The complete mitochondrial genome of a threatened loach (Sinibotia reevesae) and its phylogeny

Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae)

The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) for the first time. We compared the mitogenomes with the mitogenomes of 11 other Channidae fish. The newly sequenced mitogenomes were 16,714 - 16,895 bp in length and contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. Positive AT-skews and negative GC-skews were found in the mitogenomes of Channidae. Most PCGs started with the conventional start codon, ATN; however, the sequence of the stop codon was variable. There was no essential difference in relative synonymous codon usage (RSCU) among the Channidae mitogenomes. The fastest-evolving gene atp8 and slowest-evolving gene cox1 were identified using Ka/Ks and pairwise relative genetic distance (p-distance). The displacement loop (D-loop) regions showed great variability, which affected the size of Channa mitogenomes. One origin of replication on the light strand (O_L) region was found between trnN and trnC in the mitogenomes of Channidae. Phylogenetic analysis revealed three new sister pairs (C. andrao + C. bleheri, C. ornatipinnis + C. pulchra, and C. stewartii + C. gachua). Phylogenetic relationships established between the five Channa species based on mitogenomes were also supported by their morphological characteristics and geographical distribution. The novel information we obtained about these mitogenomes will contribute to elucidating the complex relationships among Channa species.

Reanalysis and Revision of the Complete Mitochondrial Genome of Artemia urmiana Günther, 1899 (Crustacea: Anostraca)

In the previously published mitochondrial genome sequence of Artemia urmiana (NC_021382 [JQ975176]), the taxonomic status of the examined Artemia had not been determined, due to parthenogenetic populations coexisting with A. urmiana in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of Artemia (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. With regard to coexisting populations in Urmia Lake, and intra- and inter-specific variations in the pooled samples, NC_021382 [JQ975176] cannot be recommended as a valid sequence and any attempt to attribute it to A. urmiana or a parthenogenetic population is unreasonable. With the aid of next-generation sequencing methods, we characterized and assembled a complete mitochondrial genome of A. urmiana with defined taxonomic status. Our results reveal that in the previously published mitogenome (NC_021382 [JQ975176]), tRNA-Phe has been erroneously attributed to the heavy strand but it is encoded in the light strand. There was a major problem in the position of the ND5. It was extended over the tRNA-Phe, which is biologically incorrect. We have also identified a partial nucleotide sequence of 311 bp that was probably erroneously duplicated in the assembly of the control region of NC_021382 [JQ975176], which enlarges the control region length by 16%. This partial sequence could not be recognized in our assembled mitogenome as well as in 48 further examined specimens of A. urmiana. Although, only COX1 and 16S genes have been widely used for phylogenetic studies in Artemia, our findings reveal substantial differences in the nucleotide composition of some other genes (including ATP8, ATP6, ND3, ND6, ND1 and COX3) among Artemia species. It is suggested that these markers should be included in future phylogenetic studies.

Characterization of the mitochondrial genome of Microphysogobio tungtingensis (Cypriniformes) and its taxonomic status

In the present study, the complete mitochondrial genome of Microphysogobio tungtingensis has been amplified with 16 pairs of primers. There are 16 627 base pairs has been identified and deposited in the GenBank with accession numbers MN970213. The arrangement was similar to typical vertebrate mitochondrial, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region. The overall base composition of M. tungtingensis was G + C: 42.9%, A + T: 57.1%, apparently with a slight AT bias. Phylogenetic analysis showed that M. tungtingensis was close to M. fukiensis.

Characterization of two kcnk3 genes in rabbitfish (Siganus canaliculatus): Molecular cloning, distribution patterns and their potential roles in fatty acids metabolism and osmoregulation

KCNK3 is a two-pore-domain (K_2P) potassium channel involved in maintaining ion homeostasis, mediating thermogenesis, controlling breath and modulating electrical membrane potential. Although the functions of this channel have been widely described in mammals, its roles in fishes are still rarely known. Here, we identified two kcnk3 genes from the euryhaline rabbitfish (Siganus canaliculatus), and their roles related to fatty acids metabolism and osmoregulation were investigated. The open reading frames of kcnk3a and kcnk3b were 1203 and 1176 bp in length, encoding 400 and 391 amino acids respectively. Multiple sequences alignment and phylogenetic analysis revealed that the two isotypes of kcnk3 were extensively presented in fishes. Quantitative real-time PCRs indicated that both genes were widely distributed in examined tissues but showed different patterns. kcnk3a primary distributed in adipose, eye, heart, and spleen tissues, while kcnk3b was mainly detectable in heart, kidney, muscle and spleen tissues. In vivo experiments showed that fish fed diets with fish oil as dietary lipid (rich in long chain polyunsaturated fatty acids, LC-PUFA) induced higher mRNA expression levels of kcnk3 genes in comparison with fish fed with plant oil diet at two different salinity environments (32 and 15‰). Meanwhile, the expression levels of kcnk3 genes were higher in seawater (32‰) than that in brackish water (15‰) when fishes were fed with both types of feeds. In vitro experiments with rabbitfish hepatocytes showed that LC-PUFA significantly improved hepatic kcnk3a expression level compared with treatment of linolenic acid. These results suggest that two kcnk3 genes are widely existed and they might be functionally related to fatty acids metabolism and osmoregulation in the rabbitfish.

Characterization and phylogenetic analysis of the complete mitochondrial genome of a tropical sea cucumber, Holothuria fuscocinerea

In this study, the mitochondrial genome (mitogenome) of Holothuria fuscocinerea was unraveled to be 15,890 bp in length, containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The PCGs were initiated by four initiation codons (ATG, TAC, ATC, and ATA). Only one PCG (nad6) and five tRNA genes (tRNA^Ser(UCN), tRNA^Gln, tRNA^Ala, tRNA^Val, and tRNA^Asp) were encoded on the light chain, and the other genes were encoded on the heavy chain. A phylogenetic tree constructed with 16S rRNA sequences showed that H. fuscocinerea is most closely related to H. leucospilota.

Molecular characterization of two leptin genes and their transcriptional changes in response to fasting and refeeding in Northern snakehead (Channa argus)

Leptin has been proved to play critical roles in energy metabolism, body weight regulation, food intake, reproduction and immunity in mammals. However, its roles are still largely unclear in fish. Here, we report two leptin genes (lepA and lepB) from the Northern snakehead (Channa argus) and their transcriptions in response to different feeding status. The snakehead lepA is 781 bp in length and contains a 480 bp open reading frame (ORF) encoding a 159-aa protein, while the snakehead lepB is 553 bp in length and contains a 477 bp ORF encoding a 158-aa protein. Multi-sequences alignment, three-dimensional (3D) model prediction, syntenic and genomic comparison, and phylogenetic analysis confirm two leptin genes are widely existing in teleost. Tissue distribution revealed that the two leptin genes exhibit different patterns. In a post-prandial experiment, the hepatic lepA and brain lepB showed a similar transcription pattern. In a long-term (2-week) fasting and refeeding experiment, the hepatic lepA and brain lepB showed a similar transcription change pattern induced by food deprivation stimulation but differential changes after refeeding. These findings suggest snakehead lepA and lepB are differential both in tissue distribution and molecular functions, and they might play as an important regulator in energy metabolism and food intake in fish, respectively.

Molecular cloning of two kcnk3 genes from the Northern snakehead (Channa argus) for quantification of their transcriptions in response to fasting and refeeding

Potassium channel subfamily K member 3 (KCNK3) has been reported to play important roles in membrane potential conduction, pulmonary hypertension and thermogenesis regulation in mammals. However, its roles remain largely unknown and scarce reports were seen in fish. In the present study, we for the first time identified two kcnk3 genes (kcnk3a and kcnk3b) from the carnivorous Northern snakehead (Channa argus) by molecular cloning and a genomic survey. Subsequently, their transcription changes in response to different feeding status were investigated. Full-length coding sequences of the kcnk3a and kcnk3b genes are 1203 and 1176 bp, encoding 400 and 391 amino acids, respectively. Multiple alignments, 3D-structure prediction and phylogenetic analysis further suggested that these kcnk3 genes may be highly conserved in vertebrates. Tissue distribution analysis by real-time PCR demonstrated that both the snakehead kcnk3s were widely transcribed in majority of the examined tissues but with different distribution patterns. In a short-term (24-h) fasting experiment, we observed that brain kcnk3a and kcnk3b genes showed totally opposite transcription patterns. In a long-term (2-week) fasting and refeeding experiment, we also observed differential change patterns for the brain kcnk3 genes. In summary, our findings suggest that the two kcnk3 genes are close while present different transcription responses to fasting and refeeding. They therefore can be potentially selected as novel target genes for improvement of production and quality of this economically important fish.

Characterization the mitochondrial genome of Acrossocheilus Labiatus (Cypriniformes, Acrossocheilus) and its phylogeny

The first complete mitochondrial genome of Acrossocheilus Labiatus from the Qingshui River were reported in this study with accession number MG878098. The overall nucleotide composition was 31.13% A, 25.10% T, 27.52% C, 16.24% G, respectively. Phylogenetic analysis shows that the A. parallens and A. Hemispinus showed a closest phylogenetic relationship, then clustal with A. Labiatus.

Complete mitochondrial genome of a kind of snakehead fish Channa siamensis and its phylogenetic consideration

The snakehead fish, Channa siamensis, belongs to the genus of Channa (perciformes: Channidae) and was first reported by Günther in 1861. Despite it has been described approximately for 15 decades, the genetic information is limited and the taxon status of this kind of fish is still unclear. The primary objective of this study is to get more genomic data and calculate the taxon location of this kind of fish. The next generation sequencing method was used to obtain the whole mitochondrial DNA information, and bioinformatic analysis was performed to investigate the evolutionary status and taxon location of C. siamensis. The circular mitochondrial DNA was 16,570 bp in length, and which showed typical piscine structure and arrangement. The overall nucleotide composition was 29.28% A, 24.72% T, 30.71% C, 15.29% G, with 54.1% AT, respectively. Phylogenetic analyses using concatenated amino acid and nucleotide sequences of the 13 protein-coding genes with two different methods (Maximum likelihood and Bayesian analysis) both highly supported C. siamensis belongs to the genus Channa and shows a close relationship with C. micropeltes. These data will provide more useful information for a better understanding of the mitochondrial genomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.

Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, Sinocyclocheilus multipunctatus (Cypriniformes: Cyprinidae)

The genus Sinocyclocheilus is a representative group of cave creatures. However, genetic studies on Sinocyclocheilus are rare. The primary objective of this study was to explore the structure and feature of the complete mitochondrial genome of S. multipunctatus, and reconstruct the mitogenomic phylogeny of Sinocyclocheilus. The mitochondrial DNA of S. multipunctatus was amplified by overlapping PCR fragments. The mitogenome was assembled by the SeqMan and annotated using MitoAnnotator. The phylogenetic tree was established using the Bayesian inference and Maximum likelihood methods. The mitogenome of S. multipunctatus is a typical circular molecule of 16,586 bp with base composition A (31.25%), T (25.90%), G (16.35%), and C (26.50%), and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) genes, two ribosomal RNAs, and a 931 bp control region. Phylogenetic analysis reveals two clades in the Sinocyclocheilus with robust support. S. multipunctatus is close to a newly discovered cavefish, S. ronganensis. We obtained and described the complete mitogenome of S. multipunctatus, and investigated its phylogenetic status, which may provide a valuable resource for future phylogenetic analyses and population genetic studies in Sinocyclocheilus.

Uncoupling protein 1 in snakehead (Channa argus): Cloning, tissue distribution, and its expression in response to fasting and refeeding

In mammals, uncoupling protein 1 (UCP1) is well known for its thermogenic role in brown adipose tissue (BAT). However, the UCP1 physiological roles are still unclear in fish, although several teleost ucp1 genes have been identified. The aim of this study is to investigate the potential roles of fish UCP1 involved in food intake regulation and energy homeostasis. We herein report on the molecular cloning, tissue distribution and the effect of fasting and refeeding on the expression of ucp1 in Channa argus. UCP1 consisted of a 921 bp open reading frame predicted to encode 306 amino acids. Sequence analysis revealed that snakehead UCP1 was highly conserved (>80%) with teleost UCP1, but shared a lower identity (60-72%) with mammals. Phylogenetic analysis supported that snakehead UCP1 was closely related to piscine UCP1. In addition, ucp1 was found to extensively expressed in all detected tissues, with the highest level in liver. Futhermore, the hepatic ucp1 was found to significantly increased after short-term and long-term food deprivation, and dramatically increased following refeeding. These findings suggested that snakehead UCP1 might play important roles in food intake regulation and fatty acid metabolism in snakehead fish, and it could be as a potential target locus to improve commercial production of this kind of fish.

Sequence identification and phylogenetic analysis of the mitochondrial genome of Microphysogobio kiatingensis (Cypriniformes: Cyprinidae)

Microphysogobio kiatingensis is endemic freshwater fish of China and mainly distributed in the middle and upper reaches of the Yangtze River. The complete mitogenome of M. kiatingensis was first determined by using the next-generation sequencing in present study. The circular mitogenome followed the expected pattern for vertebrates, being 16,603 bp in length. It contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one displacement loop (D-loop) locus and an origin of replication on the light-strand (OL). Most of the genes are encoded on the heavy strand except ND6 and eight tRNA genes. The overall base composition was 30.78% A, 26.09% T, 26.59% C, 16.54% G, with 56.87% AT. Thirteen intergenic spacers and nine gene overlaps exist in the complete mitochondrial genome. Phylogenetic analysis based on the tandem 13 coding protein genes nucleotide sequences with two different methods (maximum likelihood and neighbour-joining analysis) indicated that M. kiatingensis was grouped in one clade with the same genus. The complete mitogenome of M. kiatingensis can provide a useful data for the further research in Gobioninae. Meanwhile, it also provides help for biological genetics and classification of species.

Molecular cloning, tissue distribution, and effect of fasting and refeeding on the expression of neuropeptide Y in Channa argus

Neuropeptide Y (NPY) is a 36 amino-acid amidated peptide of the pancreatic polypeptide (PP) family, which plays an important role in appetite regulation and energy expenditure in mammals. Although several teleost NPY have been identified, its roles remain unclear in fish. We herein reported on the molecular cloning, tissue distribution and the effect of fasting on the expression of NPY in Channa argus, and designated as CaNPY. It consisted of a 300 bp open reading frame predicted to encode a prepro-NPY of 99 amino acids. Sequence analysis revealed that CaNPY was highly conserved (>60%) with other vertebrate NPY. Phylogenetic analysis highly supported CaNPY was closely related to piscine NPY. In addition, except for muscle and spleen tissues, CaNPY was found to extensively expressed in all other detected tissues, with the highest level in brain. Futhermore, the CaNPY transcript was found to significantly increase after short-term and long-term food deprivation, and dramatically decrease following refeeding. These findings suggested that CaNPY might be involved in food intake regulation and it could be as a potential target locus to improve commercial production of this kind of fish.

Identification and analysis of the complete mitochondrial genome of Acheilognathus omeiensis (Cypriniformes, Cyprinidae)

Acheilognathus omeiensis is a small-size freshwater ornamental fish. In this study, the complete mitochondrial genome sequence of A. omeiensis was first determined. This mitogenome was 16,774 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 2 main noncoding regions. Most mitochondrial genes were encoded on the H-strand, except for ND6 and eight tRNA genes. The base composition was 28.97% A, 27.72% T, 26.02% C, and 17.29% G, with 56.69% AT, respectively. Phylogenetic tree was constructed based on the nucleotide sequence of 13 PCGs of A. omeiensis and closely related 12 species ticks to assess their phylogenic relationship and evolution. These data should be helpful for a better understanding of the mitochondrial genomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.

Complete mitochondrial genome and phylogenetic analysis of Sinogastromyzon szechuanensis (Teleostei, Cypriniformes, Homalopteridae)

Sinogastromyzon szechuanensis is endemic to the Upper Yangtze River in China. In this study, we first determined the complete mitochondrial genome of S. szechuanensis. The circular mitogenome was 16,565 bp in length, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 2 main noncoding regions. Most mitochondrial genes were encoded on the H-strand, except for ND6 and eight tRNA genes. The overall nucleotides composition was 30.38% A, 25.26% T, 27.74% C, and 16.62% G, with AT bias of 55.64%, respectively. Phylogenetic analysis using concatenated nucleotide sequences of the 13 PCGs with two different methods (ML and NJ) both highly supported that S. szechuanensis showed a close relationship with S. puliensis and S. sichangensis. These data would be useful for further studies on genetic diversity and molecular phylogenetic relationship of the family Homalopteridae.

The complete mitochondrial genome of Ancherythroculter wangi and its phylogeny

Ancherythroculter wangi, is a unique freshwater fish and mainly distributed in the upper stream of Yangtze River and its tributary. In this study, the complete mitochondrial genome of A. wangi was first determined. The total length of the complete mitochondrial genome is 16,622 bp, contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, one D-loop locus, and an origin of replication on the light-strand (OL). The overall nucleotide composition was 31.19% A, 24.84% T, 27.79% C, 16.18% G, with 56.03% AT, respectively. Phylogenetic analysis both highly supported that A. wangi showed a close relationship with Culter mongolicus and A. kurematsui. These data would contribute to elucidate the evolutionary mechanisms and biogeography of Ancherythroculter and is useful for the conservation of genetics and stock evaluation for A. wangi.