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.

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). 

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.

Characterisation of the complete mitochondrial genome of the insect-parasitic nematode Heterorhabditis bacteriophora: an idiosyncratic gene order and the presence of multiple long non-coding regions

Nematology ◽  
2021 ◽  
pp. 1-18
Author(s):  
Sassia Omar Regeai ◽  
David A. Fitzpatrick ◽  
Ann M. Burnell ◽  
Thomais Kakouli-Duarte
Keyword(s):  
Control Region ◽  
Insect Pests ◽  
Biological Control Agent ◽  
Complete Mitochondrial Genome ◽  
Heterorhabditis Bacteriophora ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Entire Genome ◽  
Coding Regions

Summary We present here the complete mtDNA genome (mitogenome) of Heterorhabditis bacteriophora, an important biological control agent of soil-dwelling insect pests in agriculture and horticulture. This is the first description of a mitogenome for a member of the family Heterorhabditidae. The genome contains the typical chromadorean complement of 12 protein-coding genes, 22 tRNA genes and two rRNA genes. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. For the entire genome, the nucleotide contents are 47.02% (T), 28.81% (A), 16.10% (G), 8.08% (C) and 75.83% (AT). Heterorhabditis bacteriophora has a unique, idiosyncratic gene arrangement. It differs from that of Caenorhabditis elegans in having a block of seven genes: trnQ-trnF-cytb-trnL1-cox3-trnT-nad4 translocated to a position between nad3 and nad5, as well as having a change in the position of the four tRNA block gene cluster, trnC-trnM-trnD-trnG, where trnC and trnM have switched places and trnD and trnG have translocated between nad4 and nad5 genes. The H. bacteriophora mitogenome is 18 128 bp long, and thus is ca 4 kb larger than the mitogenomes of most chromadoreans. This relatively large genome is due to the presence of five non-coding regions (NCR): NCR1 (114 bp), NCR2 (159 bp), NCR3 (498 bp), NCR4 (1917 bp) and NCR5 (2154 bp), which make up 26.7% of the genome. The NCR5 had the highest A + T content of 83.47% indicating that this region is the likely AT-rich control region. The complete 498 bp NCR3 sequence is duplicated in NCR4 and in NCR5 (the putative AT-rich control region). Such an organisation has not been reported previously in nematode mtDNA.

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 Analysis of the Complete Mitochondrial Genome Sequence of the Diploid CottonGossypium raimondiiby Comparative Genomics Approaches

2016 ◽  
Vol 2016 ◽  
pp. 1-18 ◽  
Author(s):  
Changwei Bi ◽  
Andrew H. Paterson ◽  
Xuelin Wang ◽  
Yiqing Xu ◽  
Dongyang Wu ◽  
...  
Keyword(s):  
Natural Fiber ◽  
Animal Feed ◽  
Higher Plants ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Mt Dna ◽  
Transfer Event ◽  
Mt Genome

Cotton is one of the most important economic crops and the primary source of natural fiber and is an important protein source for animal feed. The complete nuclear and chloroplast (cp) genome sequences ofG. raimondiiare already available but not mitochondria. Here, we assembled the complete mitochondrial (mt) DNA sequence ofG. raimondiiinto a circular genome of length of 676,078 bp and performed comparative analyses with other higher plants. The genome contains 39 protein-coding genes, 6 rRNA genes, and 25 tRNA genes. We also identified four larger repeats (63.9 kb, 10.6 kb, 9.1 kb, and 2.5 kb) in this mt genome, which may be active in intramolecular recombination in the evolution of cotton. Strikingly, nearly all of theG. raimondiimt genome has been transferred to nucleus on Chr1, and the transfer event must be very recent. Phylogenetic analysis reveals thatG. raimondii, as a member of Malvaceae, is much closer to another cotton (G. barbadense) than other rosids, and the clade formed by twoGossypiumspecies is sister to Brassicales. TheG. raimondiimt genome may provide a crucial foundation for evolutionary analysis, molecular biology, and cytoplasmic male sterility in cotton and other higher plants.

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

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yan Cheng ◽  
Xiaoxue He ◽  
S. V. G. N. Priyadarshani ◽  
Yu Wang ◽  
Li Ye ◽  
...  
Keyword(s):  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Sandy Beaches ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Gene Migration ◽  
Protein Coding Genes ◽  
Suaeda Glauca ◽  
Mt Genome

Abstract Background Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific research value. The S. glauca chloroplast (cp) genome has recently been reported; however, the mitochondria (mt) genome is still unexplored. Results The mt genome of S. glauca were assembled based on the reads from Pacbio and Illumina sequencing platforms. The circular mt genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (28.00%), T (27.93%), C (21.62%), and G (22.45%). S. glauca mt genome contains 61 genes, including 27 protein-coding genes, 29 tRNA genes, and 5 rRNA genes. The sequence repeats, RNA editing, and gene migration from cp to mt were observed in S. glauca mt genome. Phylogenetic analysis based on the mt genomes of S. glauca and other 28 taxa reflects an exact evolutionary and taxonomic status of S. glauca. Furthermore, the investigation on mt genome characteristics, including genome size, GC contents, genome organization, and gene repeats of S. gulaca genome, was investigated compared to other land plants, indicating the variation of the mt genome in plants. However, the subsequently Ka/Ks analysis revealed that most of the protein-coding genes in mt genome had undergone negative selections, reflecting the importance of those genes in the mt genomes. Conclusions In this study, we reported the mt genome assembly and annotation of a halophytic model plant S. glauca. The subsequent analysis provided us a comprehensive understanding of the S. glauca mt genome, which might facilitate the research on the salt-tolerant plant species.

scholarly journals Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis

ZooKeys ◽  
2021 ◽  
Vol 1012 ◽  
pp. 135-150
Author(s):  
Wenjuan Shan ◽  
Mayinur Tursun ◽  
Shiyu Zhou ◽  
Yucong Zhang ◽  
Huiying Dai
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Genetic Research ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Associated Sequences ◽  
Complete Mitogenome ◽  
Hot Environments

Lepus yarkandensis is a national second-class protected animal endemic to China and distributed only in the hot and arid Tarim Basin in Xinjiang. We sequenced and described the complete mitogenome of L. yarkandensis to analyze its characteristics and phylogeny. The species’ DNA is a 17,047 bp circular molecule that includes 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The overall base composition was as follows: A, 31.50%; T, 29.40%; G, 13.30% and C, 25.80%, with a high A+T bias of 60.9%. In the PCGs, ND6 had deviation ranges for AT skew (–0.303) and GC skew (0.636). The Ka/Ks values of ND1 (1.067) and ND6 (1.352) genes were >1, indicating positive selection, which might play an important role in the adaptation of L. yarkandensis to arid and hot environments. The conserved sequence block, the central conserved domain, and the extended termination-associated sequences of the control region and their features were identified and described. The phylogenetic tree based on the complete mitogenome showed that L. yarkandensis was closely related to the sympatric Lepus tibetanus pamirensis. These novel datasets of L. yarkandensis can supply basic data for phylogenetic studies of Lepus spp., apart from providing essential and important resource for further genetic research and the protection of this species.

scholarly journals Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plantSalix suchowensis

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3148 ◽  
Author(s):  
Ning Ye ◽  
Xuelin Wang ◽  
Juan Li ◽  
Changwei Bi ◽  
Yiqing Xu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Gc Content ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Shrub Willow ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Mt Genome

Willow is a widely used dioecious woody plant ofSalicaceaefamily in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence ofS. suchowensiswith the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of theS. suchowensismt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported thatSalixas a sister toPopulus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research ofS. suchowensismt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.

scholarly journals Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 724 ◽  
Author(s):  
Xiaolei Yu ◽  
Wei Tan ◽  
Huanyu Zhang ◽  
Weiling Jiang ◽  
Han Gao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Ground Beetle ◽  
Purifying Selection ◽  
Trna Genes ◽  
Stem Loop ◽  
Protein Coding

In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.

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