tRNA Pro Gene Research Articles

The Mitogenome of the Subarctic Octocoral Alcyonium digitatum Reveals a Putative tRNAPro Gene Nested within MutS.

We sequenced and analyzed the complete mitogenome of a Norwegian isolate of the octocoral Alcyonium digitatum using the Ion Torrent sequencing technology. The 18,790 bp circular mitochondrial genome was found to harbor the same set of 17 genes, which encode 14 protein subunits, two structural ribosomal RNAs and one tRNA, as reported in other octocorals. In addition, we detected a new tRNAPro-like gene sequence nested within the MutS protein coding region. This putative tRNA gene feature appears to be conserved among the octocorals but has not been reported previously. The A. digitatum mitogenome was also shown to harbor an optional gene (ORFA) that encodes a putative protein of 191 amino acids with unknown function. A mitogenome-based phylogenetic analysis, presented as a maximum likelihood tree, showed that A. digitatum clustered with high statistical confidence with two other Alcyonium species endemic to the Mediterranean Sea and the Southeast Pacific Ocean.

Human T-cell leukemia virus type 1 uses a specific tRNAPro isodecoder to prime reverse transcription.

Human T-cell leukemia virus type 1 (HTLV-1) is the only oncogenic human retrovirus discovered to date. All retroviruses are believed to use a host cell tRNA to prime reverse transcription (RT). In HTLV-1, the primer-binding site (PBS) in the genomic RNA is complementary to the 3' 18 nucleotides (nt) of human tRNAPro The human genome encodes 20 cytoplasmic tRNAPro genes representing seven isodecoders, all of which share the same 3' 18 nt sequence but vary elsewhere. Whether all tRNAPro isodecoders are used to prime RT in cells is unknown. A previous study showed that a 3' 18 nt tRNAPro-derived fragment (tRFPro) is packaged into HTLV-1 particles and can serve as an RT primer in vitro. The role of this tRNA fragment in the viral life cycle is unclear. In retroviruses, N1-methylation of the tRNA primer at position A58 (m1A) is essential for successful plus-strand transfer. Using primer-extension assays performed in chronically HTLV-1-infected cells, we found that A58 of tRNAPro is m1A-modified, implying that full-length tRNAPro is capable of facilitating successful plus-strand transfer. Analysis of HTLV-1 RT primer extension products indicated that full-length tRNAPro is likely to be the primer. To determine which tRNAPro isodecoder is used as the RT primer, we sequenced the minus-strand strong-stop RT product containing the intact tRNA primer and established that HTLV-1 primes RT using a specific tRNAPro UGG isodecoder. Further studies are required to understand how this primer is annealed to the highly structured HTLV-1 PBS and to investigate the role of tRFPro in the viral life cycle.

Comparative Analysis of Complete Mitochondrial Genome of Ariosoma meeki (Jordan and Snider, 1900), Revealing Gene Rearrangement and the Phylogenetic Relationships of Anguilliformes

The mitochondrial genome structure of a teleostean group is generally considered to be conservative. However, two types of gene arrangements have been identified in the mitogenomes of Anguilliformes. In this study, we report the complete mitochondrial genome of Ariosoma meeki (Anguilliformes (Congridae)). For this research, first, the mitochondrial genome structure and composition were analyzed. As opposed to the typical gene arrangement pattern in other Anguilliformes species, the mitogenome of A. meeki has undergone gene rearrangement. The ND6 and the conjoint tRNA-Glu genes were translocated to the location between the tRNA-Thr and tRNA-Pro genes, and a duplicated D-loop region was translocated to move upstream of the ND6 gene. Second, comparative genomic analysis was carried out between the mitogenomes of A. meeki and Ariosoma shiroanago. The gene arrangement between them was found to be highly consistent, against the published A. meeki mitogenomes. Third, we reproduced the possible evolutionary process of gene rearrangement in Ariosoma mitogenomes and attributed such an occurrence to tandem repeat and random loss events. Fourth, a phylogenetic analysis of Anguilliformes was conducted, and the clustering results supported the non-monophyly hypothesis regarding the Congridae. This study is expected to provide a new perspective on the A. meeki mitogenome and lay the foundation for the further exploration of gene rearrangement mechanisms.

Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae.

The family Ophichthidae has the largest number and the most various species (about 359 valid species) in the order Anguilliformes worldwide. Both morphological and molecular characteristics have been used to assess their taxonomic status. However, due to the ambiguous morphological features, molecular data such as mitochondrial DNA sequences have been implemented for the correct identification and classification of these fishes. In this study, the gene arrangement and structure characteristics of two Ophichthidae mitochondrial genomes were investigated for the first time. The total mitogenome lengths of O. evermanni and O. erabo were 17,759 bp and 17,856 bp, respectively. Comparing with the ancestral mitochondrial gene order, the irregular gene rearrangement happened between ND6 and tRNA-Pro (P) genes with another similar control region emerging between tRNA-Thr (T) and ND6 genes, which could be explained by the tandem duplication and random loss (TDRL) model appropriately. ML phylogenetic tree demonstrated that the family Ophichthidae was monophyletic origin, but genus Ophichthus might be polyphyletic because of the confused cluster relationships among different species.

A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA.

Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.

Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae.

Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes’ sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.

The complete mitochondrial genome of Hapalogenys analis (Perciformes, Haemulidea) except for control region, obtained by whole genome sequencing

In this study, we obtained the complete mitochondrial genome of Hapalogenys analis using whole genome sequencing. With the exception for control region, this mitochondrial genome, consisting of 16,355 base pairs (bp), contains 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 21 transfer RNAs (tRNAs). This mitochondrial genome also lacks a tRNA-Pro gene after tRNA-Thr gene. The overall base composition shows 25.45% of T, 29.73% of C, 28.68% of A and 16.14% of G, with a slight A + T rich feature (54.13%). Sanger sequencing is needed to confirm the accuracy of control region, as well as the lack of tRNA-Pro gene. The mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

The complete mitochondrial genome of the Garra tibetana (Cypriniformes: Cyprinidae)

The Garra tibetana, an important economic fish belonging to the genus Garra, family Cyprinidae, is mainly distributed in Tibet with rare biological resources. Here, we sequenced and characterized the complete mitochondrial genome of G. tibetana for the first time, and the results showed that the total length of G. tibetana mitogenome was 16,861 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 control regions. Unlike the typical mitochondrial genome organization in vertebrate, the D-loop region was separated into two part by a tRNAPro gene. To further explore the phylogenetic relationship of the G. tibetana, we constructed the phylogenetic tree and verified that the G. tibetana was a new species of the genus Garra and had a closer relationship with Garra kempi. This study not only provided valuable evidence on phylogenetic relationship of the G. tibetana at the molecular level, but also provided an essential resource for further population genetics research and germplasm conservation on this species.

Complete mitochondrial genome of South American sea lion Otaria byronia (Carnivora: Otariidae)

The complete mitochondrial genome of Otaria byronia was sequenced for the first time. The mitogenome is 16,640 bp long and encodes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, one origin of light strand replication (OL), and a control region (CR). The overall base composition is 33.1%, 27.0%, 14.2%, and 25.7% for A, C, G, and T, respectively. The CR with 1186 bp is in the position between tRNA-Phe and tRNA-Pro genes. Phylogenetic analyses show the classification status of the pinniped species and reveal that O. byronia is grouped to the Family Otariidae.

Next-generation sequencing yields a nearly complete mitochondrial genome of The Yarkand toad-headed agama (Phrynocephalus axillaris) from the Turpan Depression

The Yarkand toad-headed agama, Phrynocephalus axillaris, is endemic to an arid region in Northwest China from the Taklamakan Desert eastward to Dunhuang and Turpan depressions. A nearly complete mitochondrial genome of one individual from the Turpan Depression was determined using next-generation sequencing. The mitogenome is 15,883 bp in length, comprising two ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and a control region (CR). The gene arrangement and composition is similar to those of other Agaminae lizards, albeit with one part of CR (651 bp) existing between the tRNA-Thr gene and tRNA-Pro gene and another part of CR (with 107 bp already sequenced) inserting between the tRNA-Phe and 12S rRNA. Bayesian phylogenetic analyses confirmed the monophyly of both genus Phrynocephalus and its viviparous species. The mitogenome sequence may provide fundamental data to investigate altitude-related evolution of mitochondrial genes in Phrynocephalus.

The phylogenomic position of the Critically Endangered Largetooth Sawfish Pristis pristis (Rhinopristiformes, Pristidae), inferred from the complete mitochondrial genome

The complete mitogenome of the Critically Endangered Largetooth Sawfish Pristis pristis (Rhinopristiformes, Pristidae) is presented in this study. The genome is 16,912 bp in length with a nucleotide base composition of 32.0% A, 26.5% C, 13.2% G, and 28.3% T, containing 37 genes typical of vertebrates. Two start (GTG and ATG) and two stop (TAG and TAA/T) codons are found in the protein-coding genes. The 22 tRNA genes range from 66 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The tRNA-Pro gene is duplicated with an unknown sequence between the two copies. Bayesian phylogenetic reconstruction showed that P. pristis clusters with the Pristis clade with strong posterior probability (100%).

The complete mitochondrial genomes of two schizothoracine fishes (Teleostei, Cypriniformes): A novel minisatellite in fish mitochondrial genomes

Minisatellites, a class of variable number tandem repeats (VNTRs), are abundant throughout the control region in animal mitochondrial DNA (mtDNA) but rare in other regions of animal mtDNA. Here, we reported a novel minisatellite in fish mitochondrial genomes. We first determined the complete mitochondrial genomes of two schizothoracine fishes (Herzensteinia microcephalus and Schizopygopsis pylzovi) and found a type of minisatellites in a novel region between the tRNA-Thr and tRNA-Pro genes in their mtDNA. To explore the origin and evolution of the minisatellites in different schizothoracine and closely related fishes, we analyzed the available 80 fish mitogenomes which represent five closely related tribes of cyprinine fishes. The results from the phylogenetic analyses show that the schizothoracine fishes sensu stricto is not a monophyletic group and is divided into two clades (Schizothoracini and Schizopygopsini); and the minisatellite is only present in Schizopygopsini distributed in the region between the two tRNA genes (tRNA-Thr and tRNA-Pro) of the mtDNA. This is the first record of a minisatellite in a non-control region of fish mitogenome.

Complete mitogenome of the toad species Oreolalax multipunctatus (Anura: Megophryidae) and phylogenetic analyses of Megophryidae

Oreolalax multipunctatus: is a type of alpine toad species belonging to Megophryidae. Here we firstly determined the complete mitochondrial genome of the species. It has a total length of 17,358 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 23 tRNA genes and a control region. Different from the typical type of gene organization in amphibian mitochondrial genomes, the new mitochondrial genome has a tandem duplication of tRNA-Met gene and a translocation of tRNA-Trp gene from the typical “WANCY” region to the position between the tRNA-Pro gene and control region. Phylogenetic analyses using mitochondrial genomes of 19 Megophryidae species supported Megophryidae as a monophyletic group containing three subfamilies with the relationship as [Megophryinae, (Leptolalaginae, Leptobrachiinae)].

The complete mitochondrial genome of Myanmar warty newt Tylototriton shanorum (Salamandridae: Tylototriton)

Tylototriton shanorum, an endemic species of Myanmar, is threatened by illegal capture and environmental destruction. Here, the complete mitochondrial genome (mitogenome) of T. shanorum is described. The entire mitogenome sequence of T. shanorum is 17,096 bp long, containing 13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes, one control region. In addition, two additional 3′ Cytb like sequences and two complete tRNAThr genes, one pseudo tRNAThr, and three noncoding sequences (NC1, NC1′ and NC2) were situated between Cytb and tRNAPro genes. The new complete mitogenome sequence of T. shanorum will be useful for conservation genetics, evolutionary biology, phylogeography, as well as phylogenetic relationships studies of this threatened species.

The entire mitochondrial genome of Vietnam Warty Newt Paramesotriton deloustali (Salamandridae: Paramesotriton) with a new distribution record from China

The Vietnam Warty Newt (Paramesotriton deloustali) is threatened by habitat loss and illegal capture for traditional medicines use and domestic pet trade. In this study, we described the complete mitochondrial genome (mitogenome) of P. deloustali. The entire mitogenome sequence of P. deloustali is 16,391 bp long, containing 13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes, one control region and an additional 261 bp non-coding sequence between tRNAThr and tRNAPro genes. Our new data of the complete mitogenome of P. deloustali will offer solid genetic information for further conservation genetics research of this threatened species.

The complete mitochondrial genome of Euphlyctis karaavali (Amphibia: Anura) with a note on its range expansion

The complete mitochondrial genome of skittering frog Euphlyctis karaavali (Karaavali Skittering Frog) was sequenced. The mitogenome is a circular molecule of 15,505 bp in length containing 13 protein-coding genes, two ribosome RNA genes, 21 transfer RNA (tRNA) genes and a non-coding D-loop region (control region). Its gene arrangements are similar to the typical neobatrachian-type except for the loss of tRNAPro gene. Our data which represent the first mitogenome for the species Euphlyctis karaavali is a newly reported species and known only from the type locality (coastal plain of Karnataka, India) at an elevation of 2 m Mean Sea Level. Our data revealed that the geographical distribution range of this species is extended up to the southern part of Kerala State and recorded at an elevation of 68 m from the Mean Sea Level. Our data will serve as a reference for further studies on the conservation genetics of the Euphlyctis genus in India.

The complete mitochondrial genome sequence of spotted linsang (Prionodon pardicolor pardicolor)

In this study, the complete mitochondrial genome sequence of Prionodon pardicolor pardicolor has been reported for the first time in China. The total length of the mitogenome was 16,689 bp. It contained the typical structure, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop). tRNASer lost the stem of DHC loop and failed to form a typical cloverleaf secondary structure. Mitochondrial control region of P. p. pardicolor was 1242 bp long, laying between the tRNAPro and tRNAPhe genes. Based on the 13 PCG sequences, homology and single-nucleotide mutation loci were performed between P. p. pardicolor and P. pardicolor. As a result, the homology between two species was 99.6% on average, and Nucleotide mutation loci was 41. Also, in view of their mitochondrial control region comparison, P. p. pardicolor drop 28 bp nucleotides.

Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems.

Casposons are a recently discovered group of large DNA transposons present in diverse bacterial and archaeal genomes. For integration into the host chromosome, casposons employ an endonuclease that is homologous to the Cas1 protein involved in protospacer integration by the CRISPR-Cas adaptive immune system. Here we describe the site-preference of integration by the Cas1 integrase (casposase) encoded by the casposon of the archaeon Aciduliprofundum boonei. Oligonucleotide duplexes derived from the terminal inverted repeats (TIR) of the A. boonei casposon as well as mini-casposons flanked by the TIR inserted preferentially at a site reconstituting the original A. boonei target site. As in the A. boonei genome, the insertion was accompanied by a 15-bp direct target site duplication (TSD). The minimal functional target consisted of the 15-bp TSD segment and the adjacent 18-bp sequence which comprises the 3′ end of the tRNA-Pro gene corresponding to the TΨC loop. The functional casposase target site bears clear resemblance to the leader sequence-repeat junction which is the target for protospacer integration catalyzed by the Cas1–Cas2 adaptation module of CRISPR-Cas. These findings reinforce the mechanistic similarities and evolutionary connection between the casposons and the adaptation module of the prokaryotic adaptive immunity systems.

The phylogenomic position of the sabre squirrelfish Sargocentron spiniferum (beryciformes: holocentridae) inferred from the mitochondrial genome

In this study, the complete mitochondrial genome of the sabre squirrelfish Sargocentron spiniferum, one member of family Holocentridae, is determined. It is a circular molecule whose length reaches 16,548 bp, consisting of 37 genes with typical order to most Chinese vertebrates. The nucleotide composition is: 30.3% A, 29.0% C, 15.3% G and 25.5% T. Located in gene junctions, there are total 39 bp short intergenic spaces and 30 bp overlaps. Two initial codons (GTG and ATG) and three terminal codons (TAG, AGG and TAA/T) are used in the protein-coding genes. Twenty-two tRNAs range from 67 to 74 bp. The control region (865 bp) is located between the tRNA-Pro and tRNA-Phe genes. The phylogenetic results show that S. spiniferum is sister to S. rubrum.

The complete mitochondrial genome of the fulvous parrotbill Paradoxornis fulvifrons (Passeriformes: Muscicapidae)

The complete mitochondrial genome of the fulvous parrotbill (Paradoxornis fulvifrons) has been determined from Illumina sequencing data. The circular genome is 17 059 bp long, comprising 37 genes (13 protein-coding genes/PCGs, 22 tRNA genes and two rRNA genes) and a putative control region. Except for COX1 with GTG as its start codon, all PCGs are initiated with the ATR (ATA/ATG) codons. One PCG (COX1) is terminated with AGG, three PCGs (COX3, ND2 and ND4) with the incomplete stop codon T––/TA–, while all the others with TAA. The 22 tRNAs range in size from 64 bp (tRNA-Ser) to 75 bp (tRNA-Leu). The two rRNAs are 982 bp (12S rRNA) and 1600 bp (16S rRNA) long, respectively. The putative control region is located between tRNA-Thr and tRNA-Pro genes with a length of 1235 bp. The base composition is biased (29.06% A, 31.10% C, 14.97% G and 24.87% T) with an overall A + T content of 53.93% (“light strand”). Phylogenetic analysis indicated that P. fulvifrons is closely related to the congeneric vinous-throated parrotbill (P. webbianus).