Mitochondrial genome of Silurus asotus (Teleostei: Siluriformes)

The complete mitogenome sequence of the Amur catfish Silurus asotus was determined using long PCRs. The genome was 16,528 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region; the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand is 30.5% A, 25.8% T, 28.0% C, and 15.8% G, with an AT content of 56.3%. The mtDNA sequence of S. asotus shared 93.6% and 90.6% sequence identity with that of Silurus meridionalis and Silurus glanis. This mitogenome sequence data would play an important role in silurid catfish phylogenetics and siluriform catfish systematics in general.     

Complete mitochondrial genome of blackchin tilapia Sarotherodon melanotheron (Perciformes, Cichlidae)

Blackchin tilapia, Sarotherodon melanotheron, is a highly salt-tolerant species in tilapias. In this paper, the complete mitochondrial genome of S. melanotheron was determined first. The mitogenome (16,627 bp) had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding, 22 tRNA, 2 rRNA genes, and 1 putative control region. It shared 95.1%, 93.2%, and 92.2% mitogenome sequence with Oreochromis aureus, Oreochromis niloticus, and Oreochromis mossambicus, respectively.     

Complete mitochondrial genome of the Antarctic amphipod Gondogeneia antarctica (Crustacea, amphipod)

The complete sequence of the mitochondrial genome of the Antarctic amphipod Gondogeneia antarctica was determined to be 18,424 bp in length, and to contain 13 protein-coding genes (PCGs), 22 tRNA genes, and large (rrnL) and small (rrnS) rRNA genes. Its total A+T content is 70.1%. The G. antarctica mitogenome is the largest known among those of crustaceans, due to the existence of two relatively large intergenic non-coding sequences. The PCG arrangement of G. antarctica is identical to that of the ancestral pancrustacean ground pattern, although the tRNA arrangement differs somewhat. The complete mitogenome sequences of 68 species of pancrustacea have been added to the NCBI database, only 4 of which represent complete mitogenome sequences from amphipods. This is the first report of a mitogenome sequence of an Antarctic amphipod, and provides insights into the evolution of crustacean mitochondrial genomes, particularly in amphipods.     

The complete mitochondrial genome of Solen strictus (Bivalvia: Solenidae)

In this paper, we determined the complete mitochondrial genome of Solen strictus (Bivalvia: Solenidae). The whole mitogenome of S. strictus is 16,535?bp in length with a base composition of 21.7% A, 41.0% T, 25.6% C, and 11.7% G and contains 12 protein-coding genes (atp8 is missing), 2 ribosomal RNA genes, 22 transfer RNA genes, and a major non-coding region (MNR). Some peculiar patterns including tandem repeats and microsatellite-like elements are found in the MNR of S. strictus.     

Complete mitochondrial genome of Spilosoma lubricipedum (Noctuoidea: Erebidae) and implications for phylogeny of noctuid insects

Mitochondrial genomes (mitogenomes) have been widely used for studies on phylogenetic relationships and molecular evolutionary biology. Here, the complete mitogenome sequence of Spilosoma lubricipedum (Noctuoidea: Erebidae: Arctiinae) was determined (total length 15,375 bp) and phylogenetic analyses S. lubricipedum were inferred from available noctuid sequence data. The mitogenome of S. lubricipedum was found to be highly A + T-biased (81.39%) and exhibited negative AT- and GC-skews. All 13 protein-coding genes (PCGs) were initiated by ATN codons, except for cox1 with CGA. All tRNAs exhibited typical clover-leaf secondary structures, except for trnS1. The gene order of the S. lubricipedum mitogenome was trnM-trnI-trnQ-nad2. The A + T-rich region of S. lubricipedum contained several conservative features common to noctuid insects. Phylogenetic analysis within Noctuoidea was carried out based on mitochondrial data. Results showed that S. lubricipedum belonged to Erebidae and the Noctuoidea insects could be divided into five well-supported families (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))).     

Complete mitochondrial genome sequence of the dragonet Callionymus curvicornis (Perciformes: Callionymoidei: Callionymidae)

We determined the complete mitochondrial genome (mitogenome) sequence of the dragonet Callionymus curvicornis. The total length of C. curvicornis mitogenome is 16,406 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. It has the typical vertebrate mitochondrial gene arrangement. This is the first report of a complete mitochondrial genome in the fish suborder Callionymoidei.     

Complete nucleotide sequence and organization of the mitochondrial genome of eri-silkworm,Samia cynthia ricini (Lepidoptera: Saturniidae)

Samia cynthia ricini is a commercial silk-producing insect that is now reared year-round in Korea, with the expectation of being utilized for diverse purposes. In this report, we present the complete mitochondrial genome (mitogenome) of S. c. ricini. The 15,384-bp long S. cynthia ricini mitogenome was amplified into 26 short fragments using three long overlapping fragments using primers designed from reported lepidopteran mitogenome sequences. The genome comprises 37 genes (13 protein-coding genes, two rRNA genes, and 22 tRNA genes), and one large non-coding region termed the A + T-rich region. The A/T content of the third codon position was 91.7%, which was 18.8% and 21.6% higher than those of first and second codon positions, respectively. The high A/T content in the genome is reflected in codon usage, accounting for 39.5% of A/T-composed codons (TTA, ATT, TTT, and ATA). Unlike a previous report on the start codon for the COI gene, the S. c. ricini COI gene commences with a typical ATT codon. A total of 221 bp of non-coding sequences are dispersed in 17 regions, ranging in size from 1 to 54 bp, which comprise 1.4% of the total genome. One of the non-coding sequence located between tRNA^Gln and ND2 (54 bp) has 77% sequence homology with the 5′-sequence of the neighboring ND2 gene, suggesting partial duplication of the sequence during evolution. The 361-bp long A + T-rich region contains an 18 bp-long poly-T stretch, ATAGA motif, ATTTA element, microsatellite-like A/T sequence, poly-A stretch and one tRNA-like sequence, as typically found in Lepidoptera including Bombycoidea.     

Complete mitochondrial genome sequence of the Arctic gammarid,Onisimus nanseni (Crustacea; Amphipoda): Novel gene structures and unusual control region features

To analyze the mitogenome of the amphipod Onisimus nanseni, we amplified the complete mitogenome of O. nanseni using long-PCR and genome walking techniques. The mitogenome of O. nanseni is circular and contains all the typical mt genes (2 rRNAs, 22 tRNAs, and 13 protein-coding genes). It has two peculiar non-coding regions of 148 bp and 194 bp. The latter can be involved in replication and termination processes. The total length of the pooled protein-coding, rRNA, and tRNA genes is shorter than those of other crustaceans. In addition, the intergenic spacers of the O. nanseni mitogenome are considerably shorter in length than those of other crustaceans. Fourteen adjacent genes overlap, resulting in a compact mitogenomic structure. In the O. nanseni mitogenome, the AT composition is elevated, particularly in the control regions (78.9% AT), as has been demonstrated for two other amphipods. The tRNA order is highly rearranged compared to other arthropod mitogenomes, but the order of protein-coding genes and rRNAs is largely conserved. The gene cluster between the CO1 and CO3 genes is completely conserved among all amphipods compared. This provides insights into the evolution and gene structures of crustacean mitochondrial genomes, particularly in amphipods.     

栽培大豆和野生大豆线粒体基因组密码子使用偏性的比较分析

为分析栽培大豆和野生大豆线粒体基因组的密码子使用特征差异,该文以其线粒体基因组编码序列为研究对象,比较其密码子偏性形成的影响因素和演化过程。结果表明:(1)栽培大豆和野生大豆线粒体基因组编码区的GC含量分别为44.56%和44.58%,说明栽培大豆和野生大豆线粒体编码基因均富含A/T碱基。(2)栽培大豆和野生大豆线粒体基因组密码子第1位、第2位GC含量平均值与第3位GC含量的相关性均呈极显著水平,说明突变在其密码子偏性形成中的作用不可忽略; PR2-plot分析显示,在同义密码子第3位碱基的使用频率上,嘌呤低于嘧啶; Nc-plot分析中Nc比值位于-0.1～0.2区间的基因数占总基因数的95%以上;突变和选择等多重因素共同作用影响了大豆线粒体基因组编码序列密码子使用偏性的形成。(3)有20、21个密码子分别被确定为栽培大豆和野生大豆线粒体基因组编码序列的最优密码子,其中除丝氨酸TCC密码子外均以A或T结尾。综上结果认为,栽培大豆线粒体密码子偏性的形成受选择的影响要高于野生大豆,这可能是栽培大豆由野生大豆经长期人工栽培驯化的结果。     

The complete mitogenome of the Formosan termite, Coptotermes formosanus Shiraki

The Formosan termite Coptotermes formosanus Shiraki is a well-known invasive pest that causes severe damage to wooden structures in many parts of the world. Although several studies examined its phylogeographic patterns using a few mitochondrial genes, the phylogenetic relationships among C. formosanus are poorly understood because of the small number of mutations known among its mitochondrial genes. To provide a useful genetic tool for further analyses, we analyzed the complete mitochondrial genome sequence of C. formosanus using specimens collected from three isolated islands in the Ryukyu Archipelago of Japan. The circular mitogenome of these termites consisted of genes encoding 22 transfer RNAs, two ribosomal RNAs, and 13 mitochondrial proteins, as is the case for most animal mitochondrial genomes. The G + C content was 34.1%, and the total length varied slightly between 16,234 and 16,236 base pairs. The complete mitochondrial genomes of the three populations were more than 99.9% identical to each other and showed differences at six nucleotide positions. The COII, 12S rRNA, and 16S rRNA genes that are commonly used for phylogenetic analyses revealed only one substitution or no substitutions. The mitogenome sequences determined here should contribute to the design of new molecular markers for the clarification of the historical distribution process of C. formosanus and for further phylogenetic analyses with this and related termite species.     

Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other Lepidopterans

We present the complete sequence of the mitochondrial genome (mitogenome) of the cotton bollworm Helicoverpa armigera. The 15,347-bp mitogenome of H. armigera was arranged in the same order described for all other sequenced lepidopterans, which differs from the most common type found in insects, due to the movement of trnM to a position 5'-upstream of trnI. The gene overlap in the H. armigera mitogenome is totally 23 bp in six locations. The H. armigera mitogenome has a total of 175 bp of intergenic spacer sequences spread over 14 regions ranging in size from 1 to 45 bp. The nucleotide composition of the whole mitogenome of H. armigera is highly A+T biased, accounting for 80.97%, with a slightly positive AT skewness and negative GC skewness, indicating the occurrence of more A than T, C more than G. The protein-encoding genes have typical mitochondrial start codons, except for cox1, which contains the unusual CGA. The cox1, cox2, and nad4 genes have incomplete stop codons (T). The lrRNA and srRNA genes are 1395 and 794-bp long, respectively. All tRNAs have a typical cloverleaf structure of mitochondrial tRNAs, except for trnS1(AGN), the dihydrouridine arm of which could not form a stable stem-loop structure. The H. armigera A+T-rich region contains a conserved structure combining the motif ATAGA and a 19-bp poly-T stretch, but absence of the 9-bp poly-A element upstream of trnM.     

Mitochondrial genome of Onychostoma lini (Teleostei, Cypriniformes)

The complete mitogenome sequence of a vulnerable species Onychostoma lini was determined using polymerase chain reaction and directly sequenced with primer walking method. The complete mitogenome was 16,595?bp in length, containing 37 genes of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene order and composition of O. lini was similar to most other fishes. The descending order of the base composition on heavy strand was 31.6% A, 27.9% C, 24.6% T, and 15.9% G, with a relatively lower level of G and a slight AT bias of 56.2%. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). The complete mitogenome sequence of O. lini provides fundamental data for further conversation genetics and captive breeding studies on this species.     

The complete mitochondrial genome of Eriocheir japonica sinensis (Decapoda: Varunidae) and its phylogenetic analysis

The complete mitochondrial genome (mitogenome) can provide novel insights into understanding the mechanisms underlying mitogenome evolution. In this study, the complete mitogenome of Eriocheir japonica sinensis (Decapoda: Varunidae) was determined to be 16,378 bp, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a D-loop region. The AT skew of the E. j. sinensis mitogenome was slightly negative (−0.016), indicating a higher number of T compared with A nucleotides. The nucleotide composition of the mitogenome was also biased toward A + T nucleotides (71.6%). All PCGs were initiated by ATN codons. Eight of the 13 PCGs harbored the incomplete termination codon by T, or TA. All other tRNA genes displayed a typical clover-leaf structure of mitochondrial tRNA. The D-loop region of the E. j. sinensis mitogenome was 918 bp in length. Based on 13 PCGs, phylogenetic analysis confirmed the placement of E. j. sinensis within the Varunidae.     

Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, <Emphasis Type="Italic">Sinocyclocheilus multipunctatus</Emphasis> (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.     

Complete mitochondrial genome of <Emphasis Type="Italic">Taharana fasciana</Emphasis> (Insecta,Hemiptera: Cicadellidae) and comparison with other Cicadellidae insects

Here, we describe the first complete mitochondrial genome (mitogenome) sequence of the leafhopper Taharana fasciana (Coelidiinae). The mitogenome sequence contains 15,161 bp with an A?+?T content of 77.9%. It includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding (A?+?T-rich) region; in addition, a repeat region is also present (GenBank accession no. KY886913). These genes/regions are in the same order as in the inferred insect ancestral mitogenome. All protein-coding genes have ATN as the start codon, and TAA or single T as the stop codons, except the gene ND3, which ends with TAG. Furthermore, we predicted the secondary structures of the rRNAs in T. fasciana. Six domains (domain III is absent in arthropods) and 41 helices were predicted for 16S rRNA, and 12S rRNA comprised three structural domains and 24 helices. Phylogenetic tree analysis confirmed that T. fasciana and other members of the Cicadellidae are clustered into a clade, and it identified the relationships among the subfamilies Deltocephalinae, Coelidiinae, Idiocerinae, Cicadellinae, and Typhlocybinae.     

Complete mitochondrial genome sequence of the Indian pipistrelle Pipistrellus coromandra (Vespertilioninae)

We characterized the complete mitogenome of Pipistrellus coromandra (Indian pipistrelle) for comparative analysis of mitogenomes and for resolving the phylogenetic relationship of four tribes in the subfamily Vespertilioninae. The mitogenome size of P. coromandra was 17,153?bp, with a control region and a typical set of 37 mitochondrial genes. The nucleotide composition of the P. coromandra mitogenome showed an AT bias with a nucleotide composition of 33.5% A, 30.7% T, 13.3% G, and 22.5% C. The mitochondrial protein-coding genes in P. coromandra use the standard start codon (ATN), two stop codons (TAA and AGA), and two incomplete stop codons (TA- and T--). The intertribal relationship of four tribes was highly resolved from the phylogenetic analysis of mitogenome sequences.     

The complete mitochondrial genome of the Korean red-backed vole, Myodes regulus (Rodentia, Murinae) from Korea

We have determined the complete mitochondrial genome (NC_016427) of the Korean red-backed vole, Myodes regulus, which is distributed in South Korea. The total length of the M. regulus mitogenome is 16,379?bp, with a base composition of 33.0% A, 26.7% T, 27.1% C, and 13.2% G. The total length of the 13 protein-coding genes is 11,396?bp long.     

The complete mitochondrial genome of the spotted steed, Hemibarbus maculatus (Teleostei, Cypriniformes)

The complete mitogenome sequence of the spotted steed (Hemibarbus maculatus) was determined using long PCR reactions. The genome is 16,611 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. maculatus was similar to that of most other vertebrates. The base composition of H-strand in descending order is A (29.16%), C (27.41%), T (25.93%), and G (17.50%), with an AT content of 55.09%. The Kimura two-parameter distances between mitogenome sequences of H. maculatus and Hemibarbus labeo, Hemibarbus barbus, Hemibarbus longirostris, Hemibarbus mylodon were 2.09%, 2.35%, 12.77%, and 13.92%, respectively. The phylogenetic relationships among the five Hemibarbus species based on the whole mitogenome sequence data were (((H. barbus, H. labeo), H. maculatus), (H. longirostris, H. mylodon)).     

Complete mitochondrial genome of Chilo suppressalis (Walker) (Lepidoptera: Crambidae)

The complete sequence of the mitochondrial genome (mitogenome) of the rice stem borer Chilo suppressalis (Walker) (Lepidoptera: Crambidae) was determined to be 15,465 bp. It contains 13 protein-coding genes (PCGs), 22 tRNA genes, the large and small rRNA genes, and an A+T-rich region. The nucleotide composition of the mitogenome of C. suppressalis is highly A+T biased, accounting for 79.70% in whole mitogenome, 77.74% in PCGs, 84.70% in tRNAs, 81.20% in rRNAs and 94.19% in A+T-rich region, respectively. The PCGs have typical ATN start codons, except for cox1, which contains the unusual CGA. The C. suppressalis A+T-rich region contains a conserved structure combining the motif ATAGA and a 19-bp poly-T stretch, but absence of the 9-bp poly-A element upstream trnM.     

The complete mitochondrial genome of Calicogorgia granulosa (Anthozoa: Octocorallia): potential gene novelty in unidentified ORFs formed by repeat expansion and segmental duplication

Mitochondrial genomes of many nonbilaterian animals show high diversity of genome size and gene content, revealing many intergenic regions (IGRs), diverse repeats and additional genes. Here we present a new complete mitogenome of the cnidarian sea fan species, Calicogorgia granulosa (Anthozoa: Octocorallia) and its novel genomic features. The 20,246 bp of the complete mitogenome, which is the largest among the nine octocorals sequenced to date, contains 13 protein coding genes, 2 rRNAs and a tRNA within its circular form of mitochondrial DNA. We found an identical segmental duplication (S1 and S2, 913 bp) composed of an ORF (672 bp) coding for a hypothetical protein within which Direct Variant Repeat (DVR) expansions reside in-frame to the coding sequence. Additionally, the duplicated segmental DNA showed no variation in nucleotide sequences both between S1 and S2 and across multiple individual samples. Upon these observations, we discuss plausible causes for the intramitochondrial segmental duplication and the absence of sequence variation, and a need for further investigation of the novel ORF as well. In conclusion the present mitogenome of C. granulosa adds more information to our understanding of the diversity and evolution of mitogenomes of nonbilaterian animals.