viral nervous necrosis (VNN) disease in aquatic animals and has been a major threat in aquaculture. Thus, it is essential for the development of a prevention method to minimize economic losses caused by NNV such as the identification of NNV resistance genes and application of these genes in molecular breeding to increase disease resistance. gab3 is an important NNV resistance gene in Asian seabass. However, the mechanism of gab3 in NNV resistance has not been elucidated. In this study, knockdown of gab3 in NNV-infected Asian seabass cells resulted in a significant decrease in viral RNA and virus titers. Knockout of gab3 in zebrafish led to an increased survival rate and resistant time after NNV infection. Cellular localization of the GAB3 and NNV by immunofluorescence staining showed that the GAB3 was translocated from the nucleus to the cytoplasm, and finally reached the cell membrane of SB cells after 48 h post NNV infection. Our study suggests that gab3 plays an important role in NNV replication and silencing gab3 can inhibit virus replication.

EgSPEECHLESS Responses to Salt Stress by Regulating Stomatal Development in Oil Palm.

Oil palm is the most productive oil producing plant. Salt stress leads to growth damage and a decrease in yield of oil palm. However, the physiological responses of oil palm to salt stress and their underlying mechanisms are not clear. RNA-Seq was conducted on control and leaf samples from young palms challenged under three levels of salts (100, 250, and 500 mM NaCl) for 14 days. All three levels of salt stress activated EgSPCH expression and increased stomatal density of oil palm. Around 41% of differential expressed genes (DEGs) were putative EgSPCH binding target and were involved in multiple bioprocesses related to salt response. Overexpression of EgSPCH in Arabidopsis increased the stomatal production and lowered the salt tolerance. These data indicate that, in oil palm, salt activates EgSPCH to generate more stomata in response to salt stress, which differs from herbaceous plants. Our results might mirror the difference of salt-induced stomatal development between ligneous and herbaceous crops.

A chromosome-level genome assembly of chia provides insights into high omega-3 content and coat color variation of its seeds.

Chia (Salvia hispanica) is a functional food crop for humans. Although its seeds contain high omega-3 fatty acids, the seed yield of chia is still low. Genomic resources available for this plant are limited. We report the first high-quality chromosome-level genome sequence of chia. The assembled genome size was 347.6 Mb and covered 98.1% of the estimated genome size. A total of 31 069 protein-coding genes were predicted. The absence of recent whole-genome duplication and the relatively low intensity of transposable element expansion in chia compared to its sister species contribute to its small genome size. Transcriptome sequencing and gene duplication analysis reveal that the expansion of the fab2 gene family is likely to be related to the high content of omega-3 in seeds. The white seed coat color is determined by a single locus on chromosome 4. This study provides novel insights into the evolution of Salvia species and high omega-3 content, as well as valuable genomic resources for genetic improvement of important commercial traits of chia and its related species.

Transposon-induced epigenetic silencing in the X chromosome as a novel form of dmrt1 expression regulation during sex determination in the fighting fish.

BACKGROUND: Fishes are the one of the most diverse groups of animals with respect to their modes of sex determination, providing unique models for uncovering the evolutionary and molecular mechanisms underlying sex determination and reversal. Here, we have investigated how sex is determined in a species of both commercial and ecological importance, the Siamese fighting fish Betta splendens. RESULTS: We conducted association mapping on four commercial and two wild populations of B. splendens. In three of the four commercial populations, the master sex determining (MSD) locus was found to be located in a region of ~ 80 kb on LG2 which harbours five protein coding genes, including dmrt1, a gene involved in male sex determination in different animal taxa. In these fish, dmrt1 shows a male-biased gonadal expression from undifferentiated stages to adult organs and the knockout of this gene resulted in ovarian development in XY genotypes. Genome sequencing of XX and YY genotypes identified a transposon, drbx1, inserted into the fourth intron of the X-linked dmrt1 allele. Methylation assays revealed that epigenetic changes induced by drbx1 spread out to the promoter region of dmrt1. In addition, drbx1 being inserted between two closely linked cis-regulatory elements reduced their enhancer activities. Thus, epigenetic changes, induced by drbx1, contribute to the reduced expression of the X-linked dmrt1 allele, leading to female development. This represents a previously undescribed solution in animals relying on dmrt1 function for sex determination. Differentiation between the X and Y chromosomes is limited to a small region of ~ 200 kb surrounding the MSD gene. Recombination suppression spread slightly out of the SD locus. However, this mechanism was not found in the fourth commercial stock we studied, or in the two wild populations analysed, suggesting that it originated recently during domestication. CONCLUSIONS: Taken together, our data provide novel insights into the role of epigenetic regulation of dmrt1 in sex determination and turnover of SD systems and suggest that fighting fish are a suitable model to study the initial stages of sex chromosome evolution.

Effects of rrm1 on NNV Resistance Revealed by RNA-seq and Gene Editing.

Viral nervous necrosis (VNN) disease caused by the nervous necrosis virus (NNV) is a major disease, leading to a huge economic loss in aquaculture. Previous GWAS and QTL mapping have identified a major QTL for NNV resistance in linkage group 20 in Asian seabass. However, no causative gene for NNV resistance has been identified. In this study, RNA-seq from brains of Asian seabass fingerlings challenged with NNV at four time points (5, 10, 15 and 20 days post-challenge) identified 1228, 245, 189 and 134 DEGs, respectively. Eight DEGs, including rrm1, were located in the major QTL for NNV resistance. An association study in 445 survived and 608 dead fingerlings after NNV challenge revealed that the SNP in rrm1 were significantly associated with NNV resistance. Therefore, rrm1 was selected for functional analysis, as a candidate gene for NNV resistance. The expression of rrm1 was significantly increased in the gill, liver, spleen and muscle, and was suppressed in the brain, gut and skin after NNV challenge. The rrm1 protein was localized in the nuclear membrane. Over-expression of rrm1 significantly decreased viral RNA and titer in NNV-infected Asian seabass cells, whereas knock-down of rrm1 significantly increased viral RNA and titer in NNV-infected Asian seabass cells. The rrm1 knockout heterozygous zebrafish was more susceptible to NNV infection. Our study suggests that rrm1 is one of the causative genes for NNV resistance and the SNP in the gene may be applied for accelerating genetic improvement for NNV resistance.

Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish.

Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long-fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole-genome sequencing, quantitative trait loci mapping, genome-wide association studies, and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino, and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double-tail mutant was suggested to be caused by a deletion in a zic1/zic4 coenhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.

Characterization of GAB3 and its association with NNV resistance in the Asian seabass.

Understanding the functions of genes related to disease resistance and identifying polymorphisms in these genes are essential in molecular breeding for disease resistance. Viral nervous necrosis (VNN) is one of the major diseases in the Asian seabass, Lates calcarifer. Our previous works on QTL mapping, GWAS and cell-line transcriptome analysis of the Asian seabass after NNV challenge revealed that the gene GAB3 might be a candidate gene for VNN resistance. In this study, we cloned and characterized GAB3, and identified SNPs in the gene of the Asian seabass. The cDNA of the gene was 2165 bp, containing an ORF of 1674 bp encoding 557 amino acids. The gene consisted of 10 exons and nine introns. It was ubiquitously expressed in normal fish. An analysis of the association between two SNPs in the second intron and NNV resistance in 1035 fish descended from 43 families revealed that the two SNPs were significantly associated with VNN resistance. After NNV infection, the expression of GAB3 was significantly increased in the brain, spleen, muscle and gut, and was suppressed in the liver. The GAB3 protein was localized in the nucleus. Overexpression of GAB3 with specific GAB3-pcDNA was positively correlated to increased viral RNA and titer in NNV-infected Asian seabass cells. Our study provides new evidence to support that GAB3 may be an important gene related to NNV resistance. In addition, the SNPs provide DNA markers for the selection of candidate genes resistance to NNV at the juvenile stage of Asian seabass.

The HIF1αn gene and its association with hypoxia tolerance in the Asian seabass.

Hypoxia is one of the major challenges in aquaculture industry. Breeding of fish tolerant to hypoxia is an important task in genetic improvement of aquaculture species. The Asian seabass, Lates calcarifer, is an important foodfish species. We identified and characterized the hypoxia-inducible factor inhibitor (HIF1αn) gene in the Asian seabass. The full-length cDNA sequence of the HIF1αn was 3425 bp, with an ORF of 1065 bp, encoding 354 amino acids. The genomic sequence of the gene was 8667 bp in length, and contained eight exons and seven introns. Phylogenetic analysis of the gene in fish and tetrapods revealed that the HIF1αn in the Asian seabass was closely related to that of tilapia (Oreochromis niloticus). The HIF1αn was highly up-regulated in the gill, spleen and heart after 3.5-hours hypoxia treatment. We identified three SNPs in the third and fourth introns of the HIF1αn gene. The SNP (i.e. SNP 9332241 (C/T)) in the fourth intron was significantly (P < 0.01) associated with hypoxia tolerance. This SNP might be useful in selecting Asian seabass for improved tolerance to hypoxia. Our data also provide useful information for further detailed analysis of the function of the HIF1αn gene in hypoxia tolerance.

The mitochondrial genome of Sinibotia robusta of pearl river (Cypriniformes: Cobitidae).

We present the complete mitochondrial genome of Sinibotia robusta in this study. The mitochondrial genome is 16 575 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the light strand are 31.9% A, 25.7% T, 26.9% C and 15.5% G. Except ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The genus most related to Botia Gray was Leptobotia Bleeker and Parabotia Sauvage, as revealed by phylogenetic relationships derived using a maximum likelihood tree. This mitogenome will help elucidate the morphological systematic complexity and phylogenetic structure of Cobitidae and related species.

The complete mitochondrial genome of Mastacembelus aculeatus (Cypriniformes, Mastacembelidae) from the Pearl River, China.

In this paper, the complete mitochondrial DNA (mtDNA) sequence of Mastacembelus aculeatus was determined. The mitochondrial genome is 16 543 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region as those found in other vertebrates, with the gene identical to that of typical vertebrates. The overall base composition of the heavy strand is 30.0% A, 26.4% T, 14.8% C, and 28.7% G, with an AT bias of 56.49%. Phylogeny of M. aculeatus suggested more close relationship with Mastacembelus armatus and Mastacembelus favus. The complete mitogenome may add new information to existing mitogenome data for Mastacembelidae, providing further information that may contribute to their taxonomy, evolution, and phylogeny.

The complete mitochondrial genome of Nibea coibor (Perciformes, Sciaenidae).

We present the complete mitochondrial genome of Nibea coibor in this study. The mitochondrial genome is 16,502 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. All of them are encoded on the heavy strand except ND6 and 8 tRNA genes on the light strand. The nucleotide compositions of the light strand were 31.62% of G, 26.88% of T, 25.19% of A and 16.31% of C. Three types of initiation codons are ATA (ATP6), ATG (ND2, COXI, COXII, ATP8, COXIII, ND3, ND4L, ND4, ND5, ND6, Cytb) and GTG (ND1), and 3 types of termination codons are AGA (COXI), T (ND2, COXII, ND3, ND4) and TAA (ATP6, ATP8, COXIII, ND4L, ND5, ND6, Cytb, ND1). There are 13 intergenic spacers, 7 gene overlaps and no tandem repeat sequence. Gene arrangement and distribution are consistent with the typical vertebrates.

The complete mitochondrial genome of the amoy croaker Argyrosomus amoyensis (Perciformes, Sciaenidae).

We present the complete mitochondrial genome of Argyrosomus amoyensis in this study. The mitochondrial genome is 16,490 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. All of them are encoded on the heavy strand except ND6 and 8 tRNA genes on the light strand. The nucleotide compositions of the light strand are 31.02% of G, 26.96% of T, 25.31% of A and 16.71% of C. All the protein-coding genes begin with ATG initiation codon, and 5 types of inferred termination codons are AGA (COXI), T (COXII, ND3, ND4, Cytb), TA (ND2, COXIII), TAA (ATP8, ATP6, ND4L, ND5, ND6) and TAG (ND1). There are 11 intergenic spacers, 7 gene overlaps and no tandem repeat sequence. Gene arrangement and distribution are consistent with the typical vertebrates.

The complete mitochondrial genome of the blackspotted croaker Protonibea diacanthus (Perciformes, Sciaenidae).

We present the complete mitochondrial genome of Protonibea diacanthus in this study. The mitochondrial genome is 16,535 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. All of them are encoded on the heavy strand except ND6 and 8 tRNA genes on the light strand. The nucleotide compositions of the light strand are 31.09% of G, 27.54% of T, 25.34% of A and 16.03% of C. All the protein-coding genes start with ATG initiation codon except ATP6 with GTG, and 5 types of inferred termination codons are AGA (COXI and COXII), T (ND3, ND4, Cytb), TA (ND2, COXIII and ATP6), TAA (ND1, ATP8 and ND4L) and TAG (DN5 and ND6). There are 14 intergenic spacers and 7 gene overlaps. The tandem repeat sequence is observed in 12S-rRNA, 16S-rRNA, tRNA(Trp), tRNA(Ala), COXIII, ND4L and ND4 genes. Gene arrangement and distribution are consistent with the typical vertebrates.

The complete mitochondrial genome of the Culter recurviceps (Teleostei, Cyprinidae).

We present the complete mitochondrial genome of the Culter recurviceps in this study. The mitochondrial genome is 16,622 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The gene order and composition of C. recurviceps mitochondrial genome was similar to that of most other vertebrates. The nucleotide compositions of the light strand are 31.36% of A, 24.77% of T, 27.77% of C and 16.09% of G. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Two copies of tandem repeat sequence (24 bp) was observed in the end of the 123 bp in control region.

The complete mitochondrial genome of the Hemibagrus guttatus (Teleostei, Bagridae).

The complete mitochondrial genome of the Hemibagrus guttatus was presented in this study. The mitochondrial genome is 16,523 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The gene order and composition of H. guttatus mitochondrial genome was similar to that of most other vertebrates. The nucleotide compositions of the light strand are 31.73% of A, 25.42% of C, 28.02% of T and 14.83% of G. With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand.

The complete mitochondrial genome of the Hemibagrus wyckioides (Siluriformes, Bagridae).

We present the complete mitochondrial genome of the Hemibagrus wyckioides in this study. The mitochondrial genome is 16,525 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. Its mitochondrial gene order and composition are similar to that of most other vertebrates. The nucleotide compositions of the light strand are 31.47% of A, 26.72 % of C, 26.62% of T, and 15.19% of G. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand.

The complete mitochondrial genome of the Clarias fuscus (Siluriformes, Clariidae).

We present the complete mitochondrial genome of the Clarias fuscus in this study. The mitochondrial genome is 16,525 bp in length and consists of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the light strand are 31.17% of A, 27.54% of C, 25.34% of T, and 14.95% of G. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. All the protein-coding genes begin with an ATG initiation codon except for COXІ with GTG. Five types of termination codons revealed are TAA (COXІ, ATP8, ND4L), T (ND2, ND3, ND4, COXП, Cytb), AGG (COXШ), TA (ATP6), and TAG (ND1, ND5, ND6). Most genes are either abutted or overlapped and many features keep consistent with the other vertebrates.