The complete mitochondrial genome of the freshwater crab Longpotamon kenliense (Decapoda, Brachyura, Potamidae) with phylogenetic consideration

Crustaceana ◽  
2020 ◽  
Vol 93 (11-12) ◽  
pp. 1277-1293
Author(s):  
Yi-Fan Wang ◽  
Shu-Xin Xu ◽  
Chun-Chao Zhu ◽  
Xin-Nan Jia ◽  
Xian-Min Zhou ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Divergence Time ◽  
Complete Sequence ◽  
Divergence Times ◽  
Mitochondrial Genomes ◽  
Freshwater Crab ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
First Time

Abstract The authors herein report for the first time the complete sequence of the mitochondrial genome of Longpotamon kenliense. The results showed that the mitochondrial genome of L. kenliense is 18,499 bp in length, shares 37 genes and 1 control region with the typical metazoan mitochondrial genome, and has a strong A + T bias (74.48%), i.e., a characteristic of the metazoan mitochondrial genome. In addition, the authors used the 13 protein-coding genes from the mitochondrial genomes of L. kenliense and 67 other species of Brachyura available from the NCBI to estimate divergence times. The divergence time of L. kenliense was 14.39 Ma, which is close to the divergence times of L. xiushuiense and L. yangtsekiense, but later than that of Sinopotamon yaanense. The results indicate that the genera Sinopotamon and Longpotamon are closely related and that the genus Sinopotamon has a longer history, which may have been caused by geological events.

scholarly journals Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu Sun ◽  
Hua Huang ◽  
Yudong Liu ◽  
Shanshan Liu ◽  
Jun Xia ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Rich Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Lepidopteran Insects

AbstractIn this study, we analyzed the complete mitochondrial genome (mitogenome) of Speiredonia retorta, which is a pest and a member of the Lepidoptera order. In total, the S. retorta mitogenome was found to contain 15,652 base pairs encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, as well as an adenine (A) + thymine (T)-rich region. These findings were consistent with the mitogenome composition of other lepidopterans, as we identified all 13 PCGs beginning at ATN codons. We also found that 11 PCGs terminated with canonical stop codons, whereas cox2 and nad4 exhibited incomplete termination codons. By analyzing the mitogenome of S. retorta using Bayesian inference (BI) and maximum likelihood (ML) models, we were able to further confirm that this species is a member of the Erebidae family.

scholarly journals The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp., and Dicyema japonicum

2018 ◽  
Author(s):  
Helen. E. Robertson ◽  
Philipp. H. Schiffer ◽  
Maximilian. J. Telford
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Small Subunit ◽  
Mitochondrial Genomes ◽  
List Type ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cell Layers

AbstractThe Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a divergent gene order compared to other metazoans. The data we present from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical across the Metazoa. The cox1 gene from dicyemid species has a series of conserved in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.Key FindingsWe report the first almost-complete mitochondrial genome from an orthonectid parasite, Intoshia linei, including 12 protein-coding genes; 20 tRNAs and putative sequences for large and small subunit rRNAs. We find that the I. linei mitochondrial genome is exceptionally AT-rich and has a novel gene order compared to other published metazoan mitochondrial genomes. These findings are indicative of the rapid rate of evolution that has occurred in the I. linei mitochondrial genome.We also report nine and eight protein-coding genes, respectively, from the dicyemid species Dicyema sp. and Dicyema japonicum, and use the cox1 genes from both species for phylogenetic inference of the internal phylogeny of the dicyemids.We find that the cox1 gene from dicyemids has a series of four conserved in-frame deletions which appear to be unique to this group.

scholarly journals Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6866 ◽  
Author(s):  
Gengyun Niu ◽  
Yaoyao Zhang ◽  
Zhenyi Li ◽  
Meicai Wei
Keyword(s):  
Mitochondrial Genome ◽  
New Genus ◽  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A New Species ◽  
High Support

A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.

scholarly journals The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum

2018 ◽  
Vol 4 ◽  
Author(s):  
Helen E. Robertson ◽  
Philipp H. Schiffer ◽  
Maximilian J. Telford
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Limited Support ◽  
Cell Layers

Abstract The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14 247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.

scholarly journals Mitochondrial Genome Sequence of Phytophthora sansomeana and Comparative Analysis of Phytophthora Mitochondrial Genomes

2020 ◽  
Author(s):  
Guohong Cai ◽  
Steven R. Scofield
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Proteins ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Circular Molecule

ABSTRACTPhytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthetase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3’ truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.

scholarly journals Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 563 ◽  
Author(s):  
Hu Li
Keyword(s):  
Mitochondrial Genome ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Future Studies ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Paraphyletic Group ◽  
Complete Mitochondrial Genomes

In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects.

scholarly journals The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae)

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Lidia Komondy ◽  
Jose Huguet-Tapia ◽  
Marina S. Ascunce ◽  
Ericka E. Helmick ◽  
Erica M. Goss ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Internal Control ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Economic Losses ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Lethal Yellowing ◽  
Primer Sets

Haplaxius crudus Van Duzee is a pest of various economically important palms due to its ability to transmit lethal yellowing, a fatal phytoplasma infection. It is also the putative vector of lethal bronzing in Florida, another lethal phytoplasma disease causing significant economic losses. To date, no mitochondrial genomes for species in the family Cixiidae are sequenced. In this study, the complete mitochondrial genome of H. crudus was sequenced, assembled, and annotated from PacBio Sequel II long sequencing reads using the University of Florida’s HiPerGator. The mitogenome of H. crudus is 15,848 bp long and encodes 37 mitochondrial genes (including 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs) in addition to a putative noncoding internal control region. The nucleotide composition of H. crudus is asymmetric with a bias toward A/T (44.8 %A, 13.4 %C, 8.5 %G, and 33.3 %T). Protein-coding genes (PCGs) possess the standard invertebrate mitochondrial start codons with few exceptions while the gene content and order of the H. crudus mitogenome is highly similar to most completely sequenced insect mitochondrial genomes. Phylogenetic analysis based on the entire mitogenome shows H. crudus resolving closely to Delphacidae, the accepted sister taxon of Cixiidae. These data provide a useful resource for developing novel primer sets that could aid in either phylogenetic studies or population genetic studies. As more full mitogenomes become available in the future for other planthopper species, more robust phylogenies can be constructed, giving more accurate perspectives on the evolutionary relationships within this fascinating and economically important group of insects.

scholarly journals The complete mitochondrial genome of the Golden Birdwing butterfly Troides aeacus: insights into phylogeny and divergence times of the superfamily Papilionoidea

2019 ◽  
Author(s):  
Si-Yu Dong ◽  
Guo-Fang Jiang ◽  
Gang Liu ◽  
Fang Hong ◽  
Yu-Feng Hsu
Keyword(s):  
Bayesian Inference ◽  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Divergence Times ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
High Bootstrap ◽  
Molecular Dataset ◽  
Troides Aeacus

AbstractBackgroundThe Lepidoptera is one of the largest insect orders. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. Here, we generated a molecular dataset with 78 species of lepidopterian insects, including a new complete mitochondrial genome (mitogenome) sequences of the Golden Birdwing Butterfly, Troides aeacus, which was listed in appendix II of CITES.MethodsBased on the concatenated nucleotide sequences of 13 protein-coding genes, we constructed phylogenetic trees with Bayesian Inference (BI) and Maximum Likelihood (ML) methods, and calculated the divergence times of Lepidoptera.ResultsMonophyly of the Papilionoidea including skippers (Hesperiidae) is strongly supported by a high bootstrap value. Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with high bootstrap supports. Additionally, Papilionidae probably diverged from the group (Hesperiidae + (Nymphalidae + Pieridae)) at 102.65 Mya, the Early Cretaceous. T. aeacus and the Golden kaiserihind Teinopalpus aureus diverged in the Cretaceous of 85.32 Mya. The age of Papilionoidea indicates that the primary break up of Gondwana may have an effect on the current distributions of butterflies.

scholarly journals First Complete Mitochondrial Genome of Melyridae(Coleoptera, Cleroidea): Genome Description and Phylogenetic Implications

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 87
Author(s):  
Lilan Yuan ◽  
Xueying Ge ◽  
Guanglin Xie ◽  
Haoyu Liu ◽  
Yuxia Yang
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Repeat Sequence ◽  
Start Codon ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Independent Families ◽  
First Time

To explore the characteristics of the mitogenome of Melyridae and reveal phylogenetic relationships, the mitogenome of Cordylepherus sp. was sequenced and annotated. This is the first time a complete mitochondrial genome has been generated in this family. Consistent with previous observations of Cleroidea species, the mitogenome of Cordylepherus sp. is highly conserved in gene size, organization and codon usage, and secondary structures of tRNAs. All protein-coding genes (PCGs) initiate with the standard start codon ATN, except ND1, which starts with TTG, and terminate with the complete stop codons of TAA and TAG, or incomplete forms, TA- and T-. Most tRNAs have the typical clover-leaf structure, except trnS1 (Ser, AGN), whose dihydrouridine (DHU) arm is reduced. In the A+T-rich region, three types of tandem repeat sequence units are found, including a 115 bp sequence tandemly repeated twice, a 16 bp sequence tandemly repeated three times with a partial third repeat and a 10 bp sequence tandemly repeated seven times. Phylogenetic analyses based on 13 protein-coding genes by both Bayesian inference (BI) and maximum likelihood (ML) methods suggest that Melyridae sensu lato is polyphyletic, and Dasytinae and Malchiinae are supported as independent families.

scholarly journals The Complete Mitochondrial Genome of The American Palm Cixiid, Haplaxius Crudus (Hemiptera: Cixiidae)

2020 ◽  
Author(s):  
Lidia Komondy ◽  
Jose Huguet-Tapia ◽  
Marina S. Ascunce ◽  
Ericka Helmick ◽  
Erica M. Goss ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Internal Control ◽  
Dna Sequences ◽  
Complete Mitochondrial Genome ◽  
Insect Pest ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
American Palm

Abstract Background Haplaxius crudus (the American palm cixiid) is a major insect pest of various economically important palms. H. crudus persists in tropical and subtropical regions where it is known to transmit the lethal yellowing (LY) phytoplasma. It has been implicated as the putative vector of Lethal bronzing (LB), a destructive phytoplasma-induced palm disease affecting over 16 species of ornamental and agricultural palms. To date, no mitochondrial genomes for species in the family Cixiidae are sequenced. Analysis of mitochondrial DNA sequences of H. crudus has proven useful for proper species diagnosis and population studies which could benefit management programs aimed at moving infective insects. These analyses describe the first mitochondrial genome from the American palm cixiid, Haplaxius crudus and an insect in the family Cixiidae. Results In this study, the complete mitochondrial genome of H. crudus was assembled and characterized from PacBio Sequel II long sequencing reads using the University of Florida’s HiPerGator supercomputer. The circular mitogenome of H. crudus is 15,845 bp long and encodes 37 mitochondrial genes (including 13 protein coding genes (PCGs), 22 tRNAs and 2 rRNAs) in addition to a putative non-coding internal control region. The nucleotide composition of H. crudus is asymmetric with a bias toward A and T (44.8 %A, 13.4 %C, 8.5 %G and 33.3 %T). Protein-coding genes (PCGs) possess the standard invertebrate mitochondrial start codons with few exceptions while the gene content and order of the H. crudus mitogenome is identical to most completely sequenced insect mitochondrial genomes. Phylogenetic analysis indicated that H. crudus is closely related to the planthopper in the family Delphacidae: N. lugens, which is the established sister group to Cixiidae. Conclusions Our studies have elucidated the first reference mitochondrial genome of Haplaxius crudus, providing structural analysis of the circular genome and encoded gene regions. The present results provide future opportunities to assess the diversity and origin of H. crudus. This study demonstrates the significance of understanding the structure and function of the mitochondrial genome to inform effective diagnostic and management strategies for insect pests.

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