Complete nucleotide sequence and gene organization of the mitochondrial genome of Paa spinosa (Anura: Ranoidae)

How Does Mitochondrial Protein-Coding Gene Expression in Fejervarya kawamurai (Anura: Dicroglossidae) Respond to Extreme Temperatures?

Unusual climates can lead to extreme temperatures. Fejervarya kawamurai, one of the most prevalent anurans in the paddy fields of tropical and subtropical regions in Asia, is sensitive to climate change. The present study focuses primarily on a single question: how do the 13 mitochondrial protein-coding genes (PCGs) respond to extreme temperature change compared with 25 °C controls? Thirty-eight genes including an extra tRNA-Met gene were identified and sequenced from the mitochondrial genome of F. kawamurai. Evolutionary relationships were assessed within the Dicroglossidae and showed that Dicroglossinae is monophyletic and F. kawamurai is a sister group to the clade of (F. multistriata + F. limnocharis). Transcript levels of mitochondrial genes in liver were also evaluated to assess responses to 24 h exposure to low (2 °C and 4 °C) or high (40 °C) temperatures. Under 2 °C, seven genes showed significant changes in liver transcript levels, among which transcript levels of ATP8, ND1, ND2, ND3, ND4, and Cytb increased, respectively, and ND5 decreased. However, exposure to 4 °C for 24 h was very different in that the expressions of ten mitochondrial protein-coding genes, except ND1, ND3, and Cytb, were significantly downregulated. Among them, the transcript level of ND5 was most significantly downregulated, decreasing by 0.28-fold. Exposure to a hot environment at 40 °C for 24 h resulted in a marked difference in transcript responses with strong upregulation of eight genes, ranging from a 1.52-fold increase in ND4L to a 2.18-fold rise in Cytb transcript levels, although COI and ND5 were reduced to 0.56 and 0.67, respectively, compared with the controls. Overall, these results suggest that at 4 °C, F. kawamurai appears to have entered a hypometabolic state of hibernation, whereas its mitochondrial oxidative phosphorylation was affected at both 2 °C and 40 °C. The majority of mitochondrial PCGs exhibited substantial changes at all three temperatures, indicating that frogs such as F. kawamurai that inhabit tropical or subtropical regions are susceptible to ambient temperature changes and can quickly employ compensating adjustments to proteins involved in the mitochondrial electron transport chain.

Characterization of Two Mitogenomes of Hyla sanchiangensis (Anura: Hylidae), with Phylogenetic Relationships and Selection Pressure Analyses of Hylidae

Hyla sanchiangensis (Anura: Hylidae) is endemic to China and is distributed across Anhui, Zhejiang, Fujian, Guangdong, Guangxi, Hunan, and Guizhou provinces. The mitogenomes of H. sanchiangensis from two different sites (Jinxiu, Guangxi, and Wencheng, Zhejiang) were sequenced. Phylogenetic analyses were conducted, including 38 mitogenomes of Hylidae from the NCBI database, and assessed the phylogenetic relationship of H. sanchiangensis within the analyzed dataset. Two mitogenomes of H. sanchiangensis showed the typical mitochondrial gene arrangement with 13 protein-coding genes (PCGs), two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and one non-coding control region (D-loop). The lengths of the 12S rRNA and 16S rRNA genes from both samples (Jinxiu and Wencheng) were 933 bp and 1604 bp, respectively. The genetic distance (p-distance transformed into percent) on the basis of the mitogenomes (excluding the control region) of the two samples was calculated as 4.4%. Hyla sanchiangensis showed a close phylogenetic relationship with the clade of (H. annectans + H. tsinlingensis), which was supported by ML and BI analyses. In the branch-site model, five positive selection sites were found in the clade of Hyla and Dryophytes: Cytb protein (at position 316), ND3 protein (at position 85), and ND5 protein (at position 400) have one site, respectively, and two sites in ND4 protein (at positions 47 and 200). Based on the results, we hypothesized that the positive selection of Hyla and Dryophytes was due to their experience of cold stress in historical events, but more evidence is needed to support this conclusion.

Characterization of the complete mitogenome of the endangered freshwater fish Gobiobotia naktongensis from the Geum River in South Korea: evidence of stream connection with the Paleo-Huanghe

Background

The freshwater fish Gobiobotia naktongensis (Teleostei, Cypriniformes, and Gobionidae) is an endangered class I species whose population size has been greatly reduced.

Objective

To successfully protect and restore the highly endangered freshwater fish G. naktongensis from the Geum River in South Korea.

Methods

The mitogenome was characterized using the primer walking method with phylogenetic relationships.

Results

The complete mitogenome of G. naktongensis Geum River was 16,607 bp, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA (tRNA) genes. Seventeen substitutions were found by comparing the tRNA regions between G. naktongensis Geum and Nakdong Rivers and G. pappenheimi; most were specific to G. naktongensis Nakdong River, with changes in their secondary structures. The comparison between G. naktongensis Geum River and G. pappenheimi revealed differences in the lengths of the D-loop and two tRNAs (tRNA^Arg and tRNA^Trp) and the secondary structures in the TΨC-arm of tRNA^His. In the phylogenetic tree, G. naktongensis Geum River did not cluster with its conspecific specimen from the Nakdong River in South Korea, but showed the closest relationship to G. pappenheimi in mainland China.

Conclusions

Our results support the existence of the Paleo-Huanghe River connecting the Korean peninsula and mainland China, suggesting that G. naktongensis in the Geum River should be treated as a different evolutionarily significant unit separated from that in the Nakdong River. The complete mitogenome of G. naktongensis Geum River provides essential baseline data to establish strategies for its conservation and restoration.

Comparative mitogenomics of Drosophilidae and the evolution of the Zygothrica genus group (Diptera, Drosophilidae)

The Zygothrica genus group of Drosophilidae encompasses more than 437 species and five genera. Although knowledge regarding its diversity has increased, uncertainties about its monophyly and position within Drosophilidae remain. Genomic approaches have been widely used to address different phylogenetic questions and analyses involving the mitogenome have revealed a cost-efficient tool to these studies. Thus, this work aims to characterize mitogenomes of three species of the Zygothrica genus group (from the Hirtodrosophila, Paraliodrosophila and Zygothrica genera), while comparing them with orthologous sequences from other 23 Drosophilidae species and addressing their phylogenetic position. General content concerning gene order and overlap, nucleotide composition, start and stop codon, codon usage and tRNA structures were compared, and phylogenetic trees were constructed under different datasets. The complete mitogenomes characterized for H. subflavohalterata affinis H002 and P. antennta present the PanCrustacea gene order with 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein coding genes and an A+T rich region with two T-stretched elements. Some peculiarities such as the almost complete overlap of genes tRNAH/ND4, tRNAF/ND5 and tRNAS2/ND1 are reported for different Drosophilidae species. Non-canonical secondary structures were encountered for tRNAS1 and tRNAY, revealing patterns that apply at different phylogenetic scales. According to the best depiction of the mitogenomes evolutionary history, the three Neotropical species of the Zygothrica genus group encompass a monophyletic lineage sister to Zaprionus, composing with this genus a clade that is sister to the Drosophila subgenus.

The complete mitochondrial genome and the phylogenetic position of Alauda gulgula (Aves: Passeriformes)

The Oriental Skylark (Alauda gulgula) is a small songbird in the Alaudidae. Here we assembled the complete mitochondrial genome of Alauda gulgula which is 17,055 bp in length and consisting of 13 protein-coding genes (PCGs), 2 ribosomal RNA, 22 transfer RNA, and 2 extensive heteroplasmic control regions. The overall A + T content of the mitogenome is 52.3%The maximum-likelihood (ML) tree based on the complete mitochondrial genome of A. gulgula revealed the close genetic relationship between A. gulgula and A. arvensis, but separate from A. cheleensis.

Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships

The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.

Complete mitochondrial genome sequence of Catla catla (Hamilton, 1822) from the Halda river of Bangladesh

Catla (Catla catla) is one of the fastest-growing major carp found in South Asia as well as Bangladesh. Catla catla is the second most popular indigenous carp species in the freshwater aquaculture industry of Bangladesh due to its relatively good taste and high market price. In this study, we disclosed the complete mitochondrial genome sequence of Bangladeshi Catla fish from Halda river located in Chittagong. The circular mitogenome of Catla catla is 16,597 bp in length and nucleotide composition is AT-based (72%), contains 37 genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a D-loop (control region).

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.

Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses

Mitogenomes are useful in analyzing phylogenetic relationships and also appear to influence energy metabolism, thermoregulation and osmoregulation. Much evidence has accumulated for positive selection acting on mitochondrial genes associated with environmental adaptation. Hence, the mitogenome is a likely target for environmental selection. The family Bufonidae (true toads) has only nine complete and four partial mitogenomes published compared to the 610 known species of this family. More mitogenomes are needed in order to obtain a clearer understanding of the phylogenetic relationships within Bufonidae that are currently controversial. To date, no mitogenomes have been reported from the genera Anaxyrus and Bufotes. Anaxyrus americanus can live in low temperature environments and Bufotes pewzowi can live in high salinity environments. We sequenced the mitogenomes of these two species to discuss the phylogenetic relationships within Bufonidae and the selection pressures experienced by specimens living in low temperature or saline environments. Like other toads, the circular mitogenomes of both species contained the typical 37 genes. Anaxyrus americanus had the highest A+T content of the complete mitogenome among the Bufonidae. In addition, A. americanus showed a negative AT-skew in the control region, whereas Bufotes pewzowi showed a positive AT-skew. Additionally, both toad species had unique molecular features in common: an ND1 gene that uses TTG as the start codon, an extra unpaired adenine (A) in the anticodon arm of trnS (AGY), and the loss of the DHU loop in trnC. The monophyly of Bufonidae was corroborated by both BI and ML trees. An analysis of selective pressure based on the 13 protein coding genes was conducted using the EasyCodeML program. In the branch model analysis, we found two branches of A. americanus and Bufotes pewzowi that were under negative selection. Additionally, we found two positively selected sites (at positions 115 and 119, BEB value > 0.90) in the ND6 protein in the site model analysis. The residue D (119) was located only in A. americanus and may be related to adaptive evolution in low temperature environments. However, there was no evidence of a positively selected site in Bufotes pewzowi in this study.

The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world's largest frogs

The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr , tRNAPro , tRNAPhe , tRNAVal , tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).

A new caruncle-bearing fanged frog (Limnonectes, Dicroglossidae) from Laos and Thailand

A new species of the dicroglossid frog genus Limnonectes is described from recent and historical museum specimens collected in central and southern Laos and northeastern Thailand. Limnonectessavansp. nov. has males that bear a caruncle on top of the head, and most closely resembles L.dabanus from adjacent southern Vietnam and eastern Cambodia. However, the new species is readily distinguished from L.dabanus, and all other caruncle-bearing species of Limnonectes in mainland Southeast Asia, by its adult and larval morphology, mitochondrial DNA, and advertisement call. Its description brings the total number of caruncle-bearing species of Limnonectes to six.

The first complete mitochondrial genome sequence of Nanorana parkeri and Nanorana ventripunctata (Amphibia: Anura: Dicroglossidae), with related phylogenetic analyses

Members of the Nanorana genus (family Dicroglossidae) are often referred to as excellent model species with which to study amphibian adaptations to extreme environments and also as excellent keystone taxa for providing insights into the evolution of the Dicroglossidae. However, a complete mitochondrial genome is currently only available for Nanorana pleskei. Thus, we analyzed the complete mitochondrial genomes of Nanorana parkeri and Nanorana ventripunctata to investigate their evolutionary relationships within Nanorana and their phylogenetic position in the family Dicroglossidae. Our results showed that the genomes of N. parkeri (17,837 bp) and N. ventripunctata (18,373 bp) encode 13 protein‐coding genes (PCGs), two ribosomal RNA genes, 23 transfer RNA (tRNA) genes, and a noncoding control region. Overall sequences and genome structure of the two species showed high degree of similarity with N. pleskei, although the motif structures and repeat sequences of the putative control region showed clear differences among these three Nanorana species. In addition, a tandem repeat of the tRNA‐Met gene was found located between the tRNA‐Gln and ND2 genes. On both the 5′ and 3′‐sides, the control region possessed distinct repeat regions; however, the CSB‐2 motif was not found in N. pleskei. Based on the nucleotide sequences of 13 PCGs, our phylogenetic analyses, using Bayesian inference and maximum‐likelihood methods, illustrate the taxonomic status of Nanorana with robust support showing that N. ventripunctata and N. pleskei are more closely related than they are to N. parkeri. In conclusion, our analyses provide a more robust and reliable perspective on the evolutionary history of Dicroglossidae than earlier analyses, which used only a single species (N. pleskei).

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 Fejervarya kawamurai (Anura: Dicroglossidae) and its phylogeny

The mitochondrial genome of Fejervarya kawamurai is a circular molecule of 17,650 bp in length, containing 13 protein-coding genes, two rRNA genes, 23 tRNA genes (including an extra tRNA-Met), and the control region. The AT content of the whole genome is 56.9%. In Bayesian inference (BI) and Maximum likelihood (ML) analyses, we found that F. kawamurai is a sister clade to F. multistriata and F. limnocharis. The monophyly of Fejervarya, Quasipaa, Nanorana was well supported (1.00 in BI and 100% in ML).

The complete mitochondrial genome of the hybrid of Hoplobatrachus chinensis (♀)×H. rugulosus (♂) and its phylogeny

The complete mitochondrial genome sequence of the hybrid of Hoplobatrachus chinensis (♀) × H. rugulosus (♂) was obtained in this study. The circular mitochondrial genome was 20,282 bp in length (including extra ND5 genes). Compared with the complete mitogenome of the parents, the results indicated that the mitochondria of the hybrid tiger frog was consistent with a maternal inheritance. Phylogenetic analyses using concatenated nucleotide sequences of the 11 protein-coding genes with two different methods (maximum likelihood and MrBayes analysis) both highly supported a close relationship of the hybrid frogs with the Chinese tiger frog (=H. chinensis).

Complete mitochondrial genomes of Nanorana taihangnica and N. yunnanensis (Anura: Dicroglossidae) with novel gene arrangements and phylogenetic relationship of Dicroglossidae

BACKGROUND

Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. Large-scale mt genomic reorganizations have been observed among many fork-tongued frogs (family Dicroglossidae). The relationships among Dicroglossidae and validation of the genus Feirana are still problematic. Hence, we sequenced the complete mt genomes of Nanorana taihangnica (=F. taihangnica) and N. yunnanensis as well as partial mt genomes of six Quasipaa species (dicroglossid taxa), two Odorrana and two Amolops species (Ranidae), and one Rhacophorus species (Rhacophoridae) in order to identify unknown mt gene rearrangements, to investigate the validity of the genus Feirana, and to test the phylogenetic relationship of Dicroglossidae.

RESULTS

In the mt genome of N. taihangnica two trnM genes, two trnP genes and two control regions were found. In addition, the trnA, trnN, trnC, and trnQ genes were translocated from their typical positions. In the mt genome of N. yunnanensis, three control regions were found and eight genes (ND6, trnP, trnQ, trnA, trnN, trnC, trnY and trnS genes) in the L-stand were translocated from their typical position and grouped together. We also found intraspecific rearrangement of the mitochondrial genomes in N. taihangnica and Quasipaa boulengeri. In phylogenetic trees, the genus Feirana nested deeply within the clade of genus Nanorana, indicating that the genus Feirana may be a synonym to Nanorana. Ranidae as a sister clade to Dicroglossidae and the clade of (Ranidae + Dicroglossidae) as a sister clade to (Mantellidae + Rhacophoridae) were well supported in BI analysis but low bootstrap in ML analysis.

CONCLUSIONS

We found that the gene arrangements of N. taihangnica and N. yunnanensis differed from other published dicroglossid mt genomes. The gene arrangements in N. taihangnica and N. yunnanensis could be explained by the Tandem Duplication and Random Loss (TDRL) and the Dimer-Mitogenome and Non-Random Loss (DMNR) models, respectively. The invalidation of the genus Feirana is supported in this study.

Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes

Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa. In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa, evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini. Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini. By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa, and a cryptic species may also exist in Q. boulengeri. However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri. Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa.

First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order

BACKGROUND

Four species of the genus Donax (D. semistriatus, D. trunculus, D. variegatus and D. vittatus) are common on Iberian Peninsula coasts. Nevertheless, despite their economic importance and overexploitation, scarce genetic resources are available. In this work, we newly determined the complete mitochondrial genomes of these four representatives of the family Donacidae, with the aim of contributing to unveil phylogenetic relationships within the Veneroida order, and of developing genetic markers being useful in wedge clam identification and authentication, and aquaculture stock management.

PRINCIPAL FINDINGS

The complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand. A long non-coding region was identified in each of the four Donax species between cob and cox2 genes, presumably corresponding to the Control Region. The Bayesian and Maximum Likelihood phylogenetic analysis of the Veneroida order indicate that all four species of Donax form a single clade as a sister group of other bivalves within the Tellinoidea superfamily. However, although Tellinoidea is actually monophyletic, none of its families are monophyletic.

CONCLUSIONS

Sequencing of complete mitochondrial genomes provides highly valuable information to establish the phylogenetic relationships within the Veneroida order. Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource.

The complete mitochondrial genome sequence of the Sichuan Digging Frog, Kaloula rugifera (Anura: Microhylidae) and its phylogenetic implications

The Sichuan Digging Frog (Kaloula rugifera) belongs to the family Dicroglossidae, which is endemic to northeastern Sichuan and southernmost Gansu provinces, in southwestern China. In this study, the complete mitochondrial genome of K. rugifera was sequenced. The mitogenome was 17,074bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the K. rugifera is 30.32% A, 25.76% C, 29.72% T, and 14.20% G, which is consistent with the lowest frequency for G content in typical amphibian animals' mitochondrial genomes. The alignment of the Kaloula species control regions exhibited high genetic variability and rich A+T content. Besides, 3 types of tandem repeat units were also identified in the control region. Phylogenetic tree demonstrated that K. rugifera was clustered together with K. borealis and K. verrucosa and they had a close relationship with each other. The complete mitogenome of K. rugifera can provide an important data for the studies on phylogenetic relationship to further explore the taxonomic status of Kaloula species.

Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri

Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.

Do cryptic species exist in Hoplobatrachus rugulosus? An examination using four nuclear genes, the cyt b gene and the complete MT genome

he Chinese tiger frog Hoplobatrachus rugulosus is widely distributed in southern China, Malaysia, Myanmar, Thailand, and Vietnam. It is listed in Appendix II of CITES as the only Class II nationally-protected frog in China. The bred tiger frog known as the Thailand tiger frog, is also identified as H. rugulosus. Our analysis of the Cyt b gene showed high genetic divergence (13.8%) between wild and bred samples of tiger frog. Unexpected genetic divergence of the complete mt genome (14.0%) was also observed between wild and bred samples of tiger frog. Yet, the nuclear genes (NCX1, Rag1, Rhod, Tyr) showed little divergence between them. Despite this and their very similar morphology, the features of the mitochondrial genome including genetic divergence of other genes, different three-dimensional structures of ND5 proteins, and gene rearrangements indicate that H. rugulosus may be a cryptic species complex. Using Bayesian inference, maximum likelihood, and maximum parsimony analyses, Hoplobatrachus was resolved as a sister clade to Euphlyctis, and H. rugulosus (BT) as a sister clade to H. rugulosus (WT). We suggest that we should prevent Thailand tiger frogs (bred type) from escaping into wild environments lest they produce hybrids with Chinese tiger frogs (wild type).

The complete mitochondrial genome of Hyla annectans (Anura: Hylidae)

The complete mitochondrial genome sequence of the Hyla annectans (Anura: Hylidae) was determined in this study. It is a circular molecule of 17,973 bp in length including 37 genes for 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region, showing a typical neobatrachian-type arrangement. The A + T content of H-strand and the control region is 60.7% and 64.6%, respectively. The control region is 2554 bp in length and possesses distinct repeat regions at both 5' and 3' ends.

The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization

Background

Although mitochondrial (mt) gene order is highly conserved among vertebrates, widespread gene rearrangements occur in anurans, especially in neobatrachians. Protein coding genes in the mitogenome experience adaptive or purifying selection, yet the role that selection plays on genomic reorganization remains unclear. We sequence the mitogenomes of three species of Glandirana and hot spots of gene rearrangements of 20 frog species to investigate the diversity of mitogenomic reorganization in the Neobatrachia. By combing these data with other mitogenomes in GenBank, we evaluate if selective pressures or functional constraints act on mitogenomic reorganization in the Neobatrachia. We also look for correlations between tRNA positions and codon usage.

Results

Gene organization in Glandirana was typical of neobatrachian mitogenomes except for the presence of pseudogene trnS (AGY). Surveyed ranids largely exhibited gene arrangements typical of neobatrachian mtDNA although some gene rearrangements occurred. The correlation between codon usage and tRNA positions in neobatrachians was weak, and did not increase after identifying recurrent rearrangements as revealed by basal neobatrachians. Codon usage and tRNA positions were not significantly correlated when considering tRNA gene duplications or losses. Change in number of tRNA gene copies, which was driven by genomic reorganization, did not influence codon usage bias. Nucleotide substitution rates and d_N/d_S ratios were higher in neobatrachian mitogenomes than in archaeobatrachians, but the rates of mitogenomic reorganization and mt nucleotide diversity were not significantly correlated.

Conclusions

No evidence suggests that adaptive selection drove the reorganization of neobatrachian mitogenomes. In contrast, protein-coding genes that function in metabolism showed evidence for purifying selection, and some functional constraints appear to act on the organization of rRNA and tRNA genes. As important nonadaptive forces, genetic drift and mutation pressure may drive the fixation and evolution of mitogenomic reorganizations.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-691) contains supplementary material, which is available to authorized users.

Complete mitogenome sequences of four flatfishes (Pleuronectiformes) reveal a novel gene arrangement of L-strand coding genes

Background

Few mitochondrial gene rearrangements are found in vertebrates and large-scale changes in these genomes occur even less frequently. It is difficult, therefore, to propose a mechanism to account for observed changes in mitogenome structure. Mitochondrial gene rearrangements are usually explained by the recombination model or tandem duplication and random loss model.

Results

In this study, the complete mitochondrial genomes of four flatfishes, Crossorhombus azureus (blue flounder), Grammatobothus krempfi, Pleuronichthys cornutus, and Platichthys stellatus were determined. A striking finding is that eight genes in the C. azureus mitogenome are located in a novel position, differing from that of available vertebrate mitogenomes. Specifically, the ND6 and seven tRNA genes (the Q, A, C, Y, S₁, E, P genes) encoded by the L-strand have been translocated to a position between tRNA-T and tRNA-F though the original order of the genes is maintained.

Conclusions

These special features are used to suggest a mechanism for C. azureus mitogenome rearrangement. First, a dimeric molecule was formed by two monomers linked head-to-tail, then one of the two sets of promoters lost function and the genes controlled by the disabled promoters became pseudogenes, non-coding sequences, and even were lost from the genome. This study provides a new gene-rearrangement model that accounts for the events of gene-rearrangement in a vertebrate mitogenome.

Complete mitochondrial genome of the Antlered sculpin Enophrys diceraus (Scorpaeniformes, Cottidae)

The complete mitochondrial genome (mitogenome) sequence of Enophrys diceraus (Cottidae) was determined for the first time by primer walking methods. It was 16,976 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (CR). Within the CR, the extended termination-associated sequence, the central conserved sequence block (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B, CSB-A) and the conserved sequence block (CSB-1, CSB-2, CSB-3) were identified. This first mitogenome information among marine sculpins is expected to enrich the knowledge on phylogenetic studies of this taxon.

Phylogeographic analyses strongly suggest cryptic speciation in the giant spiny frog (Dicroglossidae: Paa spinosa) and interspecies hybridization in Paa

Species identification is one of the most basic yet crucial issues in biology with potentially far-reaching implications for fields such as conservation, population ecology, and epidemiology. The widely distributed but threatened frog Paa spinosa has been speculated to represent a complex of multiple species. In this study, 254 individuals representing species of the genus Paa were investigated along the entire range of P. spinosa: 196 specimens of P. spinosa, 8 specimens of P. jiulongensis, 5 specimens of P. boulengeri, 20 specimens of P. exilispinosa, and 25 specimens of P. shini. Approximately 1333 bp of mtDNA sequence data (genes 12S rRNA and 16S rRNA) were used. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood and Bayesian inference. BEAST was used to estimate divergence dates of major clades. Results suggest that P. spinosa can be divided into three distinct major lineages. Each major lineage totally corresponds to geographical regions, revealing the presence of three candidate cryptic species. Isolation and differentiation among lineages are further supported by the great genetic distances between the lineages. The bifurcating phylogenetic pattern also suggests an east-west dispersal trend during historic cryptic speciation. Dating analysis estimates that P. spinosa from Western China split from the remaining P. spinosa populations in the Miocene and that P. spinosa from Eastern China diverged from Central China in the Pliocene. We also found that P. exilispinosa from Mainland China and Hong Kong might have a complex of multiple species. After identifying cryptic lineages, we then determine the discrepancy between the mtDNA and the morphotypes in several individuals. This discrepancy may have been caused by introgressive hybridization between P. spinosa and P. shini.

The complete mitochondrial genome of Lithobates catesbeianus (Anura: Ranidae)

The complete mitochondrial genome of Lithobates catesbeianus (Anura: Ranidae) is sequenced to analyze the gene arrangement. It is a circular molecule of 18,241 bp in length including 37 genes typically found in other frogs. The AT content of the overall base composition of L. catesbeianus is 59.9%. The length of control region is 2783 bp with 66.0% AT content. Protein-coding genes begin with ATG as start codon except except ND1 and ATP6 began with ATA, COI and ND4L with GTG, and ND2 with ATT. COI end with AGG as stop codon, COII and ND6 end with AGA, ND2 end with TAG, ATP8. ND4L. ND5 and Cytb end with TAA, and the other five PCGs end with a incomplete stop codon (a single stop nucleotide T).

Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)

Background

A skewed assemblage of two epi-, meso- and bathypelagic fish families makes up the order Myctophiformes – the blackchins Neoscopelidae and the lanternfishes Myctophidae. The six rare neoscopelids show few morphological specializations whereas the divergent myctophids have evolved into about 250 species, of which many show massive abundances and wide distributions. In fact, Myctophidae is by far the most abundant fish family in the world, with plausible estimates of more than half of the oceans combined fish biomass. Myctophids possess a unique communication system of species-specific photophore patterns and traditional intrafamilial classification has been established to reflect arrangements of photophores. Myctophids present the most diverse array of larval body forms found in fishes although this attribute has both corroborated and confounded phylogenetic hypotheses based on adult morphology. No molecular phylogeny is available for Myctophiformes, despite their importance within all ocean trophic cycles, open-ocean speciation and as an important part of neoteleost divergence. This study attempts to resolve major myctophiform phylogenies from both mitogenomic sequences and corroborating evidence in the form of unique mitochondrial gene order rearrangements.

Results

Mitogenomic evidence from DNA sequences and unique gene orders are highly congruent concerning phylogenetic resolution on several myctophiform classification levels, corroborating evidence from osteology, larval ontogeny and photophore patterns, although the lack of larval morphological characters within the subfamily Lampanyctinae stands out. Neoscopelidae is resolved as the sister family to myctophids with Solivomer arenidens positioned as a sister taxon to the remaining neoscopelids. The enigmatic Notolychnus valdiviae is placed as a sister taxon to all other myctophids and exhibits an unusual second copy of the tRNA-Met gene – a gene order rearrangement reminiscent of that found in the tribe Diaphini although our analyses show it to be independently derived. Most tribes are resolved in accordance with adult morphology although Gonichthyini is found within a subclade of the tribe Myctophini consisting of ctenoid scaled species. Mitogenomic sequence data from this study recognize 10 reciprocally monophyletic lineages within Myctophidae, with five of these clades delimited from additional rearranged gene orders or intergenic non-coding sequences.

Conclusions

Mitogenomic results from DNA sequences and unique gene orders corroborate morphology in phylogeny reconstruction and provide a likely scenario for the phylogenetic history of Myctophiformes. The extent of gene order rearrangements found within the mitochondrial genomes of myctophids is unique for phylogenetic purposes.

Complete mitochondrial genome sequence of Catla catla and its phylogenetic consideration

Complete nucleotide sequence of mitochondrial genome (mitogenome) of the Catla catla (Ostariophysi: Cypriniformes: Cyprinidae) was determined in the present study. Its length is 16,594 bp and contains 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs and one non-coding control region. Most of the genes were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. The reading frames of two pair of genes overlapped: ATPase 8 with 6 and ND4L with ND4 by seven nucleotides each. The main non-coding region was 929 bp, with three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and an unusual simple sequence repeat, (TA)(7). Phylogenetic analyses based on complete mitochondrial genome sequences were in favor of the traditional taxonomy of family Cyprinidae. In conclusion present mitogenome of Catla catla adds more information to our understanding of diversity and evolution of mitogenome in fishes.

A de novo case of floating chromosomal polymorphisms by translocation in Quasipaa boulengeri (Anura, Dicroglossidae)

Very few natural polymorphisms involving interchromosomal reciprocal translocations are known in amphibians even in vertebrates. In this study, thirty three populations, including 471 individuals of the spiny frog Quasipaa boulengeri, were karyotypically examined using Giemsa stain or FISH. Five different karyomorphs were observed. The observed heteromorphism was autosomal but not sex-related, as the same heteromorphic chromosomes were found both in males and females. Our results indicated that the variant karyotypes resulted from a mutual interchange occurring between chromosomes 1 and 6. The occurrence of a nearly whole-arm translocation between chromosome no. 1 and no. 6 gave rise to a high frequency of alternate segregation and probably resulted in the maintenance of the translocation polymorphisms in a few populations. The translocation polymorphism is explained by different frequencies of segregation modes of the translocation heterozygote during meiosis. Theoretically, nine karyomorphs should be investigated, however, four expected karyotypes were not found. The absent karyomorphs may result from recessive lethal mutations, position effects, duplications and deficiencies. The phylogenetic inference proved that all populations of Q. boulengeri grouped into a monophyletic clade. The mutual translocation likely evolved just once in this species and the dispersal of the one karyomorph (type IV) can explain the chromosomal variations among populations.

Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae

The monophyly and phylogenetic relationships of Pseudosciaeniae have long been controversial. Here we describe the mitochondrial genome (mitogenome) sequence of Collichthys niveatus. It is a circular double-stranded DNA molecule of 16,450 base pairs (bp) in length with a standard set of 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes as well as a non-coding control region. The mitogenome of C. niveatus shared common features with those of other bony fishes in terms of gene arrangement, base composition, and tRNA structures. The C. niveatus mitogenome exhibited pronounced strand-specific asymmetry in nucleotide composition, which was also reflected in the codon usage of genes oriented in opposite directions. Contrary to the typical structure of the control region, the central conserved blocks (CSB-D, -E, and -F) could not be detected in C. niveatus mitogenome. Phylogenetic analysis based on whole mitogenome sequences provided strong support for the monophyly of Pseudosciaeniae, and sister-group relationships of C. niveatus+Collichthys lucidus and Larimichthys crocea+Larimichthys polyactis, which was consistent with the traditional taxonomy. Unexpected divergence was found in two C. niveatus mitogenomes and several hypotheses were proposed to explain this observation including misidentification and introgressive hybridization between C. niveatus and L. polyactis, and polyphyletic origin of C. niveatus. We considered species misidentification to be the main hypothesis. However, additional data is essential to test these proposed hypotheses.

Mitochondrial genome organization and divergence in hybridizing central European waterfrogs of the Pelophylax esculentus complex (Anura, Ranidae)

Natural transfer of mitochondrial DNA has occurred between three western Palaearctic waterfrog taxa: Pelophylax lessonae, Pelophylax ridibundus and their hybridogenetic hybrid, Pelophylax kl. esculentus. The transfer is asymmetric with most P. kl. esculentus and approximately one third of all central European P. ridibundus having mtDNA derived from P. lessonae (L-mtDNA). We obtained complete nucleotide sequences of multiple mitochondrial genomes (15,376-78 bp without control regions) from all 3 taxa, including a P. ridibundus frog with introgressed L-mtDNA. The gene content and organization of the mitogenomes correspond to those typical of neobatrachians. Divergence between the mtDNAs of P. lessonae and P. ridibundus is high with an uncorrected p-distance of 11.9% across the entire mitogenome. However, the rate of nucleotide substitution depends on the degree of functional constraint with up to 30-fold differences in levels of divergence. In general, mitochondrial genes encoding the translational machinery evolve very slowly, whereas genes encoding polypeptides of the electron transport system, especially the ND genes, evolve rapidly. Only 25 of 211-213 observed amino acid replacements could be classified as radical and are therefore more likely to be exposed to selection. A disproportionately high number of amino acid substitutions has occurred in the ND4, ND4L and cytb genes of the P. lessonae lineage (including 36% of all radical changes). In contrast to the interspecific divergence, nucleotide polymorphism within L- and R-mtDNA is very low: L-mtDNA haplotypes differed on average by only 19 nucleotides, while there was no variation within two mtDNAs derived from P. ridibundus. This is an expected finding considering that we have sampled a post-glacial expansion area. Moreover, the introgressed L-mtDNA on a P. ridibundus background differed from other L-mtDNAs by only a few substitutions, indicative of a very recent introgression event. We discuss our findings in the context of natural selection acting on L-mtDNA and its potential significance in cytonuclear epistasis.

Complete mitochondrial genome sequence of the spinyhead croaker Collichthys lucidus (Perciformes, Sciaenidae) with phylogenetic considerations

The complete mitochondrial genome of the spinyhead croaker Collichthys lucidus was determined using long-PCR and primer walking methods. It is a circular molecule of 16,451 bp in length with a standard set of 22 tRNAs, 2 rRNAs, 13 protein-coding genes as well as a non-coding control region in the same order as those of the other bony fishes. C. lucidus mitogenome exhibited a clear strand-specific bias in nucleotide composition, as evidence by a GC- skew of the H-strand of -0.319. The strand-specific bias was also reflected in the codon usage of genes oriented in opposite directions. All tRNA genes except for tRNA( Ser(AGY)) harbored the typical cloverleaf secondary structures and possessed anticodons that matched the vertebrate mitochondrial genetic code. Contrary to the typical structure of control region consistig of TAS, central, and CSB domains, there were no central conserved blocks available in C. lucidus mitogenome. Despite extensive studies based on both morphology and molecules, phylogenetic position of C. lucidus with Sciaenidae is still controversial. Our phylogenetic results provided more evidence to support previous morphological studies and consistently placed C. lucidus as a sister taxon to Collichthys niveatus, with both of these taxa forming the monophyletic Collichthys.

Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, Hoplobatrachus tigerinus and Euphlyctis hexadactylus, from Bangladesh

We determined the complete nucleotide sequences of mitochondrial (mt) genomes from two dicroglossid frogs, Hoplobatrachus tigerinus (Indian Bullfrog) and Euphlyctis hexadactylus (Indian Green frog). The genome sizes are 20462 bp in H. tigerinus and 20280 bp in E. hexadactylus. Although both genomes encode the typical 37 mt genes, the following unique features are observed: 1) the ND5 genes are duplicated in H. tigerinus that have completely identical sequences, whereas duplicated ND5 genes in E. hexadactylus possessed dissimilar substitutions; 2) duplicated control region (CR) in H. tigerinus has almost identical sequences whereas single control region (CR) was found in E. hexadactylus; 3) the tRNA-Leu (CUN) gene is translocated from the LTPF tRNA cluster to downstream of ND5-1 in H. tigerinus, and the tRNA-Pro gene is translocated from the LTPF tRNA cluster to downstream of CR in E. hexadactylus; 4) pseudo tRNA-Leu (CUN) and tRNA-Pro genes are observed in E. hexadactylus; and 5) two tRNA-Met genes are encoded in both species, as observed in the previously reported dicroglossid mt genomes. Almost all observed gene rearrangements in H. tigerinus and E. hexadactylus can be explained by the tandem duplication and random loss model, except translocation of tRNA-Pro in E. hexadactylus. The novel mt genomic features found in this study may be useful for future phylogenetic studies in the dicroglossid taxa. However, the mt genome with interesting features found in the present study reveal a high level of variation of gene order and gene content, inspiring more research to understand the mechanisms behind gene and genome evolution in the dicroglossid and as well as in the amphibian taxa in future studies.

Complete mitochondrial DNA sequence and phylogenetic analysis of Zhikong scallop Chlamys farreri (Bivalvia: Pectinidae)

The complete mitochondrial genome of Zhikong scallop Chlamys farreri is 21,695 bp in length and contains 12 protein-coding genes (the atp8 gene is absent, as in most bivalves), 2 ribosomal RNA genes, and 22 transfer RNA genes. The heavy strand has an overall A+T content of 58.7%. GC and AT skews for the mt genome of C. farreri are 0.337 and -0.184, respectively, indicating the nucleotide bias against C and A. The mitochondrial gene order of C. farreri differs drastically from the scallops Argopecten irradians, Mimachlamys nobilis and Placopecten magellanicus, which belong to the same family Pectinidae. 6623 bp non-coding nucleotides exist intergenically in the mitogenome of C. farreri, with a large continuous sequence (4763 bp) between tRNA ( Val ) and tRNA ( Asn ). Two repeat families are found in the large continuous sequence, which seems to be a common feature of scallops. Phylogenetic analysis based on 12 concatenated amino acid sequences of protein-coding genes supports the monophyly of Pectinidae and paraphyletic Pteriomorphia with respect to Heteroconchia.