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Background and Aim: Catfish has a high economic value and is popular among consumers. To ensure well-stocked catfish stocks, good fisheries management must also be ensured. The high demand for catfish must be supplemented by preventive measures against pathogenic bacterial infections using probiotics with high potential for Lactobacillus casei and Bacillus subtilis. The aim of this study was to determine the effect of probiotic supplementation consisting of a combination of L. casei and B. subtilis probiotics on the growth, immune system, water quality, proximate value of feed, and body composition of catfish infected with Aeromonas hydrophila. Materials and Methods: This study used a completely randomized study with eight treatments and three replications. The manipulated factor was the probiotic concentration [0% (A), 0.5% (B), 10% (C), and 15% (D)] in groups of catfish infected and uninfected with A. hydrophila. Combination of B. subtilis, and L. casei that were used in a 1:1 ratio of 108 colony forming unit/mL. The study lasted for 42 days. On the 35th day, A. hydrophila was infected by intramuscular injection into fish. The Statistical Package for the Social Sciences (SPSS) software version 23.0 (IBM SPSS Statistics) was used to analyze data on growth, immune system, and water quality. Results: Providing probiotics in feed can increase the nutritional value of feed based on proximate test results. There were significant differences in average daily gain (ADG), feed conversion ratio (FCR), and survival rate (SR) parameters in the group of catfish infected with A. hydrophila (p > 0.05); however, there were no significant differences in final body weight, specific growth rate (SGR), and percentage weight gain. Interleukin-1ß (IL-1ß) levels were significantly different between treatments C and D. The tumor necrosis factor (TNF) α parameters were significantly different between treatments A and C, whereas the phagocytic activity of treatment A was significantly different from that of treatment D. There was a significant difference (p > 0.05) in the growth parameters of SGR, ADG, and FCR in the group of fish that were not infected with A. hydrophila, with the best treatment being a probiotic concentration of 15%, but there was no significant difference in the SR parameters. IL-1ß and TNF-α levels significantly differed between E and E0 (15% probiotics) but were not significantly different in terms of phagocytosis parameters. Conclusion: Based on the results of this study, it can be concluded that using a combination of probiotics L. casei and B. subtilis can improve the growth, immune system, water quality, proximate value of feed, and body composition of catfish infected with A. hydrophila.
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The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost's, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.
Assuntos
Bass , Genoma Mitocondrial , Animais , Filogenia , Bass/genética , Teorema de Bayes , Composição de Bases , RNA de Transferência/genética , RNA Ribossômico/genética , Serina/genéticaRESUMO
As one of efforts to conserve a genetic resource of the endemic cobitid species in the Korean peninsula, the complete mitogenome of Cobitis hankugensis (Kim, Park, Son & Nalbant, 2003) was determined using Illumina MiSeq system. The circular mitogenome was 16,557 bp length and encoded 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 tRNA genes, and a control region. Only the COX1 gene was identified with an aberrant initiation codon GTG, and an incomplete termination codon (T-/TA-) was identified in six PCGs including COX2, COX3, ND2, ND3, ND4, and Cytb genes. Phylogenetic analysis using 30 mitochondrial genomes belonging to Cobitidae, Botiidae, and Gyrinocheilidae showed that the highest identity (92.38%) with Kichulchoia brevifasciata (NC_027166). The complete mitogenome of C. hankugensis, an endemic species in Korea, will provide fundamental data on the evolutionary relationship of Cobitidae species.
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The complete mitochondrial DNA information of Pseudotolithus typus Bleeker, 1863, collected from Sierra Leone was determined using next-generation sequencing (NGS) and bioinfromatic analysis. Its mitogenome (16,504 bp) encoded the typical 13 protein-coding genes (PCGs), 2 ribosomal RNAs (12S & 16S), and 22 tRNAs. All 13 PCGs showed a standard start codon (ATG) but an unusual stop codon (AGA) was identified in COX1 gene. Except for ND6, all 12 PCGs were encoded on the light strand. Except for tRNASer-GCT, 21 tRNAs formed the typical clover-leaf structures. Phylogenetic analysis showed three mitochondrial genomes in the genus Pseudotolithus formed a clade distinct from the other species in the same family. The mitogenome of P. typus identified in this study exhibited 96.27% and 88.86% identity to T. typus in the Guinean water and P. elongatus, respectively. Additional mitogenome sequences of Pseudotolithus species will provide useful information for their scientific management in western African countries.
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Caranx crysos was collected from offshore of Sierra Leone and its complete mitochondrial genome was determined using next-generation sequencing (NGS). The circular mitogenome encoded a typical 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (12S rRNA and 16S rRNA), and 22 tRNA genes. An unusual start codon (GTG) was identified for the COX1 gene, and incomplete stop codons (T-/TA-) were found in seven genes, including ND2, ND3, ND4, COX2, COX3, ATP6, and CytB. All tRNAs were predicted to fold into the typical clover-leaf structures, except for tRNASer-GCT, which lacks the D-arm. C. crysos formed a monoclade with the tree other species belonging to the genus Caranx, apart from the others. Among them, C. crysos was most closely related to Caranx melampygus and Caranx tille. The mitogenome sequence of C. crysos provides information for a better understanding of evolutionary relationships, systemic, and mitogenomic study within the family Carangidae.
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The first mitochondrial genome of Ophiocara porocephala was determined by the combination of next-generation sequencing (NGS) and Sanger sequencing methods. A complete circular mitogenome of O. porocephala (16,529 bp) consisted of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two non-coding regions, including a control region (D-loop) and a light strand origin of replication (OL). Two start codons (ATG and GTG) and four stop codons (TAG, TAA, TA-, and T-) were used in all the PCGs. Except for ND6 and eight transfer RNAs (tRNAs), all the other genes were encoded in the heavy strand. Based on phylogenetic analysis, O. porocephala formed a clade with three other species in the subfamily Butinae, while the other 10 made a subfamily Eleotrinae clade.
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Environmental DNA (eDNA) metabarcoding is a cost-effective novel approach to estimate biodiversity in an ecosystem. In this study, the MiFish pipeline was employed to test if the system methodology is sufficiently reliable to estimate fish biodiversity in Korean rivers. A total of 125 unique haplotypes and 73 species were identified at the species level from 16 water samples collected from a single survey in four Korean rivers (Hyeongsan, Taehwa, Seomjin, and Nakdong). Among the four rivers, the highest species richness was recorded in the Seomjin River (52 species), followed by the Taehwa (42 species) and Hyeongsan (40 species) rivers. The Nakdong River (26 species) presented the lowest species richness and number of endemic species, presumably due to its metropolitan location and anthropogenic impacts, such as dams or weirs. We were also able to detect that five exotic species (Carassius cuvieri, Cyprinus carpio, Cyprinus megalophthalmus, Lepomis macrochirus, and Micropterus salmoides) are widely distributed in all surveyed rivers, a situation that might be problematic in terms of conservation. Our findings indicate that the eDNA metabarcoding technique is one of the most cost-effective scientific tools available for the management and conservation of the freshwater fish resources available in Korea. However, the low number of 12S sequences of endemic species in the database and low resolution of the MiFish region for differentiating several taxa should be upgraded for their wide use.
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The complete mitochondrial genome of green shrimp, Chlorotocus crassicornis (Costa, 1871) was generated by the combination of next-generation sequencing platform and long PCR technique. The mitochondrial genome of C. crassicornis was 16,500 bp, in which 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a putative control region was encoded. Based on the 13 protein-coding genes region, the phylogenetic tree was clearly demonstrated that C. crassicornis is closest to Pandalopsis japonica and Pandalus borealis with 77% identity. This mitogenome information will be helpful for the further studies of deep-sea fisheries resources management strategies in Korea including C. crassicornis species.
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The first complete mitochondrial genome sequence of Ailia coila from Bangladesh was determined by the bioinformatic assembly of the next generation sequencing (NGS) reads. The constructed circular mitogenome for A. coila was 16,565 bp in length which harbored the canonical 13 protein-coding genes, 22 tRNAs, 2 rRNAs. Two non-coding regions, control region, D-loop (927 bp), and origin of light strand replication, OL (30 bp) were also well conserved in the mitogenome. Among the currently reported mitochondrial genomes in the order Siluriformes, A. coila was most closely related to Eutropiichthys vacha (AB919123) with 85.63% sequence identity.
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The complete mitochondrial genome of Silurus soldatovi firstly collected from a native Korean river was determined by the bioinformatics assembly of the next-generation sequencing (NGS) reads. The circular mitogenome was 16,525 bp in length which harbored canonical 13 protein-coding genes, 22 tRNAs, and 2 rRNAs, which was identical to those of family Siluridae. Twenty-eight genes were located on H strand, whereas the remaining nine genes were on L strand. Except for COX1 gene (GTG), other 12 protein-coding genes were predicted typical start codons (ATG). Among the currently known mitogenome sequences, S. soldatovi showed highest identity (99.38%) to the Chinese haplotype of S. soldatovi (NC022723) followed by the Chinese haplotype of Silurus asotus (JX087351). Interestingly, intraspecies variations of S. asotus are higher than those of interspecies and further study should be made to elucidate the evolutional relationship between two Silurus species.
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The complete mitochondrial genome of Odontobutis platycephala collected from a native Korean river was determined by the bioinformatics assembly of the next-generation sequencing (NGS) reads. The circular mitogenome was 17,590 bp length which harbored canonical 13 protein-coding genes, 22 tRNAs, and 2 rRNAs, which was identical to those of family Odontobutidae. Twenty-eight genes were located on H strand, whereas remaining nine genes were on L strand. Except for COX1 gene (GTG), other 12 protein-coding genes were predicted typical start codons (ATG). Among the currently known mitogenome sequences, O. platycephala showed highest identity (96.98%) to Korean haplotype of O. platycephala (NC010199).
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The complete mitochondrial genome sequence of the Icefish, Chionobathyscus dewitti was determined by the Next Generation Sequencing (NGS) analysis. The complete mitogenome was 17,452 bp in length, which encoded the canonical 13 protein-coding genes, 22 tRNAs, two rRNAs, and two non-coding regions. As shown in the other notothenids, translocation of ND6 and an additional non-coding region were identified, which is different from the typical vertebrate mitochondrial genomes. The C. dewitti was clustered distinctly from the those in the Chinodraco and Chaenocephalus, which supported the idea that this species should be classified in the different genus, Chionobathyscus in the family Channichthyidae.
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The two-spot swimming crab Charybdis bimaculata (Miers, 1886) is an important decapod species in the benthic ecosystem of Korean waters. In this study, we determined its complete mitochondrial genome by the combination of NGS analysis using MiSeq platform and PCR-based cloning method. The circular mitochondrial genome of C. bimaculata was 15,714 bp in length in which the standard set of 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes were encoded. Phylogenic analysis showed that C.bimaculata is most closely related to Charybdis feriata. The complete mitogenome sequence information of C. bimaculata would provide useful data for the conservation of their population in the Pacific ocean.
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The complete mitochondrial genome of Argentine red shrimp, Pleoticus muelleri (Bate, 1888) was determined using the MiSeq platform. Its mitogenome (16,189 bp) encoded the canonical 13 protein-coding genes, 22 tRNA genes, two rRNA genes. Start codons of all protein-coding genes were ATN except for ATP8, while incomplete stop codons (T-) were identified in six genes including COXI, COXII, COXIII, NAD3, NAD5, and NAD6. The mitogenome of P. muelleri showed highest sequence identity with Parapenaeopsis hardwickii (82%) and Solenocera crassicornis (81%). Phylogenetic analysis showed three shrimps in Solenoceridae including P. muelleri were grouped together from those in Penaeidae, which suggests taxonomic reexamination for those in those family.
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The complete mitochondrial genome of the brownstripe red snapper, Lutjanus vitta was determined by MiSeq sequencing platform. The mitogenome of L. vitta (16,498 bp) encoded the typical 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions (origin of light strand replication; OL and D-Loop control region; CR). Phylogenetic analysis based on the full mitochondrial genome sequences showed that L. vitta is most closely related to L. russellii. The complete mitogenome sequence of L. vitta would provide the information of the genetic biodiversity in Lutjanus fishes, which would be further used for their scientific management in Indonesian waters.
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The complete mitogenome of the Senegalese tonguesole, Cynoglossus senegalensis was determined by Illumina MiSeq platform. The complete mitochondrial genome of C. senegalensis was 16,519 bp in length. The mitochondrial genome of C. senegalensis showed a cynoglosidae-characteristic gene organization, in which translocation of control region to the position between ND1 and tRNA-Gln gene, and also inversions in tRNA-Gln gene from L-strand position to H-strand position. Phylogenetic analysis showed that C. senegalensis is most closely related to C. sinicus and S.bilineatus, which supports the previous result that genus Cynoglossidae is evolutionary paraphyletic.
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We here report the complete mitochondrial genome of Chrysichthys nigrodigitatus, which is 16,514 bp in length. Mitogenome of C. nigrodigitatus showed the conserved 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions including the light-strand replication origin (OL) and a putative control region (CR). All tRNA genes were predicted to fold into the typical cloverleaf secondary structures with the typical base-pairing except for tRNA-Ser(AGC). Phylogenetic analysis with currently known complete mitogenome sequences in Siluriformes showed that C. nigrodigitatus is most closely related to Auchenoglanis occidentalis forming a family Claroteidae cluster.
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Penaeid shrimps are widely distributed from Indian to western Pacific Oceans and some which are economically important. In this study, we reported full mitochondrial genome of an endemic shrimp species, Penaeus acehensis, which inhabits exclusively in the coastal water of Aceh, Indonesia. Full length of circular mitogenome of P. acehensis was 15,991 bp in length, which contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. Start codons of all protein-coding genes were ATN except for COX1 in which ACG was used. Incomplete stop codon (T- -) was found in five genes including COX2, COX3, NAD5, NAD4, and NAD4L. Among its relatives, P. acehensis was most closely related to Penaeus monodon showing 89% sequence identity in its mitogenome, which was corresponding to morphological analysis. Phylogenetic tree result showed that P. acehensis was clustered together with those were distributed in Indo-West Pacific region (clade II), which is distinct from Eastern Pacific region (clade I).
