tRNAPhe Gene Research Articles

Application of High-Resolution Melting and DNA Barcoding for Discrimination and Taxonomy Definition of Rocket Salad (Diplotaxis spp.) Species.

Nuclear and cytoplasmic DNA barcoding regions are useful for plant identification, breeding, and phylogenesis. In this study, the genetic diversity of 17 Diplotaxis species, was investigated with 5 barcode markers. The allelic variation was based on the sequences of chloroplast DNA markers including the spacer between trnL and trnF and tRNA-Phe gene (trnL-F), the rubisco (rbcl), the maturase K (matk), as well as the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. A highly polymorphic marker (HRM500) derived from a comparison of cytoplasmic genome sequences in Brassicaceae, was also included. Subsequently, a real-time PCR method coupled with HRM analysis was implemented to better resolve taxonomic relationships and identify assays suitable for species identification. Integration of the five barcode regions revealed a grouping of the species according to the common chromosomal set number. Clusters including species with n = 11 (D. duveryrieriana or cretacea, D. tenuifolia, D. simplex and D. acris), n = 8 (D. ibicensis, D. brevisiliqua and D. ilorcitana), and n = 9 (D. brachycarpa, D. virgata, D. assurgens, and D. berthautii) chromosomes were identified. Both phylogenetic analysis and the genetic structure of the collection identified D. siifolia as the most distant species. Previous studies emphasized this species' extremely high glucosinolate content, particularly for glucobrassicin. High-resolution melting analysis showed specific curve patterns useful for the discrimination of the species, thus determining ITS1 as the best barcode for fingerprinting. Findings demonstrate that the approach used in this study is effective for taxa investigations and genetic diversity studies.

Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation

The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-Seq, RNA-seq, ribo-profiling and proteomics we observed distinct molecular consequences of single tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoder genes buffer the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least six tRNA-Phe alleles is required for embryonic viability and tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA genes is required to buffer translation and viability in mammals.

Emergence of rare carbapenemases (FRI, GES-5, IMI, SFC and SFH-1) in Enterobacterales isolated from surface waters in Japan.

Carbapenemase-producing Enterobacterales (CPE) pose serious threats to public health. Compared with clinical CPE, the genetic characteristics of environmental CPE are not well understood. This study aimed to characterize the genetic determinants of carbapenem resistance in CPE isolated from environmental waters in Japan. Eighty-five water samples were collected from rivers and a lake in Japan. CPE were identified using selective media, and genome sequencing was performed for the obtained isolates (n = 21). Various rare/novel carbapenemases were identified: GES-5 in Raoultella planticola (n = 1), FRI-8 and FRI-11 in Enterobacter spp. (n = 8), IMI-22 and IMI-23 in Serratia ureilytica (n = 3), and SFC-1, SFC-2 and SFH-1 in Serratia fonticola (n = 9). Genomes of 11 isolates could be closed, allowing the elucidation of the genetic contexts of the carbapenemase genes. The blaGES-5 gene was located within a class 1 integron, In2071 (cassette array, blaGES-5-aacA3-aadA16), on a 33 kb IncP6 plasmid. The blaFRI-8 genes were carried on IncFII(Yp) plasmids ranging in size from 191 kb to 244 kb, and the blaFRI-11 genes were carried on 70 kb and 74 kb IncFII(pECLA)/IncR plasmids. The blaIMI-22 and blaIMI-23 genes were co-located on a 107 kb plasmid. The blaSFC and blaSFH-1 genes were found on putative genomic islands inserted at tRNA-Phe genes in chromosomes. This study revealed the presence of rare/novel carbapenemases among CPE in aquatic environments, suggesting that the environment may act as a potential reservoir of these minor carbapenemases.

The complete mitochondrial genome of common Shelduck Shengjin Lake Tadorna tadorna

The complete mtDNA of Shengjin Lake Tadorna tadorna 16622 bp in length, containing 13 protein-coding genes, 2 rRNAs, 22 tRNAs and one D-loop. Mitochondrial genes of the Shengjin Lake Tadorna tadorna was arranged in the same order and orientation as those of reported Tadorna tadorna. All the start codon of the protein-coding genes is ATG, TAA is the most frequent stop codon. The 12S rRNA and 16S rRNA genes are located between the tRNALeu and tRNAPhe genes and separated by the tRNAVal gene. The control region, located between the tRNAGlu and tRNAPhe genes and is rich in A and T. Phylogenetic trees show Shengjin Lake Tadorna tadorna has close relative with Cairina moschata.

The complete mitochondrial genome of Mallard Shengjin Lake Anas platyrhynchos

The complete mtDNA of Mallard Shengjin Lake Anas platyrhynchos is 16,604 bp in length, containing 13 protein-coding genes, two rRNAs, 22 tRNAs, and one D-loop. Mitochondrial genes of the Mallard Shengjin Lake A. platyrhynchos were arranged in the same order and orientation as those of other reported A. platyrhynchos and Chinese domestic ducks. The most frequent start codon of the protein-coding genes is ATG; TAA is the most frequent stop codon. The 12S rRNA and 16S rRNA genes are located between the tRNALeu and tRNAPhe genes and separated by the tRNAVal gene. The control region, located between the tRNAGlu and tRNAPhe genes is 1049 bp and is rich in A and T. Phylogenetic trees show Mallard Shengjin Lake A. platyrhynchos has close relative with Mallard Anas platyrhynchos (EU009397).

Phylogenetic relationships and cryptic species diversity in the Brazilian egg-brooding tree frog, genus Fritziana Mello-Leitão 1937 (Anura: Hemiphractidae)

The genus Fritziana (Anura: Hemiphractidae) comprises six described species (F. goeldii, F. ohausi, F. fissilis, F. ulei, F. tonimi, and F. izecksohni) that are endemic to the Brazilian Atlantic Forest. Although the genus has been the subject of studies dealing with its taxonomy, phylogeny, and systematics, there is considerable evidence for cryptic diversity hidden among the species. The present study aims to understand the genetic diversity and phylogenetic relationships among the species of Fritziana, as well as the relationships among populations within species. We analyzed 107 individuals throughout the distribution of the genus using three mitochondrial gene fragments (12S, 16S, and COI) and two nuclear genes (RAG1 and SLC8A3). Our data indicated that the species diversity in the genus Fritziana is underestimated by the existence of at least three candidate species hidden amongst the group of species with a closed dorsal pouch (i.e. F. fissilis and F. ulei). We also found four species presenting geographical population structures and high genetic diversity, and thus require further investigations. In addition, we found that two candidate species show a new arrangement for the tRNA-Phe gene, unique in Anura so far. Based on our results, we suggest that the conservation status of the species, as well as the species diversity in the genus Fritziana, needs to be reviewed.

Late onset nonsyndromic hearing loss in a Dongxiang Chinese family is associated with the 593T > C variant in the mitochondrial tRNAPhe gene

We report here the clinical, genetic, molecular and biochemical characterization of a four-generation Dongxiang Chinese pedigree with suggestively maternally transmitted non-syndromic hearing loss. Five of 10 matrilineal relatives exhibited variable severity and age at onset of sensorineural hearing loss. The average ages at onset of hearing loss in matrilineal relatives of this family were 29years. Molecular analysis of their mitochondrial genomes identified the tRNAPhe 593T>C variant belonging to Asian haplogroup G2a2a. The m.593T>C variant resided at the position 17 of DHU-loop, where the position is important for the structure and function of tRNA. It was anticipated that the m.593T>C variant altered the structure and function of tRNAPhe. By using lymphoblastoid cell lines derived from the Chinese family, we showed a 46% decreases in the steady-state level of tRNAPhe in mutant cell lines. Western blotting analysis showed ∼35% reduction in the levels of mitochondrial translation in mutant cell lines carrying the m.593T>C variant. Impaired mitochondrial translation is apparently a primary contributor to the marked reduction in the rate of respiratory capacity. The respiratory deficiency lowed mitochondrial ATP production in the mutant cell lines. These data provide the evidence that mitochondrial dysfunctions caused by the m.593T>C variant lead to late-onset nonsyndromic hearing loss. Thus, our findings may provide the new insights into the understanding of pathophysiology and valuable information for management and treatment of maternally inherited hearing loss.

Mitochondrial genome sequence and gene organization of Kunar Snow trout (Schizothorax labiatus) with phylogenetic consideration

The complete mitochondrial genome is important for determining the phylogenetic relationship of species. In the current study, we sequenced the complete mitochondrial genome of Kunar Snow trout (Schizothorax labiatus). It was found to be 61,590bp in length having 37 genes (13 protein coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer (tRNA) genes and one putative control region (CR)). Out of the total 37 genes, 28 were encoded on heavy strand (H), whereas 9 on light strand (L). A+T content of nucleotide were 58.04% and G+C were 41.94%. ATG was a start codon for all the proteins except COXI which has GTG as a start codon. The stop codons were TAG and TAA or incomplete stop codons (TA- and T--). The l6S rRNA genes was located between the tRNA-Val and tRNA-Leu (UUR) genes, whereas the 12S rRNA located between the tRNA-Phe and tRNA-Val. 22 tRNA genes were interspersed along the genome, in the typical structure for S. labiatus. These tRNA genes had ranged in size from 66 to 85 nucleotides, which were predicted to fold into the expected cloverleaf secondary structures with normal base pairing. The control region was located between the tRNA-Pro and tRNA-Phe genes with 936bp. Several conserved sequence blocks (CSB) were also identified within D-loop sequences. The phylogenetic analysis based on complete mitochondrial genome sequence, showed that S. labiatus has close genetic relationships with 20 species (mostly cyprinids) and its mitogenome sequence would be useful to know the phylogenetic status of the S. labiatus.

Origin and Evolution of Allopolyploid Wheatgrass Elymus fibrosus (Schrenk) Tzvelev (Poaceae: Triticeae) Reveals the Effect of Its Origination on Genetic Diversity.

Origin and evolution of tetraploid Elymus fibrosus (Schrenk) Tzvelev were characterized using low-copy nuclear gene Rpb2 (the second largest subunit of RNA polymerase II), and chloroplast region trnL–trnF (spacer between the tRNA Leu (UAA) gene and the tRNA-Phe (GAA) gene). Ten accessions of E. fibrosus along with 19 Elymus species with StH genomic constitution and diploid species in the tribe Triticeae were analyzed. Chloroplast trnL–trnF sequence data suggested that Pseudoroegneria (St genome) was the maternal donor of E. fibrosus. Rpb2 data confirmed the presence of StH genomes in E. fibrosus, and suggested that St and H genomes in E. fibrosus each is more likely originated from single gene pool. Single origin of E. fibrosus might be one of the reasons causing genetic diversity in E. fibrosus lower than those in E. caninus and E. trachycaulus, which have similar ecological preferences and breeding systems with E. fibrosus, and each was originated from multiple sources. Convergent evolution of St and H copy Rpb2 sequences in some accessions of E. fibrosus might have occurred during the evolutionary history of this allotetraploid.

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.

Particular gene order and complete mitochondrial genome of Beach conger (Conger japonicus)

Beach conger (Conger japonicus) is a demersal and carnivorous species belonging to the family Congridae. In the present study, the complete mitochondrial genome of the C. japonicus was first determined. The mitochondrial genome of C. japonicus is 17,778 nucleotides, comprising 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and 2 main non-coding regions (the control region and the origin of the light strand replication), which is consistent with other vertebrates. However, its gene order is different from other vertebrates (except for C. myriaster). The Cytb gene, tRNAThr and the control region are located between the ND5 gene and the ND6 gene in C. japonicus while they are between the ND6 gene and the tRNAPhe gene in other vertebrates. The same gene order also appeared in C. myriaster. The mitochondrial genome of C. japonicus and C. myriaster, which are currently the only two members of Conger genus with complete mitochondrial genome, appeared in the gene rearrangement, so we speculated that the mitochondrial genome of all species from Conger genus may appear in the gene rearrangement. However, to clarify the speculation, more mitochondrial genomes of Conger genus will be needed in the future. In addition, phylogenetic analysis result demonstrated that C. japonicus and C. myriaster clustered in a clade and formed a sister relationship.

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.

Complete mitogenome of Nemacheilus subfusca (Cypriniformes: Cobitidae)

The Nemacheilus subfusca (N. subfusca) is a species of the Noemacheilinae in the Cobitidae family, which has been few reported. The first complete mitochondrion of the N. subfusca is 16 585 bp in length, containing 13 protein-coding genes, two rRNA genes (12S and 16S rRNA), 22 tRNA genes and a control region (D-loop region). The longest protein-coding gene of this mitochondrion was ND5 (1839 bp), and the 22 tRNA genes were range from 66 (tRNACys) to 76 (tRNALys) in length. The 12S rRNA (957 bp) and 16S rRNA (1677 bp) were separated by TrnaVal, and the D-loop region located between tRNAPro and tRNAPhe genes. The phylogenetic indicates that the N. subfusca was independent from other species of distinct genus in the Noemacheilinae, which provided the valuable evidence on phylogenetic relationship of the N. subfusca at the molecular level.

The complete mitochondrial genome of the black star fat minnow (Rhynchocypris semotilus), an endemic and endangered fish of Korea

The Black star fat minnow (Rhynchocypris semotilus) is an endemic and critically endangered freshwater fish in Korea. Its genome was 16 605 bp long and consisted of 13 protein-coding genes (PCG), two rRNA genes, 22 tRNA genes, and a control region. The gene order and the composition of R. semotilus were similar to that of most other vertebrates. Four overlapping regions in ATP8/ATP6, ATP6/COX3, ND4L/ND4, and ND5/ND6, among the 13 PCGs were found. The control region was located between the tRNA-Pro and tRNA-Phe genes and was determined to be 935 bp in length with the 3′ end containing a 12 TA-repeat sequence. Phylogenetic analysis suggested that R. semotilus is most closely related to R. oxycephalus.

Complete mitochondrial genome of the yellowbelly threadfin bream, Nemipterus bathybius (Perciformes, Nemipteridae)

The complete mitogenome of the yellowbelly threadfin bream, Nemipterus bathybius, has been reported for the first time in this study. The circular mtDNA molecule was 17 353 bp in size and the overall nucleotide composition of H-strand was 29.0% A, 28.3% T, 16.5% G, and 26.2% C, with an A + T bias. The complete mitogenome encoded 13 protein-coding genes, 2 rRNAs, 22 tRNAs, and 2 non-coding regions, as found in other typical vertebrate mitogenomes. The D-loop located between tRNAPro and tRNAPhe genes and the length was 1603 bp, rich in A + T (73.0%). The phylogenetic tree of complete mitogenome sequences of 12 families and 26 species showed that the family Nemipteridae was in the basal position of the suborder Percoidei, whereas its two associated families (Sparidae and Lethrinidae) were clustered together with other 7 families, which supported a non-monophyly of superfamily Sparoidea.

Origin and Reticulate Evolutionary Process of Wheatgrass Elymus trachycaulus (Triticeae: Poaceae).

To study origin and evolutionary dynamics of tetraploid Elymus trachycaulus that has been cytologically defined as containing StH genomes, thirteen accessions of E. trachycaulus were analyzed using two low-copy nuclear gene Pepc (phosphoenolpyruvate carboxylase) and Rpb2 (the second largest subunit of RNA polymerase II), and one chloroplast region trnL–trnF (spacer between the tRNA Leu (UAA) gene and the tRNA-Phe (GAA) gene). Our chloroplast data indicated that Pseudoroegneria (St genome) was the maternal donor of E. trachycaulus. Rpb2 data indicated that the St genome in E. trachycaulus was originated from either P. strigosa, P. stipifolia, P. spicata or P. geniculate. The Hordeum (H genome)-like sequences of E. trachycaulus are polyphyletic in the Pepc tree, suggesting that the H genome in E. trachycaulus was contributed by multiple sources, whether due to multiple origins or introgression resulting from subsequent hybridization. Failure to recovering St copy of Pepc sequence in most accessions of E. trachycaulus might be caused by genome convergent evolution in allopolyploids. Multiple copies of H-like Pepc sequence from each accession with relative large deletions and insertions might be caused by either instability of Pepc sequence in H- genome or incomplete concerted evolution. Our results highlighted complex evolutionary history of E. trachycaulus.

The complete sequence of the mitochondrial genome of Liangshan pig (Sus Scrofa)

Liangshan pig is one of the famous native breeds in Sichuan province in China. It lives in the mountainous areas (about 1500–2500 m altitude) and has a superior meat quality. Here, the complete mitochondrial genome sequence of Liangshan pig was first reported. The total length of mitochondrial genome is 16,760 bp, including 34.62% A, 25.79% T, 26.20%, C and 13.39% G, with an A + T bias of 60.41%. Mitochondrial genome contains a major non-coding control region (D-Loop region), two ribosomal RNA genes, 13 protein-coding genes (PCGs), and 22 transfer RNA genes. The D-loop region is located between the tRNA-Pro and tRNA-Phe genes with a length of 1324 bp, some tandem repeat sequences was found in the region. The mitochondrial genome of Liangshan pig provides an important role in genetic mechanism.

Complete mitochondrial genome of Goniurosaurus luii (Squamata, Eublepharidae)

The complete mitochondrial genome sequence of Goniurosaurus luii has been determined in the present paper. The genome was 16,519 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (CR). Its gene composition and order was similar to most other Squamate reptiles. The overall base composition of the genome in descending order was 34.11% A, 26. 01% C, 27.43% T, and 12.45% G, with a slight AT bias of 61.54%. CR was located between the tRNA-Pro and tRNA-Phe genes and was 1147 bp in length, some tandem repeat sequences and conserved elements (CSB2-3) were found in the control region.

The complete mitochondrial genome of Teratoscincus roborowskii (Squamata: Gekkonidae)

The complete nucleotide sequence of the mitochondrial genome of Teratoscincus roborowskii was sequenced here. It was determined to be 16,644 base pairs in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The 22 tRNA genes could be folded into the typical cloverleaf structure described for vertebrate mitochondrial tRNAs. The base composition of the heavy strand was 30.33% A, 30.35% C, 14.65% G and 24.67% T. The control region was located between the tRNA-Pro and tRNA-Phe genes and is 1248 bp in length and some tandem repeat sequences were found in it.

Complete mitochondrial genome of Korean yellow-throated marten, Martes flavigula (Carnivora, Mustelidae)

The complete mitogenome sequence of Martes flavigula, which is an endangered and endemic species in South Korea, was determined. The genome is 16,533 bp in length and its gene arrangement pattern, gene content, and gene organization is identical to those of martens. The control region was located between the tRNAPro and tRNAPhe genes and is 1087 bp in length. This mitogenome sequence data might be an important role in the preservation of genetic resources by allowing researchers to conduct phylogenetic and systematic analyses of Mustelidae.