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Eleusine indica , also known as goosegrass, is a serious weed in at least 42 countries. In this paper we report the complete plastid genome sequence of goosegrass obtained by de novo assembly of paired-end and mate-paired reads generated by Illumina sequencing of total genomic DNA. The goosegrass plastome is a circular molecule of 135,151 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 20,919 bases. The large (LSC) and the small (SSC) single-copy regions span 80,667 bases and 12,646 bases, respectively. The plastome of goosegrass has 38.19% GC content and includes 108 unique genes, of which 76 are protein-coding, 28 are transfer RNA, and 4 are ribosomal RNA. The goosegrass plastome sequence was compared to eight other species of Poaceae. Although generally conserved with respect to Poaceae, this genomic resource will be useful for evolutionary studies within this weed species and the genus Eleusine . [ABSTRACT FROM AUTHOR]

Background: While the CCA sequence at the mature 3é end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and Archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In Bacteria, tRNA genes template CCA sporadically. Results: In order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database version 0.8. Among 132,129 prokaryotic tRNA genes, initiator tRNA genes template CCA at the highest average frequency (74.1%) over all functional classes except selenocysteine and pyrrolysine tRNA genes (88.1% and 100% respectively). Across bacterial phyla and a wide range of genome sizes, many lineages exist in which predominantly initiator tRNA genes template CCA. Convergent and parallel retention of CCA templating in initiator tRNA genes evolved in independent histories of reductive genome evolution in Bacteria. Also, in a majority of cyanobacterial and actinobacterial genera, predominantly initiator tRNA genes template CCA. We also found that a surprising fraction of archaeal tRNA genes template CCA. Conclusions: We suggest that cotranscriptional synthesis of initiator tRNA CCA 3é ends can complement inefficient processing of initiator tRNA precursors, "bootstrap" rapid initiation of protein synthesis from a non-growing state, or contribute to an increase in cellular growth rates by reducing overheads of mass and energy to maintain nonfunctional tRNA precursor pools. More generally, CCA templating in structurally non-conforming tRNA genes can afford cells robustness and greater plasticity to respond rapidly to environmental changes and stimuli. [ABSTRACT FROM AUTHOR]

Mutations in mitochondrial tRNAThr gene were recently reported to be associated with coronary heart disease. These mutations, such as T15889C, G15927A, G15930A and A15951G, were claimed to be pathogenic. To examine whether these mutations contributed to the genetic susceptibility to coronary heart disease, we analyzed the conservation index of these mutations between different species. In particular, reports concerning the role of the G15927A mutation was the most controversial. Therefore, based on the previous and this study, we conducted that mutations in mitochondrial tRNAThr gene may not be associated with coronary heart disease. [ABSTRACT FROM AUTHOR]

The mitochondrial genome (mitogenome) ofMegachile sculpturalis(Hymenoptera: Megachilidae) has been reported in this study. This is the first sequenced mitogenome from the family Megachilidae. The sequenced region of this mitochondrial genome is determined to be 16 581 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a partial sequence of the AT-rich region, and the AT-rich region contains several characteristic repeated sequences. Additionally, we conducted a phylogenetic analysis using all the mitochondrial genomes of Apoidea that are available in Genbank. Bayesian method supported the monophyly of both Apidae and Colletidae. And Megachilidae was inferred as the sister group of Apidae. [ABSTRACT FROM PUBLISHER]

The method developed for the total synthesis of a given DNA containing biologically specific sequences consists of the following. The DNA in the double-stranded form is carefully divided into short single-stranded segments with suitable overlaps in the complementary strands. All the segments are chemically synthesized starting with protected nucleosides and mono-nucleotides. The 5′-OH ends of the appropriate oligonucleotides are then phosphorylated with the use of [γ-P]ATP and polynucleotide kinase. A few to several neighboring oligonucleotides are then allowed to form bihelical complexes in aqueous solution, and the latter are joined end to end by polynucleotide ligase to form covalently linked duplexes. Subsequent head-to-tail joining of the short duplexes leads to the total DNA. The methods are described for the construction of a biologically functional suppressor transfer RNA gene. The total work involved (i) the synthesis of a 126-nucleotide-long bihelical DNA corresponding to a known precursor to the tyrosine suppressor transfer RNA, (ii) the sequencing of the promoter region and the distal region adjoining the C-C-A end, which contained a signal for the processing of the RNA transcript, (iii) total synthesis of the 207 base-pair-long DNA, which included the control elements, as well as the Eco R1 restriction endonu-clease specific sequences at the two ends, and (iv) full characterization by transcription in vitro and amber suppressor activity in vivo of the synthetic gene. [ABSTRACT FROM AUTHOR]

Purpose: To understand the role of mitochondrial DNA (mtDNA) mutations in patients with polycystic ovary syndrome (PCOS). Methods: A total of 57 women with PCOS and 38 controls were recruited in this study, mutational analysis of mitochondrial genome was performed using polymerase chain reaction and under a direct sequence analysis. Results: Sequence characterization of mitochondrial genome showed a distinct set of polymorphisms mainly focused on oxidative phosphorylation (OXPHOS) complex, in addition, six variants in mitochondrial tRNA genes, including tRNA, tRNA, tRNA, tRNA, tRNA and tRNA were also identified in PCOS patients. Interestingly, these variants occurred at highly conserved nucleotides of corresponding tRNAs, which are important for tRNA stability level and biochemical function. Conclusions: Mutations in mtDNA, especially the OXPHOS complex and tRNAs, may be associated with PCOS patients, thus, our results shed new insight into the pathogenesis of PCOS. [ABSTRACT FROM AUTHOR]

The nucleotide variation and structural patterns of mitochondrial RNA molecule have been proposed as useful tools in molecular systematics; however, their usefulness is always subject to a proper assessment of homology in the sequence alignment. The present study describes the secondary structure of mitochondrial tRNA for the amino acid serine (UCN) on 13 Euptychiina species and the evaluation of its potential use for evolutionary studies in this group of butterflies. The secondary structure of tRNAs showed variation among the included species except between Hermeuptychia sp1 and sp2. Variation was concentrated in the ribotimidina-pseudouridine-cystosine (TψC), dihydrouridine (DHU) and variable loops and in the DHU and TψC arms. These results suggest this region as a potential marker useful for taxonomic differentiation of species in this group and also confirm the importance of including information from the secondary structure of tRNA to optimize the alignments. [ABSTRACT FROM AUTHOR]

In this work, we reported the complete mitochondrial DNA sequence of the hybrid of Squaliobarbus curriculus (♀) ×  Ctenopharyngodon idella (♂), which was obtained by artificial hybridization. The total length of the mitochondrial genome is 16,616 bp, with the base composition of 31.15% A, 25.02% T, 27.66% C, and 16.17% G. It contains 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). The arrangement of these genes is the same as that found in the teleosts. All the protein initiation codons are ATG, except for COX1 that begins with GTG. The complete mitogenome of the hybrid of S. curriculus (♀) ×  C. idella (♂) provides an important data set for the study in genetic mechanism. [ABSTRACT FROM AUTHOR]

The complete sequence (14,751 bp) of the mitochondrial DNA (mtDNA) of the opisthobranch gastropod Placida sp. was determined using long PCR and genome-walking techniques. The genome contains 13 protein-coding genes (PCG), 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) genes that are typical of metazoan mtDNA, and 2 lengthy noncoding regions with a total length of 1441 bp. All the tRNA genes have general secondary structures without reduced T or D stems. The mitochondrial gene arrangement of Placida sp. is almost identical to that of sea slugs, whereas the tRNA gene arrangement is different from other animals outside Sacoglossa in the Euthyneura. A phylogenetic analysis based on the mitochondrial genome of Euthyneura indicated that Placida sp. and Placida dendritica are closely related to Elysia chlorotica as a sister taxon, which strongly supports their close phylogenetic affinity. [ABSTRACT FROM AUTHOR]

Yellow catfish ( Pelteobagrus fulvidraco) belongs to the family Bagridae, which is one of the most important economic freshwater aquaculture species in China. In this study, we reported the complete sequence of the mitochondrial genome of P. fulvidraco. The complete mitochondrial genome is 16,527 bp in length, including the typical structure of 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes, and the non-coding control region. Both the termination-associated sequence and critical central conserved sequences (CSB-D, CSB-E, and CSB-F) was also detected. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome (mitogenome) of the seven-spotted lady beetle, Coccinella septempunctata (Coleoptera: Coccinellidae), which is one of the best known insects capable of predation, is described with an emphasis on the noteworthy composition of the A+T-rich region. The C. septempunctata genome consists of 2 rRNAs, 22 tRNAs, 13 protein-coding genes, and 1 control region, designated as the A+T-rich region in insects. Along with an unusually long A+T-rich region (4469 bp), the 18,965-bp long C. septempunctata mitogenome was the largest in Coleoptera. The A+T-rich region is composed of a 2214-bp long non-repeat region composed of 80.17% A/T nucleotides and a 2256-bp long repeat region composed of 65.71% A/T nucleotides. The repeat region harbors 32 identical 70-bp long tandem repeats plus one 15-bp long incomplete first repeat. These repeat sequences may possibly have been caused by slipped-strand mispairing and unequal crossing-over events during DNA replication. [ABSTRACT FROM AUTHOR]

The complete nucleotide sequence ofJuglans regiachloroplast genome (cpDNA) was carried out using Illumina Hiseq 2500. The genome is 160 537 bp in length, and the overall base composition of H-strand is 31.59% for A, 18.35% for C, 17.76% for G and 32.30% for T. Similar to the other higher plants, cpDNA have a large single copy (LSC) region of 90 059 bp and a small single copy(SSC) of 18 412 bp, is separated by a pair of inverted repeats (IRa and IRb) of 26 033 bp. There are 113 genes in the cpDNA, including 80 protein-coding genes, 4 ribosomal RNA genes (4 rRNA species), 36 transfer RNA genes (19 tRNA species). To further investigate the evolution status ofJ. regiain the level of chloroplast genome, tree constructed using MEGA 6.0 with NJ and ML methord demonstratedJ. regiawas clustered inFagales, which was identical with APG III. [ABSTRACT FROM PUBLISHER]

The complete nucleotide sequence of theSinopodophyllum hexandrumYing chloroplast genome (cpDNA) was determined based on next-generation sequencing technologies in this study. The genome was 157 203 bp in length, containing a pair of inverted repeat (IRa and IRb) regions of 25 960 bp, which were separated by a large single-copy (LSC) region of 87 065 bp and a small single-copy (SSC) region of 18 218 bp, respectively. The cpDNA contained 148 genes, including 96 protein-coding genes, 8 ribosomal RNA genes, and 44 tRNA genes. In these genes, eight harbored a single intron, and two (ycf3andclpP) contained a couple of introns. The cpDNA AT content ofS. hexandrumcpDNA is 61.5%. [ABSTRACT FROM PUBLISHER]

Sheep is one of the most important and widespread domestic animals. Nevertheless, the origins of most sheep breeds are poorly understood, specifically the fat-tailed sheep that maternally originates from a specific group. Here, we reported the whole mitochondrial DNA of Ujumuqin sheep (Ovis aries), derived from one of the oldest fat-tailed sheep breed-Mongolian sheep in China. It harbors 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a D-Loop region. The mitogenome is 16 617 bp in length, with a homology of 50% between the mitogenome of Ujumuqin sheep and that of Texel sheep. The unveiling of the mitochondrial DNA sequence of Ujumuqin sheep will have a significant role to play in the further studies on sheep evolution and domestication. [ABSTRACT FROM PUBLISHER]

Acer morrisonense(Aceraceae) is an important forest tree species and is endemic to Taiwan area. In this study, we determined the complete nucleotide sequence ofA. morrisonensechloroplast genome (cpDNA) by using next-generation sequencing. The cpDNA was 157 197 bp in size, contained a pair of 26 728 bp inverted repeat (IR) regions, which were separated by a large single copy region (LSC) and a small single copy (SSC) region of 85 655 and 18 086 bp, respectively. The cpDNA contained 134 genes, including 86 protein-coding genes (78 PCG species), 8 ribosomal RNA genes (four rRNA species), and 40 transfer RNA genes (31 tRNA species). The most of gene species occur as a single copy, while 21 gene species occur in double copies. The overall AT content ofA. morrisonensechloroplast genome were 62.2%, while the corresponding values of the LSC, SSC, and IR regions were 64.0%, 67.9%, and 57.3%, respectively. The phylogenetic analysis suggested that the cpDNA ofA. morrisonenseis closely related to that of congenericA. buergerianumsubsp. ningpoense. [ABSTRACT FROM PUBLISHER]

The grey-backed thrush (Turdus hortulorum) is an endangered bird species, which is mainly distributed in northern China, Korean Peninsula and Vietnam. In this study, the complete nucleotide sequence of the mitochondrial genome ofT. hortulorumis determined. The circle genome was 16,759 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop). The mtDNA ofT. hortulorumis similar to the typical mtDNA of birds and other vertebrates. [ABSTRACT FROM AUTHOR]

In this study we determined the complete mitochondrial (mt) genome of the yellowtail clownfishAmphiprion clarkiiusing eight consensus primer pairs with a long PCR technique. The circular mtDNA molecule was 16,976 bp in size and the overall nucleotide composition of the H-strand was 29.15% A, 26.15% T, 15.67% G and 29.03% C, with an A + T bias. The complete mitogenome contained 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 1 control region (D-loop), and the gene order was typical of vertebrate mitogenomes. We determined five complete continuity tandem repeat units and one imperfect tandem repeat, all located downstream in the control region. [ABSTRACT FROM AUTHOR]

In this study we determined the complete mitochondrial (mt) genome of the orange clownfishAmphiprion percula. The circular mtDNA molecule was 16,645 bp in size and the overall nucleotide composition of the H-strand was 29.20% A, 25.80% T, 16.03% G and 28.98% C, with an A + T bias. The complete mitogenome encoded 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 1 control region (D-loop), with the gene arrangement and translation direction basically identical to other typical vertebrate mitogenomes. The similarity of the complete mitogenomes betweenA. perculaandA. ocellaris(AP006017) was 95.60%, clearly different at molecular level. [ABSTRACT FROM AUTHOR]

In this study, complete nucleotide sequence of the F-type mitochondrial genome ofArconaia lanceolata(Bivalvia: Unioninae), the endemic species of freshwater pearl mussel in China, was first determined. The complete mitochondrial genome ofArconaia lanceolatais 15,782 bp in size, and encodes 35 genes, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs. Those genes are similar to most species of Unioninae in order, structure and composition. In the 13 protein-coding genes, ND2, Cytb, ND1 and ND6 are located in the light chain while the rest on the heavy chain. Also, COXI, Cytb, ND1, ND6 and ND4L with ATA as start codon, the remaining protein-coding genes initiated with the orthodox ATG as start codon. There are 28 non-coding regions in the mitochondrial genome ofA. lanceolata, the largest is of 345 bp in length, located between ND5 and tRNAGlngene. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the Japanese wobbegong Orectolobus japonicus was presented in this study. It is 16,706 bp in length with the typical gene composition and arrangement in the mitochondrial genome of vertebrates. The overall base composition is 32.6% A, 24.0% C, 13.3% G and 30.1% T. Two start codons (ATG and GTG) and two stop codons (TAG and TAA) were found in protein-coding genes. The tRNA- Ser2 lacks the dihydrouridine arm and cannot be folded into a typical cloverleaf structure. One termination associated sequence (TAS) and three conserved sequence blocks (CSB1-3) were found in the control region. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the Chinese lake gudgeon Sarcocheilichthys sinensis was first determined in this study. It is a circular DNA double strand of 16,684 bp in length, encodes genes for 13 proteins, 2 ribosomal RNA subunits, 22 transfer RNAs and an A + T-rich control region with the typical gene order in vertebrate mitogenomes. Overall nucleotide composition is 30.5% A, 26.6% C, 16.7% G and 26.3% T. Three start codons (ATG, GTG and ATA) and three stop codons (TAG, TAA and T) were found in all protein-coding genes. The tRNA- SerAGY lacked the dihydrouridine arm and could not fold into typical cloverleaf secondary structure. The origin of L-strand replication was identified between the tRNA- Asn and tRNA- Cys genes. [ABSTRACT FROM AUTHOR]