scholarly journals The First Complete Mitochondrial Genomes of Two Sibling Species from Nitidulid Beetles Pests

Insects ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 24 ◽  
Author(s):  
Yi Wu ◽  
Yangming Lan ◽  
Liyuan Xia ◽  
Miao Cui ◽  
Weiwei Sun ◽  
...  
Keyword(s):  
Control Region ◽  
Sibling Species ◽  
Transfer Rna ◽  
Mitochondrial Genomes ◽  
Identification System ◽  
Storage Pests ◽  
Nitidulid Beetles ◽  
Mt Genome ◽  
Rna Genes ◽  
Complete Mitochondrial Genomes

Carpophilus dimidiatus (Fabricius, 1792) and Carpophilus pilosellus Motschulsky are two sibling species and economically important storage pests worldwide. The first complete mitochondrial (mt) genomes of both were sequenced using next-generation sequencing. The mt genomes of C. dimidiatus and C. pilosellus are circular, with total lengths of 15,717 bp and 15,686 bp, respectively. Gene order and content for both species are similar to what has been observed in ancestral insects and consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. Comparing the mt genome data of C. dimidiatus and C. pilosellus, they are similar in organization, arrangement patterns, GC contents, transfer RNA (tRNA) secondary structures, and codon usage patterns. Small differences were noted with regards to the nucleotide similarity of coding regions and the control region. This is the first publication of the complete mitochondrial genomes of two sibling species. The mt genome sequences can supplement the nuclear markers of the Carpophilus genus in research species identification, system evolution, and population genetic structure, and also will be valuable molecular marker for further genetic studies.

Mitochondrial genomes of Vanhornia eucnemidarum (Apocrita: Vanhorniidae) and Primeuchroeus spp. (Aculeata: Chrysididae): evidence of rearranged mitochondrial genomes within the Apocrita (Insecta: Hymenoptera)

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 752-766 ◽  
Author(s):  
Lyda Raquel Castro ◽  
Kalani Ruberu ◽  
Mark Dowton
Keyword(s):  
Molecular Evolution ◽  
Gene Duplication ◽  
Ribosomal Rna ◽  
Nucleotide Composition ◽  
Gene Organization ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Noncoding Regions ◽  
Mt Genome ◽  
Rna Genes

We sequenced most of the mitochondrial (mt) genomes of 2 apocritan taxa: Vanhornia eucnemidarum and Primeuchroeus spp. These mt genomes have similar nucleotide composition and codon usage to those of mt genomes reported for other Hymenoptera, with a total A + T content of 80.1% and 78.2%, respectively. Gene content corresponds to that of other metazoan mt genomes, but gene organization is not conserved. There are a total of 6 tRNA genes rearranged in V. eucnemidarum and 9 in Primeuchroeus spp. Additionally, several noncoding regions were found in the mt genome of V. eucnemidarum, as well as evidence of a sustained gene duplication involving 3 tRNA genes. We also report an inversion of the large and small ribosomal RNA genes in Primeuchroeus spp. mt genome. However, none of the rearrangements reported are phylogenetically informative with respect to the current taxon sample.Key words: mitochondrial genomes, molecular evolution, hymenoptera.

scholarly journals Complete mitochondrial genomes of five raptors and implications for the phylogenetic relationships between owls and nightjars

2019 ◽  
Author(s):  
Gang Liu ◽  
Lizhi Zhou ◽  
Guanghong Zhao
Keyword(s):  
Control Region ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Stop Codon ◽  
Mitochondrial Genomes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Independent Families ◽  
Complete Mitochondrial Genomes

The phylogenetic relationships between owls and nightjars are rather complex and controversial. To clarify these relationships, we determined the complete mitochondrial genomes of Glaucidium cuculoides, Otus scops, Glaucidium brodiei, Caprimulgus indicus, and Strix leptogrammica, and estimated phylogenetic trees based on the complete mitochondrial genomes and aligned sequences from closely related species that were obtained in GenBank. The complete mitochondrial genomes were 17392, 17317, 17549, 17536, and 16307 bp in length. All mitochondrial genomes contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a putative control region. All mitochondrial genomes except for that of Strix leptogrammica contained a pseudo-control region. ATG, GTG, and ATA are generally start codons, whereas TAA is the most frequent stop codon. All tRNAs in the new mtDNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN) , which missing the “DHU” arm. The phylogenetic relationships demonstrated that Strigiformes and Caprimulgiformes are independent orders, and Aegothelidae is a family within Caprimulgiformes. The results also revealed that Accipitriformes is an independent order, and Pandionidae and Sagittariidae are independent families. The results also supported that Apodiformes is polyphyletic, and hummingbirds (family Trochilidae) belong to Apodiformes. Piciformes was most distantly related to all other analyzed orders.

scholarly journals The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Xiao-Feng Xue ◽  
Wei Deng ◽  
Shao-Xuan Qu ◽  
Xiao-Yue Hong ◽  
Renfu Shao
Keyword(s):  
Transfer Rna ◽  
Mitochondrial Genomes ◽  
Rna Genes

scholarly journals Complete mitochondrial genomes of five raptors and implications for the phylogenetic relationships between owls and nightjars

2019 ◽  
Author(s):  
Gang Liu ◽  
Lizhi Zhou ◽  
Guanghong Zhao
Keyword(s):  
Control Region ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Stop Codon ◽  
Mitochondrial Genomes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Independent Families ◽  
Complete Mitochondrial Genomes

The phylogenetic relationships between owls and nightjars are rather complex and controversial. To clarify these relationships, we determined the complete mitochondrial genomes of Glaucidium cuculoides, Otus scops, Glaucidium brodiei, Caprimulgus indicus, and Strix leptogrammica, and estimated phylogenetic trees based on the complete mitochondrial genomes and aligned sequences from closely related species that were obtained in GenBank. The complete mitochondrial genomes were 17392, 17317, 17549, 17536, and 16307 bp in length. All mitochondrial genomes contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a putative control region. All mitochondrial genomes except for that of Strix leptogrammica contained a pseudo-control region. ATG, GTG, and ATA are generally start codons, whereas TAA is the most frequent stop codon. All tRNAs in the new mtDNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN) , which missing the “DHU” arm. The phylogenetic relationships demonstrated that Strigiformes and Caprimulgiformes are independent orders, and Aegothelidae is a family within Caprimulgiformes. The results also revealed that Accipitriformes is an independent order, and Pandionidae and Sagittariidae are independent families. The results also supported that Apodiformes is polyphyletic, and hummingbirds (family Trochilidae) belong to Apodiformes. Piciformes was most distantly related to all other analyzed orders.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genomes of Two Tiny Necrophagous Phorid Flies, Metopina sagittata and Puliciphora borinquenensis (Diptera: Phoridae)

2021 ◽  
Author(s):  
Shu-Tong Dai ◽  
Dian-Xing Feng ◽  
Da-Peng Sun
Keyword(s):  
Mitochondrial Genome ◽  
Species Identification ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Rna Genes ◽  
Complete Mitochondrial Genomes

Abstract The mitochondrial genome is frequently used for species identification and phylogenetic studies. In this study, we first sequenced and annotated the complete mitochondrial genomes of two phorid species that are forensically important in buried or enclosed environments: Metopina sagittata (Liu) and Puliciphora borinquenensis (Wheeler). The complete mitochondrial genome sequences of M. sagittata and P. borinquenensis were 15,640 bp with an A+T content of 75.97% and 15,429 bp with an A+T content of 75.38%, respectively. Their circular genomes both contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region located between rrnS and trnI which was 808 bp for M. sagittata and 746 bp for P. borinquenensis. All the PCGs of both species started with ATN codons except for cox1 which used TTG codon. In addition to the common stop codon TAA and TAG, the incomplete stop codon T was used in two PCGs (cox1 and nad4) of M. sagittata and five PCGs (cox1, cox2, cox3, nad5, and nad4) of P. borinquenensis. There were 3 and 10 mismatched base pairs in the tRNA secondary structures from M. sagittata and P. borinquenensis, respectively. Both maximum likelihood and Bayesian inference analyses indicated that Platypezidae and Phoridae are sister taxa. M. sagittata is closely related to P. borinquenensis within the subfamily Metopininae. This work enhances the databases of Phoridae genomes and contributes to the further study of species identification and phylogenetics of this family.

scholarly journals Complete Mitochondrial Genomes of Two Toxin-Accumulated Nassariids (Neogastropoda: Nassariidae: Nassarius) and Their Implication for Phylogeny

2020 ◽  
Vol 21 (10) ◽  
pp. 3545
Author(s):  
Yi Yang ◽  
Hongyue Liu ◽  
Lu Qi ◽  
Lingfeng Kong ◽  
Qi Li
Keyword(s):  
Biological Significance ◽  
Morphological Characteristics ◽  
Time Estimation ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Sister Group Relationship ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Rna Genes ◽  
Complete Mitochondrial Genomes

The Indo-Pacific nassariids (genus Nassarius) possesses the highest diversity within the family Nassariidae. However, the previous shell or radula-based classification of Nassarius is quite confusing due to the homoplasy of certain morphological characteristics. The toxin accumulators Nassarius glans and Nassarius siquijorensis are widely distributed in the subtidal regions of the Indo-Pacific Ocean. In spite of their biological significance, the phylogenetic positions of N. glans and N. siquijorensis are still undetermined. In the present study, the complete mitochondrial genomes of N. glans and N. siquijorensis were sequenced. The present mitochondrial genomes were 15,296 and 15,337 bp in length, respectively, showing negative AT skews and positive GC skews as well as a bias of AT rich on the heavy strand. They contained 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and several noncoding regions, and their gene order was identical to most caenogastropods. Based on the nucleotide sequences combining 13 protein coding genes and two rRNA genes, a well-supported phylogeny of Nassarius was reconstructed, and several morphological synapomorphies were observed corresponding to the phylogenetic framework. In addition, the sister group relationship between N. variciferus and the remaining toxin-accumulated nassariids was determined, suggesting that the phylogeny might be related to their diet. The divergence time estimation analysis revealed a correlation between speciation events of nassariids and glacial cycles during the Pliocene-Pleistocene epoch.

Ancient Mitochondrial Gene Transfer between Fungi and the Orchids

2019 ◽  
Vol 37 (1) ◽  
pp. 44-57 ◽  
Author(s):  
Brandon T Sinn ◽  
Craig F Barrett
Keyword(s):  
Gene Transfer ◽  
Intimate Relationships ◽  
Mitochondrial Gene ◽  
Intergenic Spacer ◽  
Transfer Rna ◽  
Mitochondrial Genomes ◽  
Obligate Parasites ◽  
Genomic Scale ◽  
Rna Genes ◽  
Lines Of Evidence

Abstract The mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here, we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an ∼270-bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring >8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, nonplant organisms.

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