Mitochondrial phylogeny and comparative mitogenomics of closely related pine moth pests (Lepidoptera:Dendrolimus)

BackgroundPine moths,Dendrolimusspp. (Lasiocampidae), are serious economic pests of conifer forests. Six closely related species (Dendrolimus punctatus,D. tabulaeformis,D. spectabilis,D. superans,D. houi, andD. kikuchii) occur in China and cause serious damage to coniferophyte. The complete mito genomes ofDendrolimusgenus are significant to resolve the phylogenetic relationship and provide theoretical support in pest control.MethodsThe complete mitogenomes of three species (D. superans,D. houi, andD. kikuchii) were sequenced based on PCR-amplified with universal primers, which were used to amplify initial fragments. Phylogenetic analyses were carried out with 78 complete mitogenomes of lepidopteran species from 10 superfamilies.ResultsThe complete mitochondrial genomes of these three species were 15,417, 15,381, and 15,377 bp in length, separately. The phylogenetic analyses produced consistent results for sixDendrolimusspecies based on complete mitogenomes, two major clades were formed, one containingD. spectabilisclustered withD. punctatus+D. tabulaeformis, andD. superansas the sister group to this three-taxon clade, the other containingD. kikuchiiandD. houi. Comparative analyses of the congeneric mitochondrial genomes were performed, which showed that non-coding regions were more variable than the A+T rich region. The mitochondrial nucleotide diversity was more variable when compared within than among genus, and the concatenated tRNA region was the most conserved and the nd6 genes was the most variable.

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Comparative analysis of twelve mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha) and their phylogenetic implications

PeerJ ◽

10.7717/peerj.12465 ◽

2021 ◽

Vol 9 ◽

pp. e12465

Author(s):

Nian Gong ◽

Lin Yang ◽

Xiangsheng Chen

Keyword(s):

Nucleotide Diversity ◽

Stop Codon ◽

Purifying Selection ◽

Sister Group ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Phylogenetic Implications ◽

Basal Position ◽

High Support ◽

Complete Mitochondrial Genomes

Here, the complete mitochondrial genomes (mitogenomes) of 12 Caliscelidae species, Augilina tetraina, Augilina triaina, Symplana brevistrata, Symplana lii, Neosymplana vittatum, Pseudosymplanella nigrifasciata, Symplanella brevicephala, Symplanella unipuncta, Augilodes binghami, Cylindratus longicephalus, Caliscelis shandongensis, and Peltonotellus sp., were determined and comparatively analyzed. The genomes varied from 15,424 to 16,746 bp in size, comprising 37 mitochondrial genes and an A+T-rich region. The typical gene content and arrangement were similar to those of most Fulgoroidea species. The nucleotide compositions of the mitogenomes were biased toward A/T. All protein-coding genes (PCGs) started with a canonical ATN or GTG codon and ended with TAN or an incomplete stop codon, single T. Among 13 PCGs in 16 reported Caliscelidae mitogenomes, cox1 and atp8 showed the lowest and highest nucleotide diversity, respectively. All PCGs evolved under purifying selection, with atp8 considered a comparatively fast-evolving gene. Phylogenetic relationships were reconstructed based on 13 PCGs in 16 Caliscelidae species and five outgroups using maximum likelihood and Bayesian inference analyses. All species of Caliscelidae formed a steadily monophyletic group with high support. Peltonotellini was present at the basal position of the phylogenetic tree. Augilini was the sister group to Caliscelini and Peltonotellini.

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Two complete mitochondrial genomes of Crocodylus and implications for crocodilians phylogeny

Amphibia-Reptilia ◽

10.1163/156853810791769464 ◽

2010 ◽

Vol 31 (3) ◽

pp. 299-309 ◽

Cited By ~ 8

Author(s):

Peng Yan ◽

Ge Feng ◽

Xiaoqiang Li ◽

Xiaobing Wu

Keyword(s):

Phylogenetic Analyses ◽

Sister Group ◽

Molecular Data ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Nucleotide Level ◽

Protein Coding ◽

Genome Features ◽

Gavialis Gangeticus ◽

Complete Mitochondrial Genomes

AbstractThe complete mitochondrial (mt) genomes of two crocodilians: Crocodylus palustris and Crocodylus mindorensis, were sequenced in order to examine their gene and genome features. Additionally, we intended to increase the amount of molecular data suitable for phylogenetic analysis. Their gene orders conform to other crocodilians that have been sequenced, except the arrangement of two tRNA genes differ from other vertebrates, showing that the gene order of crocodilians is remarkably conserved. Phylogenetic analyses (maximum likelihood, Bayesian inference) based on the mt protein-coding genes at the nucleotide level were performed among crocodilians for which complete mt genomes were available. The results suggest that the gharial (Gavialis gangeticus) joins the false gharial (Tomistoma schlegelii) on a common branch, that constitutes a sister group to traditional Crocodylidae. In this report, Mecistops cataphractus is evidently most closely related to Osteolaemus tetraspis. They are isolated as sister taxon from the main clades in Crocodylus. Regarding Paleosuchus, it appears as sister group to Caiman within the Alligatoridae. In particular, relationships among species of Crocodylus (true crocodiles) are discussed.

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Characterization of the Complete Mitochondrial Genomes from Two Nitidulid Pests with Phylogenetic Implications

Insects ◽

10.3390/insects11110779 ◽

2020 ◽

Vol 11 (11) ◽

pp. 779

Author(s):

Xiaoxiao Chen ◽

Qing Song ◽

Min Huang

Keyword(s):

Tandem Repeats ◽

Stop Codon ◽

Phylogenetic Analyses ◽

Sister Group ◽

Start Codon ◽

Mitochondrial Genomes ◽

Sister Group Relationship ◽

Rich Region ◽

Phylogenetic Implications ◽

Complete Mitochondrial Genomes

The complete mitochondrial genomes of Xenostrongylusvariegatus and Epuraea sp. were sequenced and analyzed. The total genome lengths are 17,657 and 16,641 bp, with an A+T content of 77.2% and 76.4%, respectively. Each mitochondrial genome consists of 37 coding genes and a non-coding (AT-rich) region. All protein-coding genes (PCGs) start with the standard start codon, ATN, and end with complete stop codons, TAA and TAG, or an incomplete stop codon, T. All tRNAs can be folded into the typical clover-leaf secondary structure, with the exception of trnS1 in both species with a reduced dihydrouridine (DHU) arm. The AT-rich region has tandem repeats differing in both number and length. Genetic distance and Ka/Ks analyses show that nad6 has a higher variability and more rapid evolutionary rate than other PCGs. Both maximum likelihood and Bayesian inference phylogenetic analyses based on 13 PCGs and 2 ribosome DNAs (rDNAs) agree with the previous phylogenies in supporting the Nitidulidae monophyly and the sister-group relationship of Kateretidae + (Monotomidae + Nitidulidae).

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Three Complete Mitochondrial Genomes of Erotylidae (Coleoptera: Cucujoidea) with Higher Phylogenetic Analysis

Insects ◽

10.3390/insects12060524 ◽

2021 ◽

Vol 12 (6) ◽

pp. 524

Author(s):

Jing Liu ◽

Yuyu Wang ◽

Ruyue Zhang ◽

Chengmin Shi ◽

Weicheng Lu ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Genomic Analysis ◽

Sister Group ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Transfer Rnas ◽

Next Generation Sequencing Technology ◽

The Family ◽

Mt Genome ◽

Complete Mitochondrial Genomes

The family Erotylidae belongs to the superfamily Cucujoidea, which are phytophagous and mycophagous. So far, only two representative complete mitochondrial (mt) genomes of Erotylidae have been sequenced. Mitochondrial genomes of Tritoma metasobrina, Neotriplax arisana, and Episcapha opaca, which all belong to the subfamily Erotylinae, were sequenced using next-generation sequencing technology to better understand the diversity of mt genomes of Erotylidae. A comparative mt genomic analysis was conducted on the three sequenced representatives of Erotylinae and Languriinae sp. (Languriinae). The size of the complete mt genome of the 4 species ranged from 15,581 bp to 16,502 bp in length, including 37 genes (13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs) and the control region. The arrangements of their mt genomes are highly consistent with other Coleoptera species. The start codons of two PCGs (ND1 and ND5) and the stop codons of one PCG (ATP8) were illustrated differences between Languriinae sp. and the other three species. All tRNAs of these 4 species exhibited cloverleaf secondary structures except that the dihydorouridine (DHU) arm of tRNASer(AGN) was absent. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods all supported that Erotylidae as monophyletic. Erotylinae was monophyletic being the sister group to Xenocelinae. Languriinae was closely related to ‘Erotylinae-Xenocelinae’. Our results recovered Languriinae nested within Erotylidae.

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Complete Mitochondrial Genomes of Three Nuthatches From the Genus Sitta (Aves: Passeriformes: Sittidae) and Mitogenome-Based Phylogenetic Analysis

10.21203/rs.3.rs-1097909/v1 ◽

2021 ◽

Author(s):

Qing-Miao Yuan ◽

Xu Luo ◽

Jing Cao ◽

Yu-Bao Duan

Keyword(s):

Phylogenetic Analyses ◽

Taxonomic Status ◽

Sister Group ◽

Gene Arrangement ◽

Phylogenetic Position ◽

Mitochondrial Genomes ◽

Phylogenetic Relations ◽

Genome Data ◽

The Family ◽

Complete Mitochondrial Genomes

Abstract Background Nuthatches (genus Sitta) comprise a group of Passeriformes. With the publication of more mitochondrial genome data, there has been considerable focus on the taxonomic status of the nuthatches. To understand the phylogenetic position of Sitta and phylogenetic relations within this genus, we sequenced and analyzed the complete mitochondrial genomes of three species, S. himalayensis, S. nagaensis and S. yunnanensis, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitochondrial genomes of three Sitta species are 16,822-16,830 bp in length and consisted of 37 genes and a control region. This study recovered the same gene arrangement found in the mitogenomes of Gallus gallus, which is considered the typical ancestral avian gene order. All tRNAs were predicted to form the typical cloverleaf secondary structures. Bayesian inference and maximum likelihood phylogenetic analyses of sequences of 18 species obtained a well-supported topology. The family Sittidae is the sister-group of Troglodytidae, and the genus Sitta can be divided into 3 major clades. We demonstrated the phylogenetic relationships within genus Sitta (S. carolinensis + (S. villosa + S. yunnanensis + (S. himalayensis + (S. europaea + S. nagaensis)))).

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Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny

Insects ◽

10.3390/insects12090779 ◽

2021 ◽

Vol 12 (9) ◽

pp. 779 ◽

Cited By ~ 1

Author(s):

Ke-Ke Xu ◽

Qing-Ping Chen ◽

Sam Pedro Galilee Ayivi ◽

Jia-Yin Guan ◽

Kenneth B. Storey ◽

...

Keyword(s):

Sister Group ◽

Recent Common Ancestor ◽

Mitochondrial Genomes ◽

Sister Group Relationship ◽

Protein Coding ◽

Most Recent Common Ancestor ◽

Stick Insects ◽

Long Time ◽

Relationship Of ◽

Complete Mitochondrial Genomes

Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.

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Intergenic Spacer Length Variability in Cultivated, Weedy and Wild Rye Species

Open Life Sciences ◽

10.1515/biol-2015-0020 ◽

2015 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

L. Skuza ◽

E. Filip ◽

I. Szućko

Keyword(s):

Intergenic Spacer ◽

Repetitive Elements ◽

Universal Primers ◽

Closely Related Species ◽

Spacer Length ◽

Coding Regions ◽

Similarity Group ◽

Rdna Igs ◽

High Level ◽

Ribosomal Rrna

AbstractNon-coding rDNA spacers (IGS) can vary substantially in size due to differences in the number of repetitive elements among closely related species. Three pairs of universal primers were used in this study for the amplification of non-coding regions of ribosomal (rRNA) IGS. The amplified IGS products obtained from 19 Secale accessions, which included both cultivated and noncultivated rye and which represented three species and four subspecies of the genus Secale, showed a high level of polymorphism. The PCR results were characterized by multiple bands (1-6), different sizes (750bp-3250bp) and 100% polymorphism. Cluster analysis using the neighborjoining method based on the Dice’s coefficient of genetic similarity showed a division of the studied species into two similarity groups. All the studied Secale cereale ssp. cereale were found to belong to the same similarity group. The variation in the size of the IGS among the species which was detected in this study could be due to dissimilarity between the sequences of their respective repetitive elements or between their tandem repeat numbers. The highly interspecific polymorphisms for the rDNA IGS regions suggested that IGS might be a useful molecular marker in studies of Secale species.

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

10.7287/peerj.preprints.27478v1 ◽

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.

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Phylogeny of Terrestrial Isopods Based on the Complete Mitochondrial Genomes, Subvert the Monophyly of Oniscidea

10.21203/rs.3.rs-25479/v1 ◽

2020 ◽

Author(s):

Rui Zhang ◽

Ruru Chen ◽

Jianmei An ◽

Carlos A. Santamaria

Keyword(s):

Phylogenetic Analyses ◽

Soil Formation ◽

Taxonomic Status ◽

Mitochondrial Genomes ◽

Phylogenetic Hypothesis ◽

Terrestrial Isopods ◽

The Family ◽

Complete Mitochondrial Genomes

Abstract Background: Oniscidea is the only truly terrestrial taxon within the Crustacea, and vital to soil formation. However, the monophyly of suborder Oniscidea has been in dispute since 1995, with different studies disagreeing on whether the coastal Ligiidae are included within the suborder. To clarify the phylogenetic hypothesis of suborder Oniscidea, we sequenced the complete mitochondrial genomes of Ligia exotica (Roux, 1828) and Mongoloniscus sinensis (Dollfus, 1901).Results: Like most metazoan, the complete mitogenomes of two species with circular double strands. The structure and characters of mitogenomes of these two species are analyzed. The constructed phylogenetic analyses show that Oniscidea is polyphyletic group, with Ligia being more closely related to marine isopods (Valvifera + Cymothoida + Sphaeromatidea).Conclusions: We elevate the taxonomic status of the family Ligiidae to the suborder Ligiaidea which are with parallel rank with Oniscidea. Ligiaidea is much primitive than other exact terrestrial isopods. Crinocheta are strongly monophyly, family Agnaridae is more closely related to Porcellionidae rather than Armadillididae.

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Mitochondrial Phylogenomics of Tenthredinidae (Hymenoptera: Tenthredinoidea) Supports the Monophyly of Megabelesesinae as a Subfamily

Insects ◽

10.3390/insects12060495 ◽

2021 ◽

Vol 12 (6) ◽

pp. 495

Author(s):

Gengyun Niu ◽

Sijia Jiang ◽

Özgül Doğan ◽

Ertan Mahir Korkmaz ◽

Mahir Budak ◽

...

Keyword(s):

Host Plants ◽

Sister Group ◽

Morphological Characters ◽

Mitochondrial Genomes ◽

Origin Time ◽

Plant Utilization ◽

Group Placement ◽

Robust Evidence ◽

Close Investigation ◽

Complete Mitochondrial Genomes

Tenthredinidae represents one of the external feeders of the most diverse superfamily, Tenthredinoidea, with diverse host plant utilization. In this study, four complete mitochondrial genomes (mitogenomes), those of Cladiucha punctata, Cladiucha magnoliae, Megabeleses magnoliae, and Megabeleses liriodendrovorax, are newly sequenced and comparatively analyzed with previously reported tenthredinid mitogenomes. The close investigation of mitogenomes and the phylogeny of Tenthredinidae leads us to the following conclusions: The subfamilial relationships and phylogenetic placements within Tenthredinidae are mostly found to be similar to the previously suggested phylogenies. However, the present phylogeny supports the monophyly of Megabelesesinae as a subfamily, with the sister-group placement of Cladiucha and Megabeleses outside of Allantinae. The occurrence of the same type of tRNA rearrangements (MQI and ANS1ERF) in the mitogenomes of Megabelesesinae species and the presence of apomorphic morphological characters also provide robust evidence for this new subfamily. The divergence and diversification times of the subfamilies appear to be directly related to colonization of the flowering plants following the Early Cretaceous. The origin time and diversification patterns of Megabelesesinae were also well matched with the divergence times of their host plants from Magnoliaceae.

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