A novel rearrangement in the mitochondrial genome of tongue sole, Cynoglossus semilaevis: control region translocation and a tRNA gene inversion

Genome ◽  
2009 ◽  
Vol 52 (12) ◽  
pp. 975-984 ◽  
Author(s):  
Xiaoyu Kong ◽  
Xiaoli Dong ◽  
Yanchun Zhang ◽  
Wei Shi ◽  
Zhongming Wang ◽  
...  
Keyword(s):  
Control Region ◽  
Molecular Mechanisms ◽  
Cynoglossus Semilaevis ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Heavy Strand ◽  
Light Strand ◽  
Putative Control Region

The organization of fish mitochondrial genomes (mitogenomes) is quite conserved, usually with the heavy strand encoding 12 of 13 protein-coding genes and 14 of 22 tRNA genes, and the light strand encoding ND6 and the remaining 8 tRNA genes. Currently, there are only a few reports on gene reorganization of fish mitogenomes, with only two types of rearrangements (shuffling and translocation) observed. No gene inversion has been detected in approximately 420 complete fish mitogenomes available so far. Here we report a novel rearrangement in the mitogenome of Cynoglossus semilaevis (Cynoglossinae, Cynoglossidae, Pleuronectiformes). The genome is 16 371 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 main noncoding regions, the putative control region and the light-strand replication origin. A striking finding of this study is that the tRNAGln gene is translocated from the light to the heavy strand (Q inversion). This is accompanied by shuffling of the tRNAIle gene and long-range translocation of the putative control region downstream to a site between ND1 and the tRNAGln gene. The remaining gene order is identical to that of typical fish mitogenomes. Additionally, unique characters of this mitogenome, including a high A+T content and length variations of 8 protein-coding genes, were found through comparison of the mitogenome sequence with those from other flatfishes. All the features detected and their relationships with the rearrangements, as well as a possible rearrangement pathway, are discussed. These data provide interesting information for better understanding the molecular mechanisms of gene reorganization in fish mitogenomes.

Mitogenome of Anterastes babadaghi (Orthoptera: Tettigoniinae; Platycleidini): Frequent conserved overlapping regions within Tettigoniinae

Zootaxa ◽  
2019 ◽  
Vol 4651 (1) ◽  
pp. 173-190
Author(s):  
UĞUR KARŞI ◽  
BATTAL ÇIPLAK
Keyword(s):  
Control Region ◽  
Start Codon ◽  
Gene Location ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Stop Codons ◽  
Protein Coding Genes ◽  
Generation Sequencing

Development of next generation sequencing rapidly increased the number of total mitogenome in data bases. However, the documented number of total mitogenome from species of Tettigoniinae is still limited and a comparison at subfamily level has not been made sufficiently. This paper aims to describe total mitogenome of A. babadaghi (Orthoptera, Tettigoniidae) by comparing to the known mitogenomes of other Tettigoniinae. The total mitogenome of A. babadaghi is 15882–15883 bp, AT skewed with 70.2% AT percentage, and consists of 13 protein coding genes (PCG), 22 tRNA genes, two rRNA genes and an AT rich control region. The genes are ordered as in pancrustacean. The comparative description of mitogenomes in Tettigoniinae showed that total length varies between 15766-16788 bp, the start codon for protein coding genes almost always fits to the ATN pattern, the stop codons are incomplete T-- / TA- and rarely complete TAA, intergenic spacers (IGS) and overlapping regions (OR) in species of the subfamily are similar in number, location, length and nucleotide sequence. We arrived to following conclusion from comparative data: (i) A. babadaghi has a typical orthopteran mitogenome by general features; (ii) this generalisation seems valid for Tettigoniinae as gene content, gene location, gene order, average AT content, anticodons and secondary structure of the tRNA genes, the start and stop codons of the protein coding genes, and several IGSs/ORs are similar to other orthopteran and hexapopods, (iii) variation range in total mitogenome length is narrow in Tettigoniinae and mainly determined by the lengths of control region and total IGSs, (iv) mitogenome of the subfamily exhibits conserved patterns especially in overlapping regions, but conserved features are mostly plesiomorphic. 

scholarly journals Complete Mitochondrial Genome Sequence of Bos Frontalis (Gayal) of Bangladesh

2021 ◽  
Author(s):  
Gautam Kumar Deb ◽  
Razia Khatun ◽  
Shakh Mohammed Jahangir Hossain ◽  
Shamsur Rahaman ◽  
Md. Anamul Bahar Bhuiyan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Related Species ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract Background: Complete mitochondrial genome of Bos frontalis will aid in the investigation of evolutionary links between closely related species. Bos frontalis mitogenome contains 37 genes and a control region. We discover the first complete mitogenome of Bos frontalis found in Bangladesh which was obtained from whole-genome sequencing of Bos frontalis.Results: Bos frontalis mitogenome is 16,347 bp long, with an AT-based nucleotide composition (60.21%). It contains 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region (D-loop). This circular genome starts with ND6(negative strand) and ends at ND5(positive strand). Protein coding genes lost 24 bases and tRNA genes gained 27 bases compared to closely related species. Phylogenetic analysis of the mitochondrial genome of 26 closely related species from 8 congeneric species was conducted by the maximum likelihood method with 1000 bootstrap iteration.Conclusion: Our studied Bos frontalis mitochondrial genome has a similar gene arrangement compared with other Bos species. It has almost the same amount of AT and GC content, but notably the ND6 gene lacks AT skew and GC skew than that of the other two comparing species. PCG’s loss in size might be a continuous process of evolution. The mitochondrial genome is regarded as a critical tool for species identification and monitoring populations of conservation concern.

scholarly journals Complete Genome Sequence of Cupriavidus necator H16 (DSM 428)

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Gareth T. Little ◽  
Muhammad Ehsaan ◽  
Christian Arenas-López ◽  
Kamran Jawed ◽  
Klaus Winzer ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cupriavidus Necator ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Cupriavidus Necator H16

The hydrogen-utilizing strain Cupriavidus necator H16 (DSM 428) was sequenced using a combination of PacBio and Illumina sequencing. Annotation of this strain reveals 6,543 protein-coding genes, 263 pseudogenes, 64 tRNA genes, and 15 rRNA genes.

scholarly journals The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

2018 ◽  
Vol 94 ◽  
Author(s):  
P. Zhang ◽  
R.K. Ran ◽  
A.Y. Abdullahi ◽  
X.L. Shi ◽  
Y. Huang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Squirrel Monkey ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Rrna Genes ◽  
Saimiri Sciureus ◽  
Trna Genes ◽  
Loop Structure ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractDipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

scholarly journals The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242541
Author(s):  
Lvpei Du ◽  
Shanya Cai ◽  
Jun Liu ◽  
Ruoyu Liu ◽  
Haibin Zhang
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Cold Seep ◽  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Protein Coding Genes ◽  
High Support

Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.

scholarly journals Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8450 ◽  
Author(s):  
Sunan Huang ◽  
Xuejun Ge ◽  
Asunción Cano ◽  
Betty Gaby Millán Salazar ◽  
Yunfei Deng
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Variable Regions ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

2021 ◽  
Vol 46 (1) ◽  
pp. 162-174
Author(s):  
Ming-Hui Yan ◽  
Chun-Yang Li ◽  
Peter W. Fritsch ◽  
Jie Cai ◽  
Heng-Chang Wang
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

scholarly journals Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1354
Author(s):  
Slimane Khayi ◽  
Fatima Gaboun ◽  
Stacy Pirro ◽  
Tatiana Tatusova ◽  
Abdelhamid El Mousadik ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Important Species ◽  
Complete Chloroplast Genome ◽  
Argania Spinosa ◽  
Protein Coding Genes ◽  
Cp Genome

Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.

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

2020 ◽  
Vol 21 (13) ◽  
pp. 4685
Author(s):  
Zhenhai Li ◽  
Min Li ◽  
Shannan Xu ◽  
Li Liu ◽  
Zuozhi Chen ◽  
...  
Keyword(s):  
Divergence Time ◽  
Rrna Genes ◽  
12S Rrna ◽  
Trna Genes ◽  
Coding Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Gc Skew ◽  
The Family ◽  
Conserved Genes

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.

scholarly journals Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

2018 ◽  
Vol 19 (8) ◽  
pp. 2383 ◽  
Author(s):  
Qixiang Lu ◽  
Wenqing Ye ◽  
Ruisen Lu ◽  
Wuqin Xu ◽  
Yingxiong Qiu
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Early Pleistocene ◽  
Disjunct Distribution ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Protein Coding Genes

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia.

Sign in / Sign up

Export Citation Format

Share Document