The complete mitochondrial genome of theHemibarbus medius(Cypriniformes, Cyprinidae)

The complete mitochondrial genome of the apple snail Pomacea maculate (Gastropoda: Ampullariidae)

We present the complete mitochondrial genome of Pomacea maculate in this study. The mitochondrial genome is 15,512 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. Overall nucleotide compositions of the light strand are 41.13% of A, 30.81% of T, 15.25% of C and 12.81% of G. Its gene arrangement and distribution are different from the typical vertebrates. The absence of D-loop is consistent with the Gastropoda, but at least one lengthy non-coding region is essential regulatory element for the initiation of transcription and replication. Phylogenetic tree is constructed by the maximum-likelihood method based on the complete mitochondrial genomes of 15 species of Caenogastropoda, using Helix aspersa as outgroup to assess their actual phylogenetic relationship and evolution. The result provides fundamental data for resolving phylogenetic and genetic problems related to effective management strategies.

Characterization of the Complete Mitochondrial Genome Sequences of Three Croakers (Perciformes, Sciaenidae) and Novel Insights into the Phylogenetics

The three croakers (Nibea coibor, Protonibea diacanthus and Argyrosomus amoyensis, Perciformes, Sciaenidae) are important commercial species inhabiting the Eastern Indian Ocean and Western Pacific. Molecular data employed in previous research on phylogenetic reconstruction have not been adequate and complete, and systematic and comprehensive phylogenetic relationships for these fish are unresolved. We sequenced the complete mitochondrial genomes of the three croakers using next-generation sequencing for the first time. We analyzed the composition and phylogenies between 19 species in the family Sciaenidae using the mitochondrial protein coding sequences of 204 species in the Series Eupercaria. We present the characterization of the complete mitochondrial genome sequences of the three croakers. Gene arrangement and distribution of the three croakers are canonically identical and consistent with other vertebrates. We found that the family Sciaenidae is an independent branch that is isolated from the order Perciformes and does not belong to any extant classification. Therefore, this family is expected to belong to a new classification at the order level and needs further analysis. The evolution of Sciaenidae has lagged far behind the Perciformes differentiation. This study presents a novel insight into the phylogenetics of the family Sciaenidae from the order Perciformes and facilitates additional studies on the evolution and phylogeny of Series Eupercaria.

The complete mitochondrial genome of the Ancherythroculter lini (Cypriniformes, Cyprinidea)

Ancherythroculter lini is the endemic species of fish in China. In this study, we determined the complete mitochondrial genome of Ancherythroculter lini using the next-generation sequencing (NGS). The total length of the complete mitochondrial genome is 16 616 bp which consists of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs genes, and a control region. Most of the genes are encoded on the heavy strand except ND6 and eight tRNA genes. The genes order and locations are similar to other vertebrates. The H-strand has a nucleotide composition of 30.78% A, 24.74% T, 16.48% G, and 28.00% C. 13 intergenic spacers and five gene overlaps exist in the complete mitochondrial genome. And, we found the culter genus and Ancherythroculter nigrocauda are more closely related to Ancherythroculter lini by constructing a phylogenetic tree.

The complete mitochondrial genome of the golden apple snail Pomacea canaliculata (Gastropoda: Ampullariidae)

We present the complete mitochondrial genome of Cipangopaludina cathayensis in this study. The mitochondrial genome is 15 706 bp in length, containing 13 protein-coding genes, two rRNA genes and 22 tRNA genes. Overall nucleotide compositions of the light strand are 40.97% of A, 30.78% of T, 20.48% of C and 12.60% of G. Its gene arrangement and distribution are different from the typical vertebrates. The absence of D-loop is consistent with the Gastropoda, but, at least, one lengthy non-coding region is an essential regulatory element for the initiation of transcription and replication. A phylogenetic tree is constructed using the maximum-likelihood method based on the complete mitogenomes of the closely related 21 Gastropoda species to assess their actual phylogenetic relationship and evolution. The result provides fundamental data for resolving phylogenetic and genetic problems related to effective management strategies.

Ion Torrent next-generation sequencing reveals the complete mitochondrial genome of koi carp (Cyprinus carpio, Cyprinidae)

The complete mitochondrial genome of the koi carp (Cyprinus carpio, Cyprinidae) was sequenced in the present study by using Ion Torrent Personal Genome Machine (PGM) platform for the first time. The mitochondrial genome sequence is 16 581 bp in size and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The gene order and organization were similar to most of the other teleost. The nucleotide compositions of the light strand are 24.82% of A, 31.92% of T, 27.53% of G and 15.73% of C. With the exception of eight tRNA genes and the NADH dehydrogenase subunit 6 (ND6), all other mitochondrial genes are encoded on the heavy strand. The phylogenetic tree constructed using a maximum-likelihood model showed sister relationship of koi carp to other Cyprinidae fishes.

Complete mitochondrial genome of Rhodeus ocellatus (Cypriniformes: Cyprinidae)

The complete mitogenome sequence of Rhodeus ocellatus (Kner) was determined using the next-generation sequencing (NGS). The genome was 16 761 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a control region. The overall nucleotide composition was 30.43% A, 27.50% T, 25.94% C, and 16.13% G, with an A + T bias of 57.93%. The gene composition and the arrangement of the R. ocellatus mitochondrial genome were similar to that of most other vertebrates. The complete mitochondrial genome sequence will help to study the evolutionary relationships and population genetics of Rhodeus fish.

The complete mitochondrial genome of the mudsnail Cipangopaludina cathayensis (Gastropoda: Viviparidae)

We present the complete mitochondrial genome of Cipangopaludina cathayensis in this study. The mitochondrial genome is 17,157 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. All of them are encoded on the heavy strand except 7 tRNA genes on the light strand. Overall nucleotide compositions of the light strand are 44.51% of A, 26.74% of T, 20.48% of C and 8.28% of G. All the protein-coding genes start with ATG initiation codon except ATP6 with ATA and ND4 with TTG, and 2 types of termination codons are TAA (ATP6, ND2, COX1, COX2, ATP8, ND1, ND6, Cytb, COX3, ND4) and TAG (ND4L, ND5, ND3). There are 29 intergenic spacers and 5 gene overlaps. The tandem repeat sequences are observed in COX2, tRNA(Asp), ATP6, tRNA(Cys), S-rRNA, ND1, Cytb, ND4 and COX3 genes. Gene arrangement and distribution are different from the typical vertebrates. The absence of D-loop is consistent with the Gastropoda, but at least one lengthy non-coding region is essential regulatory element for the initiation of transcription and replication.

The complete mitochondrial genome of the giant African snail Achatina fulica (Mollusca: Achatinidae)

We present the complete mitochondrial genome of the Achatina fulica in this study. The results show that the mitochondrial genome is 15,057 bp in length, which is comprised of 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes. The nucleotide compositions of the light strand are 35.47% of A, 27.97% of T 19.46% of C, and 17.10% of G. Except the ND3, 7 tRNA, ATP6, ATP8, COX3 and 12S-rRNA on the light strand, the rest are encoded on the heavy strand. Five types of inferred initiation codons are ATA (ND1, ND5), GTG (ND6), ATG (COX3, COX2), ATT (ND4) and TTG (COX1, ND2, ND3, ND4L, ATP6, ATP8, Cytb), and 3 types of inferred termination codons are T (COX3, ND2), TAA (ND1, ND4L, ND5, ND6, ATP6), and TAG (ND3, ND4, COX1, COX2, Cytb, ATP8). There are 24 intergenic spacers and 6 gene overlaps. The tandem repeat sequence (total 52 bp) of (AATAATT)n is observed in 16S-rRNA. Gene arrangement and distribution are inconsistent 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 orange-spotted grouper Epinephelus coioides (Perciformes, Serranidae)

We present the complete mitochondrial genome of Epinephelus coioides in this study. The mitochondrial genome is 16,458 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 28.88% of G, 28.75% of T, 26.58% of A and 15.80% of C. All the protein-coding genes share ATG initiation codon except ATP6 with CTG and COXI with GTG, and four types of inferred termination codons are T (ND2, COXII, ND3, ND4 and Cytb), TA (COXIII), TAA (ND1, ATP8, ND4L, ND5, ATP6 and COXI) and TAG (ND6). There are 10 intergenic spacers, 5 gene overlaps and no tandem repeat sequence. Gene arrangement and distribution are consistent with the typical vertebrates.

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.