Mitochondrial Gene Arrangement Research Articles

The mitochondrial genome of Leuctra sp. (Plecoptera: Leuctridae) and its performance in phylogenetic analyses.

The nearly complete mitochondrial genome (mitogenome) of Leuctra sp. (Plecoptera: Leuctridae) was sequenced. The 14,585-bp long mitogenome of L. sp. contained 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). The mitochondrial gene arrangement of L. sp. was identical with other stoneflies and the putative ancestral mitogenome of Drosophila yakuba Burla. Most PCGs used standard ATN start codons and TAN termination codons. Twenty-one of the 22 tRNAs in each mitogenome exhibited the cloverleaf secondary structures, while the dihydrouridine (DHU) arm of trnSer (AGN) was reduced. Phylogenetic analyses using our new Leuctra sp. genome and all other publicly available genomes for Plecoptera and Bayesian inference (BI) and maximum likelihood methods (ML) generated identical topologies, both supporting the monophyly of all stonefly families for which tests were possible and the infraorder Systellognatha. Scopuridae and Gripopterygidae were grouped with the infraorder Euholognatha. The final relationships within Plecoptera were recovered as (((((Perlodidae + Chloroperlidae) + Perlidae) + Pteronarcyidae) + Peltoperlidae) + Styloperlidae) + (((((Capniidae + Taeniopterygidae) + Nemouridae) + Scopuridae) + Leuctridae) + Gripopterygidae).

Comparative analysis of camelid mitochondrial genomes

Camelus dromedarius has played a pivotal role in both culture and way of life in the Arabian peninsula, particularly in arid regions where other domestic animals cannot be easily domesticated. Although, the mitochondrial genomes have recently been sequenced for several camelid species, wider phylogenetic studies are yet to be performed. The features of conserved gene elements, rapid evolutionary rate, and rare recombination make the mitochondrial genome a useful molecular marker for phylogenetic studies of closely related species. Here we carried out a comparative analysis of previously sequenced mitochondrial genomes of camelids with an emphasis on C. dromedarius, revealing a number of noticeable findings. First, the arrangement of mitochondrial genes in C. dromedarius is similar to those of the other camelids. Second, multiple sequence alignment of intergenic regions shows up to 90% similarity across different kinds of camels, with dromedary camels to reach 99%. Third, we successfully identified the three domains (termination-associated sequence, conserved domain and conserved sequence block) of the control region structure. The phylogenetic tree analysis showed that C. dromedarius mitogenomes were significantly clustered in the same clade with Lama pacos mitogenome. These findings will enhance our understanding of the nucleotide composition and molecular evolution of the mitogenomes of the genus Camelus, and provide more data for comparative mitogenomics in the family Camelidae.

Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders

BackgroundIn recent years, Next Generation Sequencing (NGS) has accelerated the generation of full mitogenomes, providing abundant material for studying different aspects of molecular evolution. Some mitogenomes have been observed to harbor atypical sequences with bizarre secondary structures, which origins and significance could only be fully understood in an evolutionary framework.ResultsHere we report and analyze the mitochondrial sequences and gene arrangements of six closely related spiders in the sister genera Parachtes and Harpactocrates, which belong to the nocturnal, ground dwelling family Dysderidae. Species of both genera have compacted mitogenomes with many overlapping genes and strikingly reduced tRNAs that are among the shortest described within metazoans. Thanks to the conservation of the gene order and the nucleotide identity across close relatives, we were able to predict the secondary structures even on arm-less tRNAs, which would be otherwise unattainable for a single species. They exhibit aberrant secondary structures with the lack of either DHU or TΨC arms and many miss-pairings in the acceptor arm but this degeneracy trend goes even further since at least four tRNAs are arm-less in the six spider species studied.ConclusionsThe conservation of at least four arm-less tRNA genes in two sister spider genera for about 30 myr suggest that these genes are still encoding fully functional tRNAs though they may be post-transcriptionally edited to be fully functional as previously described in other species. We suggest that the presence of overlapping and truncated tRNA genes may be related and explains why spider mitogenomes are smaller than those of other invertebrates.

The conserved mitochondrial genomes of Drosophila mercatorum (Diptera: Drosophilidae) with different reproductive modes and phylogenetic implications

Fruit flies (Drosophilidae: Drosophila) are commonly found in daily life and have long been used as model organisms in biology researches. Drosophila mercatorum is one important member of the Drosophila genus and has been used to study centrosome assembly of cells. In this study, we sequenced and analyzed the mitochondrial genome (mitogenome) of D. mercatorum, finding that it contains the typical structure of 37 genes and a control region. The arrangement of mitochondrial genes is in accordance with that in other Drosophila species, which is considered the ancestral organization of insects' mitogenomes. Phylogenetic analyses were performed based on 23 species of Drosophila. Our results supported two monophyletic subgenera, Drosophila and Sophophora, except for D. willistoni which was presented as an early offshoot of Drosophila. The topology ((D. yakuba + D. erecta) + D. melanogaster) was supported. We further compared the mitogenomes of parthenogenesis and sexual reproduction strains of D. mercatorum. However, only one synonymous mutation in COI gene was identified, indicating mitogenomic evolution is not strongly correlated with the different reproductive modes of this species. Taken together, our results demonstrate that mitogenome is an effective molecular marker that can be further used in phylogenetic studies of Drosophila and other organisms.

Characterization of the complete mitochondrial genome of Brentisentisyangtzensis Yu & Wu, 1989 (Acanthocephala, Illiosentidae).

The mitogenome of Brentisentisyangtzensis is 13,864 bp in length and has the circular structure typical of metazoans. It contains 36 genes: 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and 12 protein-encoding genes (PCGs). All genes are transcribed from the same strand. Thirteen overlapping regions were found in the mitochondrial genome. The overall A+T content of B.yangtzensis is 68.3% versus 31.7% of G+C content (A = 27.8%, T = 40.5%, C = 9.0%, G = 22.7%). B.yangtzenensis (Illiosentidae) and Leptorhynchoidesthecatus (Rhadinorhynchidae) form a sister clade, showing the relatively close relationship between the Illiosentidae and the Rhadinorhynchidae. The mitochondrial gene arrangements of acanthocephalan species are relatively conserved, with only a few translocations of tRNAs (trnS1, trnS2, trnV, and trnK) detected. An identical gene order was found both in a sister clade (Centrorhynchusaluconis and Plagiorhynchustransversus) and across different classes (B.yangtzensis (Palaeacanthocephala), Acanthosentischeni (Eoacanthocephala) and Macracanthorhynchushirudinaceus (Archiacanthocephala), Oncicolaluehei and L.thecatus (Palaeacanthocephala)). More studies and more sequences of acanthocephalan species are needed to gain a clear understanding of the phylogenetic relationships.

A complete mitochondrial DNA genome of whitefly species (Hemiptera: Aleyrodidae) from Litchi chinensis

A novel complete mitochondrial genome (mitogenome) of whitefly species, collected from Litchi chinensis at Fujian province of China (hereafter whitefly_Litchi chinensis _China) (GenBank accession number: MH999477), was described in this study. The mitogenome of whitefly_Litchi chinensis _China is 15,360 bp in length and contains 13 protein-coding genes, 21 transfer RNAs, 2 ribosomal RNAs and a non-coding AT-rich region (D-loop). The arrangement of mitochondrial genes of whitefly_Litchi chinensis_China are identical with Aleurochiton aceris, but remarkably different from the mitogenomes of the other whitefly genus. Most protein-coding genes (PCGs) start with ATN, except for nad2, cox2 and atp6 genes starting with TTG, GTG, and TTG, respectively; 10 of the 13 PCGs use the typical stop codon TAN, whereas cox1, and cox2 stop with a single T. Phylogenetic analyses based on 13 PCGs support the close relationship of the sample with Aleurochiton aceris, which would provide us further insights on the taxonomy and phylogeny of Aleyrodidae.

Characterization of the complete mitochondrial genome of Agapornis personatus and its phylogenetic analysis

In this study, we characterized the complete mitochondrial genome of Agapornis personatus. Its mitochondrial genome is a circular molecule of 16,722 bp, with all genes exhibiting typical mitochondrial gene arrangement and transcribing directions. The overall base composition is 21.49% T, 34.6% C, 29.66% A, and 14.25% G. Phylogenetic analysis of the complete mitogenome was conducted using the neighbour-joining method based on 16 parrot species. Phylogenetic tree suggested that A. personatus was closest to the same genus specie Agapornis roseicollis. The results would be useful for further studies on molecular evolution and breeding works of A. personatus.

Complete mitochondrial genome of Agapornis lilianae (Psittaciformes: Psittacidae), with its phylogenetic analysis

In this paper, we reported the complete mitogenome of Agapornis lilianae. A. lilianae mitogenome is 16,720bp base pairs long. The overall base compositions of complete mitogenomes of A. lilianae is 29.66% A, 21.5% T, 34.59% C, 14.25% G. All genes exhibit the typical mitochondrial gene arrangement and transcribing directions. The phylogenetic analysis based on 21 mitochondrial sequence data suggested that A. lilianae are closely related to the same genus specie Agapornis roseicollis. The results obtained here would be useful for the conservation and phylogeny of A. lilianae.

The complete mitochondrial genome sequence of Yarkand hare (Lepus yarkandensis)

We first reported the mitochondrial genome of Lepus yarkandensis. The mitogenome of L. yarkandensis contains 17,011 base pairs. The overall base composition of complete mitogenome is 28.13% A, 27.67% T, 22.02% C, and 22.17% G, with 44.20% of the GC content. All genes exhibit the typical mitochondrial gene arrangement and transcribing directions. Phylogenetic analysis of 9 Lepus species was performed based on the sequence of cytochrome b gene using the Maximum Likelihood method in MEGA 7.0. The results suggested that L. yarkandensis is closely related to Lepus timidus. The results are helpful to future studies on molecular evolution, population genetics, and wildlife protection of L. yarkandensis.

Complete mitochondrial genome and phylogenetic analysis of Stonogobiops yasha (Perciformes, Gobiidae)

The complete mitochondrial genome sequence of Stonogobiops yasha was first determined in this study. The circle genome was 16,566 bp long and consisted of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. The mitochondrial gene arrangement of S. yasha is similar to those of most other gobies. The phylogenetic analysis using the neighbor-joining method showed that the kinship between Stonogobiops and Acentrogobius is closer than those between Stonogobiops and other selected genera. This is the first record of the complete mitogenome for the genus Stonogobiops.

Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients

Deaminations (A->G, C->T) increase with DNA singlestrandedness during replication, presumably creating spontaneous genomic mutational and nucleotide frequency gradients. Alternatively, genes are positioned to avoid deaminations. Deamination gradients affect directly mitogene third codon positions; conserved vertebrate mitochondrial tRNA and protein coding gene arrangements minimize deaminations in anticodons, and first and second codon positions in mitogenes. Here we describe deamination gradients across theoretical minimal RNA rings, 22 nucleotide-long RNAs designed to simulate prebiotic RNAs. These RNA rings code for a start/stop codon and a single codon for each amino acid, and form stem-loop hairpins slowing degradation. They resemble consensus tRNAs, defining potential anticodons and cognate amino acids. Theoretical minimal RNA rings are not designed to include deamination gradients, yet deamination gradients occur in RNA rings. tRNA homology produces stronger evidence for deamination gradients than RNA ring homology defined by coding properties. Deamination gradients start at predicted RNA ring anticodons, corresponding to known homologies between mitochondrial tRNAs and replication origins, and between bacterial tRNA synthetases and mitochondrial DNA polymerase gamma. Deamination gradients are strongest for RNA rings with predicted anticodons matching cognate amino acids that integrated early the genetic code. Presumably protections against deaminations evolved while amino acids integrated the genetic code. Results confirm tRNA-RNA ring homologies. Coding constraints defining RNA rings presumably produce deamination gradients starting at predicted anticodons. Hence, the universal genetic code determines nucleotide deamination gradients in theoretical minimal RNA rings, suggesting adaptation to prevent consequences of deamination mutations. Results also indicate that the genetic code's structure determined evolution of tRNAs, their cognates, tRNA synthetases, and polymerases.

Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes

Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangement. However, two types of gene arrangement have been identified in the mitochondrial genomes (mitogenomes) of Anguilliformes. Here, a newly sequenced mitogenome of Ophichthus brevicaudatus (Anguilliformes; Ophichthidae) was presented. The total length of the O. brevicaudatus mitogenome was 17,773 bp, and it contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and two identical control regions (CRs). The gene order differed from that of the typical vertebrate mitogenomes. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The duplication-random loss model was adopted to explain the gene rearrangement events in this mitogenome. The most comprehensive phylogenetic trees of Anguilliformes based on complete mitogenome was constructed. The non-monophyly of Congridae was well supported, whereas the non-monophyly of Derichthyidae and Chlopsidae was not supported. These results provide insight into gene arrangement features of anguilliform mitogenomes and lay the foundation for further phylogenetic studies on Anguilliformes.

Microsatellite loci and the complete mitochondrial DNA sequence characterised through next-generation sequencing and de novo genome assembly, and a preliminary assessment of population genetic structure for the Australian crane, Antigone rubicunda

The Brolga ( Antigone rubicunda) is a large Australian crane species with a broad distribution spanning from the tropical north to the south-eastern regions of the continent. Brolga populations throughout New South Wales, Victoria and South Australia have been in decline since the early twentieth century, with the species being listed as vulnerable in each state. To aid future conservation of the species, its taxonomic status needs to be validated, and patterns of gene flow and population connectivity across the species distribution need to be understood. To assist future genetic studies, we developed a suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence by next-generation sequencing. A total of 18 polymorphic loci were characterised using DNA extractions from 47 individuals, comprising 30 and 17 individuals from Victoria and northern Australia, respectively. We observed moderate genetic variation across loci with only a single locus deviating significantly from Hardy–Weinberg equilibrium. De novo and reference-based genome assemblies were used to assemble the A. rubicunda mitochondrial genome sequence, which consists of 16,700 base pairs, and a typical metazoan mitochondrial gene content and arrangement. We test these new markers by conducting a preliminary analysis of genetic structure between south-eastern and northern Australian Brolga populations. Mitochondrial analyses provided evidence of shared haplotypes across the species range supporting the conspecific status of extant populations, while microsatellite markers indicated weak but significant genetic differentiation suggesting gene flow is limited. We discuss the implications of these findings and the benefits that these genetic markers will provide for future population genetic research on this iconic Australian bird species.

Gene annotation errors are common in the mammalian mitochondrial genomes database

BackgroundAlthough animal mitochondrial DNA sequences are known to evolve rapidly, their gene arrangements often remain unchanged over long periods of evolutionary time. Therefore, comparisons of mitochondrial genomes may result in significant insights into the evolution both of organisms and of genomes. Mammalian mitochondrial genomes recently published in the GenBank database of NCBI show numerous rearrangements in various regions of the genome, from which it may be inferred that the mammalian mitochondrial genome is more dynamic than expected. However, it is alternatively possible that these are errors of annotation and, if so, are misleading our interpretations. In order to verify these possible errors of annotation, we performed a comparative genomic analysis of mammalian mitochondrial genomes available in the NCBI database.ResultsUsing a combination of bioinformatics methods to carefully examine the mitochondrial gene arrangements in 304 mammalian species, we determined that there are only two sets of gene arrangements, one that is shared by all of the marsupials and another that is shared by all of the monotremes and eutherians, with these two arrangements differing only by the positions of tRNA genes in the region commonly designated as “WANCY” for the genes it comprises. All of the 68 other cases of reported gene rearrangements are errors. We note that there are also numerous errors of impossibly short, incorrect gene annotations, cases where genomes that are reported as complete are actually missing portions of the sequence, and genes that are clearly present but were not annotated in these records.ConclusionsWe judge that the application of simple bioinformatic tools in the verification of gene annotation, particularly for organelle genomes, would be a very useful enhancement for the curation of genome sequences submitted to GenBank.

Complete mitochondrial genome of Stethojulis Strigiventer (Labriformes, Labridae): mitogenome characterization and phylogenetic analysis

Stethojulis strigiventer is a tropical reef-associated marine fish belonging to the family Labridae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of S. strigiventer. The complete mitochondrial genome is 16,524 bp length and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 11 species showed that Stethojulis strigiventer is clustered together with the genus Parajulis and Halichoeres and rooted with other Labridae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues of the Labriformes and studying conservation genetics.

Characterization of the complete mitochondrial genome of Periophthalmus modestus (Gobiiformes, Oxudercidae) and phylogenetic analysis

The complete mitochondrial genome was determined for the shuttles hoppfish Periophthalmus modestus belonging to the family Oxudercidae. The length of the complete mitochondrial genome is 16,510 bp and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 15 species showed that P. modestus formed a well-supported monophyletic group with genus Periophthalmus species and rooted with other Oxudercidae species.

Characterization of the complete mitochondrial genome of Sphaeramia orbicularis (Kurtiformes, Apogonidae)

The complete mitochondrial genome was determined for the orbicular cardinalfish Sphaeramia orbicularis belonging to the family Apogonidae. The length of the complete mitochondrial genome is 16,458 bp and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 9 species showed that S. orbicularis formed a well-supported monophyletic group with other Apogonidae species.

Complete mitogenomes of two Psittacula species, P. derbiana and P. eupatria

In this paper, we first reported the complete mitogenomes of Psittacula derbiana and Psittacula eupatria. Respectively, P. derbiana and P. eupatria mitogenomes are 16,887 and 17,139 bp base pairs long. The overall base compositions of complete mitogenomes of P. derbiana and P. eupatria are 30.9% A, 22.4% T, 32.8% C, 13.9% G and 31.7% A, 22.0% T, 33.2% C, 13.1% G, respectively. All genes exhibit the typical mitochondrial gene arrangement and transcribing directions. The Neighbor-joining analysis suggested that Psittacula species are closely related to Eclectus roratus. The results obtained here could contribute to future studies on molecular evolution and population genetics in Psittacula species.

The complete mitochondrial genome of an eelpout Lycodes ygreknotatus (Teleostei: Zoarcidae)

Here, we report the complete mitochondrial genome of the eelpout Lycodes ygreknotatus. The mitogenome is 16,486 bp in length and has the typical vertebrate mitochondrial gene arrangement, which contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one D-loop region. The overall nucleotide base composition of L. ygreknotatus is 26.29%, 25.32%, 30.43%, and 17.96% for A, T, C, and G, respectively. Phylogenetic analysis of 14 fish species showed that L. ygreknotatus and Lycodes toyamensis were clustered into one branch.

Complete mitochondrial genome of Pristicon trimaculatus (Kurtiformes, apogonidae): mitogenome characterization and phylogenetic analysis

Pristicon trimaculatus is a tropical reef-associated marine fish belonging to the family Apogonidae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of P. trimaculatus. The complete mitochondrial genome is 16,512 bp length and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of nine species showed that P. trimaculatus formed a monophyletic group with other Apogonidae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues of the Kurtiformes.