scholarly journals Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wen-Ge Dong ◽  
Yalun Dong ◽  
Xian-Guo Guo ◽  
Renfu Shao
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Genome Organization ◽  
Trna Gene ◽  
Trna Genes ◽  
Single Chromosome ◽  
Gene Translocation ◽  
Sucking Lice ◽  
Different Types ◽  
Mt Genome

Abstract Background The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes. Results We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes. Conclusions We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

An additional record of Fejervarya manoharani Garg and Biju from the Western Ghats with a description of its complete mitochondrial genome

Zootaxa ◽  
2017 ◽  
Vol 4277 (4) ◽  
pp. 491 ◽  
Author(s):  
S. KUMAR KIRAN ◽  
V. S. ANOOP ◽  
K. C. SIVAKUMAR ◽  
RAGHUNATHAN DINESH ◽  
J. P. MANO ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Gene Organization ◽  
Morphological Data ◽  
12S Rrna ◽  
Trna Genes ◽  
Protein Coding ◽  
Its Gene ◽  
Nd5 Gene

An additional sighting of newly described frog species, Fejervarya manoharani Garg and Biju, outside of the type locality along with their morphological data is reported herewith. We are also providing the whole DNA sequence of the mitochondrial genome with its gene organization as additional data to distinguish this species from its congeners. The mitogenome of F. manoharani was 17,654 bp in length. It contains 38 genes including two rRNAs, 23 tRNAs, 13 protein-coding genes and a control region. Similar to other dicroglossid frogs, a tandem duplication of tRNAMet was found. The ND5 gene was located at the 3' end of the control region like in three other Fejervarya species for which mitogenomic data are available. A rearrangement of four tRNA genes, namely Leucine, Threonine, Proline, and Phenylalanine, between ND5 and 12S rRNA, differing from other Fejervarya species, was also observed. 

scholarly journals Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca

2020 ◽  
Author(s):  
Yan Cheng ◽  
Xiaoxue He ◽  
S. V. G. N. Priyadarshani ◽  
Yu Wang ◽  
Li Ye ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Sandy Beaches ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Landscape Plant ◽  
Suaeda Glauca ◽  
Mt Genome ◽  
Mitochondria Genome

Abstract Background Suaeda glauca is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also a beautiful landscape plant with high development prospects and scientific research value. The S. glauca chloroplast genome has recently been reported; however, the mitochondria genome is still unexplored. Results This study assembled the mitochondria genome and annotated the mitochondrial genes of S. glauca based on the Pacbio long reads. The circular mitochondrial genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (27.96%), T (28.01%), C (21.64%), G (21.64%). S. glauca mt genome has 51 genes, including 26 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Phylogenetic analysis with common genes of 28 species resulted in similar morphological classification. Conclusions As a Chenopodiaceae species, S. glauca mt genome will provide insights into the missing pieces in the evolution of sex determination and improve genomic breeding in the future.

scholarly journals The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing

2020 ◽  
Author(s):  
Igor Filipović ◽  
James P. Hereward ◽  
Gordana Rašić ◽  
Gregor J. Devine ◽  
Michael J. Furlong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Invasive Pest ◽  
Long Control Region ◽  
Trna Genes ◽  
Oryctes Rhinoceros ◽  
Mitogenome Sequence ◽  
Long Read

AbstractThe coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts.Sequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitochondrial genome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes.The complete circular mitochondrial genome of O. rhinoceros is 20,898 bp-long, with a gene content canonical for insects (13 PCGs, 2 rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the CRB mitogenome sequence and annotation.

scholarly journals The Whole Genome Assembly and Comparative Genomic Research ofThellungiella parvula(Extremophile Crucifer) Mitochondrion

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Xuelin Wang ◽  
Changwei Bi ◽  
Yiqing Xu ◽  
Suyun Wei ◽  
Xiaogang Dai ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Genomic Research ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Protein Coding ◽  
Ssr Analysis ◽  
Brassicaceae Species ◽  
Mt Genome ◽  
Rna Genes

The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile speciesThellungiella parvula(T. parvula) have been determined with the lengths of 255,773 bp.T. parvulamt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome ofT. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species,T. parvulais related toArabidopsis thalianawhose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

The mitochondrial genome of Gyrodactylus salaris (Platyhelminthes: Monogenea), a pathogen of Atlantic salmon (Salmo salar)

Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 739-747 ◽  
Author(s):  
T. HUYSE ◽  
L. PLAISANCE ◽  
B. L. WEBSTER ◽  
T. A. MO ◽  
T. A. BAKKE ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Ribosomal Rna ◽  
Trna Gene ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Coding Regions ◽  
Mt Genome

SUMMARYIn the present study, we describe the complete mitochondrial (mt) genome of the Atlantic salmon parasite Gyrodactylus salaris, the first for any monogenean species. The circular genome is 14 790 bp in size. All of the 35 genes recognized from other flatworm mitochondrial genomes were identified, and they are transcribed from the same strand. The protein-coding and ribosomal RNA (rRNA) genes share the same gene arrangement as those published previously for neodermatan mt genomes (representing cestodes and digeneans only), and the genome has an overall A+T content of 65%. Three transfer RNA (tRNA) genes overlap with other genes, whereas the secondary structure of 3 tRNA genes lack the DHU arm and 1 tRNA gene lacks the TΨC arm. Eighteen regions of non-coding DNA ranging from 4 to 112 bp in length, totalling 278 bp, were identified as well as 2 large non-coding regions (799 bp and 768 bp) that were almost identical to each other. The completion of the mt genome offers the opportunity of defining new molecular markers for studying evolutionary relationships within and among gyrodactylid species.

The complete mitochondrial genome of Plodia interpunctella (Lepidoptera: Pyralidae) and comparison with other Pyraloidea insects

Genome ◽  
2016 ◽  
Vol 59 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Qiu-Ning Liu ◽  
Xin-Yue Chai ◽  
Dan-Dan Bian ◽  
Chun-Lin Zhou ◽  
Bo-Ping Tang
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Plodia Interpunctella ◽  
Rrna Genes ◽  
Likelihood Method ◽  
Trna Genes ◽  
Cox1 Gene ◽  
Stem Loop ◽  
Lepidoptera Pyralidae ◽  
Mt Genome

The mitochondrial (mt) genome can provide important information for the understanding of phylogenetic relationships. The complete mt genome of Plodia interpunctella (Lepidoptera: Pyralidae) has been sequenced. The circular genome is 15 287 bp in size, encoding 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The AT skew of this mt genome is slightly negative, and the nucleotide composition is biased toward A+T nucleotides (80.15%). All PCGs start with the typical ATN (ATA, ATC, ATG, and ATT) codons, except for the cox1 gene which may start with the CGA codon. Four of the 13 PCGs harbor the incomplete termination codon T or TA. All the tRNA genes are folded into the typical clover-leaf structure of mitochondrial tRNA, except for trnS1 (AGN) in which the DHU arm fails to form a stable stem–loop structure. The overlapping sequences are 35 bp in total and are found in seven different locations. A total of 240 bp of intergenic spacers are scattered in 16 regions. The control region of the mt genome is 327 bp in length and consisted of several features common to the sequenced lepidopteran insects. Phylogenetic analysis based on 13 PCGs using the Maximum Likelihood method shows that the placement of P. interpunctella was within the Pyralidae.

scholarly journals The assembled Banana dihaploid mitochondrial genome is compact with a high number of gene copies

2022 ◽  
Author(s):  
Shruthy Priya Prakash ◽  
Vaidheki Chandrasekar ◽  
Selvi Subramanian ◽  
Rahamatthunnisha Ummar
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Copy Number ◽  
Ribosomal Proteins ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Mt Genome

Banana being a major food crop all around the world, attracts various research interests in crop improvement. In banana, complete genome sequences of Musa accuminata and Musa balbisiana are available. However, the mitochondrial genome is not sequenced or assembled. Mitochondrial (mt) genes play an important role in flower and seed development and in Cytoplasmic Male Sterility. Unraveling banana mt genome architecture will be a foundation for understanding inheritance of traits and their evolution. In this study, the complete banana mt genome is assembled from the whole genome sequence data of the Musa acuminata subsp. malaccensis DH-Pahang. The mt genome sequence acquired by this approach was 409574 bp and it contains, 54 genes coding for 25 respiratory complex proteins 15 ribosomal proteins, 12 tRNA genes and two ribosomal RNA gene. Except atpB, rps11 and rps19 other genes are in multiple copies. The copy number is 12 in tRNA genes. In addition, nearly 25% tandem repeats are also present in it. These mt proteins are identical to the mt proteins present in the other members of AA genome and share 98% sequence similarity with M. balbisiana. The C to U RNA editing is profoundly higher (87 vs 13%) in transcripts of M. balbisiana (BB) compared to M. accuminata (AA). The banana AA mitochondrial genome is tightly packed with 233 genes, with less rearrangements and just 5.3% chloroplast DNA in it. The maintenance of high copy number of functional mt genes suggest that they have a crucial role in the evolution of banana.

The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)

Zootaxa ◽  
2013 ◽  
Vol 3620 (2) ◽  
pp. 260-272 ◽  
Author(s):  
WEN SONG ◽  
HU LI ◽  
FAN SONG ◽  
LI LIU ◽  
PEI WANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Repetitive Sequences ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Protein Coding ◽  
Simple Loop ◽  
Complete Mitogenome

The 16, 299 bp long mitochondrial genome (mitogenome) of a tessaratomid bug, Eusthenes cupreus (Westwood), is reported and analyzed. The mitogenome represents the first sequenced complete mitogenome of the heteropteran family Tessaratomidae. The mitogenome of E. cuopreus is a typical circular DNA molecule with a total AT content of 74.1%, and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The gene arrangement is identical with the most common type in insects. Most PCGs start with the typical ATN codon, except that the initiation codon for COI is TTG. All tRNAs possess the typical clover-leaf structure, except tRNASer (AGN), in which the dihydrouridine (DHU) arm forms a simple loop. Six domains with 45 helices and three domains with 27 helices are predicted in the secondary structures of rrnL and rrnS, respectively. The control region is located between rrnS and tRNAIle, including some short microsatellite repeat sequences. In addition, three different repetitive sequences are found in the control region and the tRNAIle-tRNAGln-tRNAMet-ND2 gene cluster. One of the unusual features of this mitogenome is the presence of one tRNAGln-like sequence in the control region. This extra tRNAGln-like sequence is 73 bp long, and the anticodon arm is identical to that of the regular tRNAGln.

scholarly journals Rapid shifts in mitochondrial tRNA import in a plant lineage with extensive mitochondrial tRNA gene loss

2021 ◽  
Author(s):  
Jessica Marie Warren ◽  
Thalia Salinas-Giegé ◽  
Deborah A. Triant ◽  
Douglas R. Taylor ◽  
Laurence Drouard ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Loss ◽  
Trna Gene ◽  
Flowering Plant ◽  
Trna Genes ◽  
Evolutionary Divergence ◽  
Mitochondrial Trna ◽  
Trna Import ◽  
History Of ◽  
Mitochondrial Trna Gene

In most eukaryotes, transfer RNAs (tRNAs) are one of the very few classes of genes remaining in the mitochondrial genome, but some mitochondria have lost these vestiges of their prokaryotic ancestry. Sequencing of mitogenomes from the flowering plant genus Silene previously revealed a large range in tRNA gene content, suggesting rapid and ongoing gene loss/replacement. Here, we use this system to test longstanding hypotheses about how mitochondrial tRNA genes are replaced by importing nuclear-encoded tRNAs. We traced the evolutionary history of these gene loss events by sequencing mitochondrial genomes from key outgroups (Agrostemma githago and Silene [=Lychnis] chalcedonica). We then performed the first global sequencing of purified plant mitochondrial tRNA populations to characterize the expression of mitochondrial-encoded tRNAs and the identity of imported nuclear-encoded tRNAs. We also confirmed the utility of high-throughput sequencing methods for the detection of tRNA import by sequencing mitochondrial tRNA populations in a species (Solanum tuberosum) with known tRNA trafficking patterns. Mitochondrial tRNA sequencing in Silene revealed substantial shifts in the abundance of some nuclear-encoded tRNAs in conjunction with their recent history of mt-tRNA gene loss and surprising cases where tRNAs with anticodons still encoded in the mitochondrial genome also appeared to be imported. These data suggest that nuclear-encoded counterparts are likely replacing mitochondrial tRNAs even in systems with recent mitochondrial tRNA gene loss, and the redundant import of a nuclear-encoded tRNA may provide a mechanism for functional replacement between translation systems separated by billions of years of evolutionary divergence.

Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

Zootaxa ◽  
2020 ◽  
Vol 4860 (3) ◽  
pp. 401-412
Author(s):  
ZHI-TENG CHEN
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeats ◽  
Evolutionary Rate ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Long Control Region ◽  
Trna Genes ◽  
Stem Loop ◽  
First Time

The complete mitochondrial genome (mitogenome) of Pteronarcys sachalina Klapálek was sequenced and compared with those of two other salmonflies for the first time. The mitogenome of P. sachalina was 16,180 bp in length, with an A+T content of 70.6%. The uniform set of 37 genes (13 PCGs, 22 tRNA genes and two rRNA genes) and a long control region (1431 bp) were all annotated. Most PCGs had standard ATN start codons and TAN stop codons. COX1 exhibited the highest evolutionary rate among the 13 PCGs of sequenced species of Pteronarcyidae. ND2 was truncated at the 3′ end when compared with congeners. Most tRNA genes had typical cloverleaf secondary structures, whereas the dihydrouridine (DHU) arm of trnS1 was reduced. Tandem repeats and stem-loop (SL) structures were predicted in the control region of P. sachalina. Conserved sequences were found in control regions of the three already sequenced salmonflies, P. sachalina, Pteronarcys princeps Banks, and Pteronarcella badia (Hagen). 

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