ATG Initiation Codon Research Articles

Complete mitochondrial genome of four pheretimoid earthworms (Clitellata: Oligochaeta) and their phylogenetic reconstruction

Among oligochaetes, the Pheretima complex within the Megascolecidae is a major earthworm group. Recently, however, the systematics of the Pheretima complex based on morphology are challenged by molecular studies. Since little comparative analysis of earthworm complete mitochondrial genomes has been reported yet, we sequenced mitogenomes of four pheretimoid earthworm species to explore their phylogenetic relationships. The general earthworm genomic features are also found in four earthworms: all genes transcribed from the same strand, the same initiation codon ATG for each PCGs, and conserved structures of RNA genes. Interestingly we find an extra potential tRNA-leucine (CUN) in Amynthas longisiphonus. The earthworm mitochondrial ATP8 exhibits the highest evolutionary rate, while the gene CO1 evolves slowest. Phylogenetic analysis based on protein-coding genes (PCGs) strongly supports the monophyly of the Clitellata, Hirudinea, Oligochaeta, Megascolecidae and Pheretima complex. Our analysis, however, reveals non-monophyly within the genara Amynthas and Metaphire. Thus the generic divisions based on morphology in the Pheretima complex should be reconsidered.

The complete mitochondrial genome sequence of Plotosus japonicus (Siluriformes: Plotosidae) and phylogenetic studies of Siluriformes

In this study, we first determined and described the complete mitogenome sequence of Plotosus japonicus, which is a kind of marine fish widely distributed in Northwest Pacific. The complete mitogenome sequence is 16 472 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region (CR) and a light-strand replication origin (OL). The overall base composition is 31.9% A, 24.7% T, 27.7% C, 15.7% G, with a slight AT bias (56.6%), similar to other vertebrate mitochondrial genomes. All the protein-coding genes use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, while COII and ND4 use AGA, COIII and Cytb use an incomplete stop codon TA or T. Maximum Likelihood (ML) tree and Bayesian analyses based on concatenated nucleotide sequences of 12 mitochondrial protein-coding genes were constructed and both yielded identical topologies. These results are expected to provide useful molecular data for species identification and further phylogenetic studies of Siluriformes.

The complete mitochondrial genome of silver fox (Caniformia: Canidae)

Silver fox is color variant of Vulpes vulpes. At present, there are few studies on phylogeny of Canidae and Caniformia. In this article, we determined and described the complete mitogenome of silver fox for the first time, which is 16,723 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, one origin of replication on the light-strand (OL) and a putative control region (CR). The overall base composition is 31.4% A, 27.9% T, 26.0% C, 14.7% G, respectively, with a AT bias (59.3%). Ten protein-coding genes use the initiation codon ATG while ND2, ND3 and ND5 use ATA. Most of them have TAA as the stop codon, except ND2 uses TAG, Cytb uses AGA, and COX3, ND3, ND4 use an incomplete stop codon TA. The information is expected to provide useful molecular data for further taxonomic and phylogenetic studies of Canidae and Caniformia.

The complete mitochondrial genome of Xinong Saanen dairy goat (Capra hircus)

Xinong Saanen dairy goat (Capra hircus), a breed distributed widely and adapted highly in China, has the characteristics of high milk production and high litter size. Our research revealed that the complete mitochondrial genome of Xinong Saanen dairy goat was 16,639 bp in length. The contents of A, C, G and T in the mitochondrial genome were 33.6%, 26.0%, 13.1% and 27.3%, respectively. It had a typical mitogenome structure, containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and 1 control region. Most of the PCGs have ATG initiation codons, whereas ND2, ND3 and ND5 start with ATA. These results provide essential information for phylogeographic history and population genetic structure, genetic diversity of domestic goats and mitochondrial genome editing based on the goat model.

The complete mitochondrial genome of Shaannan White goat (Capra hircus)

The Shaannan White goat (Capra hircus), a breed native to China, has the characteristics of high fecundity and white fur. In this study, we sequenced the complete mitochondrial genome and found its length to be 16,641 bp with the base composition of 33.5% A, 26.1% C, 13.1% G and 27.3% T. It has a typical mitogenome structure, containing 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and a non-coding control region. Most of the genes have ATG initiation codons, whereas ND2, ND3 and ND5 genes start with ATA. These results provide important reference sequence for future phylogenetic studies.

Complete mitochondrial genome of Tree Sparrow Passer montanus saturatus (Passeriformes: Passeridae)

Tree Sparrow Passer montanus is an Eurasian distribution passerine bird, which has 9 subspecies. In this study, we determined the complete mitochondrial genome of Passer montanus saturatus. The mitochondrial DNA is 16,904 bp long with A + T contents of 52.56%. The mitochondrial genome is typical circular that encodes the complete set of 37 genes. All protein-coding genes use the standard mitochondrial initiation codon ATG, except for COI starts with GTG and ND3 starts with ATA. TAN is the most frequent stop codon, and AGN and T– – are also occurred very common. All tRNAs possess the classic clover leaf secondary structure except for tRNASer (AGN) and tRNACys (CUN), which lack the “DHU” stem, only forming a simple loop.

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, tRNAAsp, ATP6, tRNACys, 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 mitogenome of the Black-tailed gull Larus crassirostris (Charadriiformes: Laridae)

The complete mitogenome (KM507782) of the Black-tailed gull L. crassirostris was 16,746 bp long, with A 30.6% (5128 bp), T 24.3% (4076 bp), C 30.9% (5176 bp), and G 14.1% (2366 bp). Total length of 13 protein-coding genes was 11,396 bp and 12 of them except for ND6 were encoded in heavy strand. The three initiation codons ATG, GTG and ATT were used in the protein-coding genes. The ATG was a common initiation codon which was found in most of the protein-coding genes, whereas GTG was used in COX1 and ND5 and ATT in only ND3, respectively. The total length of 22 tRNA genes was 1550 bp, ranging from 66 bp (tRNASer(AGY)) to 74 bp (tRNALeu(UUR) and tRNASer(UCN)).

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, tRNATrp, tRNAAla, 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 striped lynx spider Oxyopes sertatus (Araneae: Oxyopidae)

The complete mitochondrial genome of Oxyopes sertatus is a circular molecule of 14,442 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The A + T content of the overall base composition of H-strand is 75.9% (T: 42.9%; C: 8.2%; A: 33.0%; G: 15.9%). COII, COIII and ND4 genes begin with TTG as start codon; ATP6, COI, ND1 and ND5 genes begin with ATA as start codon, ATP8, Cyt b, ND2 and ND3 genes begin with ATT as start codon, ND6 gene begins with GTG as start codon, while ND4L gene start with a typical ATG initiation codon. ND2 gene is terminated with TAG as stop codon, Cyt b and ND5 end with TA, COI, ND1 and ND4L end with T, ATP6, ATP8, COII, COIII, ND3, ND4 and ND6 end with TAA.

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 pantropical jumping spider Plexippus paykulli (Araneae: Salticidae)

The complete mitochondrial genome of Plexippus paykulli is a circular molecule of 14,316 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The A + T content of the overall base composition of H-strand is 73.5% (T: 40.6%; C: 9.0%; A: 32.9%; G: 17.5%). ATP6, Cyt b, ND2, ND5 and ND4 genes begin with ATA as start codon; ATP8, ND1, ND3 and ND4L genes begin with ATT as start codon; COII and COIII genes begin with TTG as start codon; COI gene begins with AGA as start codon, while ND6 gene start with a typical ATG initiation codon. ATP6, COI, COII, COIII and ND3 genes are terminated with TAA as stop codon, ND6 ends with TA, ATP8, ND1 and ND2 end with TAG, Cyt b, ND5, ND4 and ND4L end with T.

Complete mitochondrial genome of Nanjiang Yellow goat (Capra hircus)

Nanjiang Yellow goat (Capra hircus) is the first cultured mutton breed in China. In this study, the complete mitochondrial genome sequence of Nanjiang Yellow goat has been identified for the first time. The total length of the mitochondrial genome was 16,639 bp, with the base composition of 33.54% A, 26.05% C, 13.11% G and 27.30% T. It contained 37 genes (22 transfer RNA genes, 2 ribosomal RNA genes, and 13 protein-coding genes) and a major non-coding control region (D-loop). Most of the genes have ATG initiation codons, whereas ND2, ND3 and ND5 start with ATA. The complete mitochondrial genome sequence of Nanjiang Yellow goat provides an important data set for further estimation on the phylogeographic structure of domestic goats.

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.

The complete mitochondrial genome of Chinese tibetan goat (Capra hircus)

The Tibetan goat (Capra hircus), a breed native to China, is adapted to cold and hypoxia. Here, we describe the complete mitochondrial genome sequence of Tibetan goat. The mitochondrial genome is 16,640 bp in length, with a base composition of 33.6% A, 26.0% C, 13.1% G and 27.3% T. It has a typical mitogenome structure, containing 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and a non-coding control region (D-loop region). Most of the genes have ATG initiation codons, whereas ND2, ND3 and ND5 start with ATA. This genomic data provides a strating point for future phylogenetics studies.

Complete mitochondrial genome of Naumann’s thrush Turdus naumanni (Passeriformes: Turdidae)

The mitochondrial DNA of Naumann’s thrush Turdus naumanni (Passeriformes: Turdidae) is 16,750 bp long with A + T contents of 52.79%. It has typical circular mitochondrial genomes that encode the complete set of 37 genes which are usually found in birds. All protein-coding genes use the standard mitochondrial initiation codon ATG, except for ND2 and COI start with GTG. TAN is the most frequent stop codon, and AGN and T– – are also occurred very common. All tRNAs possess the classic clover leaf secondary structure except for tRNASer(AGN) and tRNALys(CUN), which lack the “DHU” stem, only forming a simple loop.

The complete mitochondrial genome of the Hemibarbus medius (Cypriniformes, Cyprinidae)

We present the complete mitochondrial genome of the Hemibarbus medius in this study. The mitochondrial genome is 16,611 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 29.82% of A, 27.22% of C, 25.93% of T, and 17.04% 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. Four types of termination codons revealed are TAA (ND1, COXІ, ATP8, ND4L, ND5), T (ND2, ND3, COXП, COXШ, CYTB), TA (ND4, ATP6), and TAG (ND6). Most genes are either abutted or overlapped and many features keep consistent with the other vertebrates.

The complete mitochondrial genome of long-legs spider Pholcus sp. (Araneae: Pholcidae)

The complete mitochondrial genome of Pholcus sp. is a circular molecule of 14,279 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The A + T content of the overall base composition of H-strand is 65.8% (T: 39.1%; C: 10.7%; A: 26.7%; G: 23.5%). COII and ND2 genes begin with GTG as start codon, COI, ND4L and ND5 genes begin with ATA as start codon, ATP8, ND1 and ND3 genes begins with ATT as start codon, while other five protein-coding genes start with a typical ATG initiation codon. ATP6, ATP8, COIII, ND2, ND4, ND4L and ND6 genes are terminated with TAA as stop codon, COI, Cyt b, ND1 and ND3 end with TAG, while COII and ND5 end with T.

The complete mitochondrial genome of the Anabas testudineus (Perciformes, Anabantidae)

We present the complete mitochondrial genome of the Anabas testudineus in this study. The mitochondrial genome is 16,603 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 29.40% of C, 28.63% of A, 25.79% of T, and 16.18% 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. Four types of termination codons revealed are TAA (COXІ, ATP8, ND4L, CYTB), T (COXП, ND3, ND4), TA (ND2, ATP6, COXШ), and TAG (ND1, ND5, ND6). Most genes are either abutted or overlapped and many features keep consistent with the other vertebrates.