Mitochondrial DNA dataset suggest that the genus Sphaerirostris Golvan, 1956 is a synonym of the genus Centrorhynchus Lühe, 1911

AbstractOur present genetic data of Acanthocephala, especially the mitochondrial (mt) genomes, remains very limited. In the present study, the nearly complete mt genome sequences of Sphaerirostris lanceoides (Petrochenko, 1949) was sequenced and determined for the first time based on specimens collected from the Indian pond heron Ardeola grayii (Sykes) (Ciconiiformes: Ardeidae) in Pakistan. The mt genome of S. lanceoides is 13 478 bp in size and contains 36 genes, including 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Moreover, in order to clarify the phylogenetic relationship of the genera Centrorhynchus and Sphaerirostris, and to test the systematic position of S. lanceoides in the Centrorhynchidae, the phylogenetic analyses were performed using Bayesian inference and maximum likelihood methods, based on concatenated nucleotide sequences of 12 PCGs, rRNAs and tRNAs. The phylogenetic results further confirmed the monophyly of the order Polymorphida and the paraphyly of the order Echinorhynchida in the class Palaeacanthocephala. Our results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) and showed a sister relationship between S. lanceoides and S. picae (Rudolphi, 1819).

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The mitochondrial genome of Leuctra sp. (Plecoptera: Leuctridae) and its performance in phylogenetic analyses

Zootaxa ◽

10.11646/zootaxa.4671.4.8 ◽

2019 ◽

Vol 4671 (4) ◽

pp. 571-580 ◽

Cited By ~ 1

Author(s):

YUE SHEN ◽

YU-ZHOU DU

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Mitochondrial Gene ◽

Gene Arrangement ◽

Likelihood Methods ◽

Protein Coding ◽

Maximum Likelihood Methods ◽

Rna Genes ◽

Drosophila Yakuba

The nearly complete mitochondrial genome (mitogenome) of Leuctra sp. (Plecoptera: Leuctridae) was sequenced. The 14,585-bp long mitogenome of L. sp. contained 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). The mitochondrial gene arrangement of L. sp. was identical with other stoneflies and the putative ancestral mitogenome of Drosophila yakuba Burla. Most PCGs used standard ATN start codons and TAN termination codons. Twenty-one of the 22 tRNAs in each mitogenome exhibited the cloverleaf secondary structures, while the dihydrouridine (DHU) arm of trnSer (AGN) was reduced. Phylogenetic analyses using our new Leuctra sp. genome and all other publicly available genomes for Plecoptera and Bayesian inference (BI) and maximum likelihood methods (ML) generated identical topologies, both supporting the monophyly of all stonefly families for which tests were possible and the infraorder Systellognatha. Scopuridae and Gripopterygidae were grouped with the infraorder Euholognatha. The final relationships within Plecoptera were recovered as (((((Perlodidae + Chloroperlidae) + Perlidae) + Pteronarcyidae) + Peltoperlidae) + Styloperlidae) + (((((Capniidae + Taeniopterygidae) + Nemouridae) + Scopuridae) + Leuctridae) + Gripopterygidae).

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The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

Scientific Reports ◽

10.1038/s41598-019-57065-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Vikas Kumar ◽

Kaomud Tyagi ◽

Rajasree Chakraborty ◽

Priya Prasad ◽

Shantanu Kundu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Start Codon ◽

Gene Arrangement ◽

Sister Relationship ◽

Protein Coding ◽

Relationship Of ◽

Rna Genes ◽

Boundary Mapping ◽

Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

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The complete mitochondrial genome of Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

PeerJ ◽

10.7717/peerj.8762 ◽

2020 ◽

Vol 8 ◽

pp. e8762

Author(s):

Yue Shen ◽

Yu-Zhou Du

Keyword(s):

Mitochondrial Genome ◽

Northern Hemisphere ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Trna Genes ◽

Protein Coding ◽

The Family ◽

Maximum Likelihood Methods ◽

Rna Genes

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

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Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

Plants ◽

10.3390/plants9091116 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1116 ◽

Cited By ~ 1

Author(s):

Xue-Li Zhao ◽

Zhang-Ming Zhu

Keyword(s):

Phylogenetic Analyses ◽

Evolutionary Process ◽

Rrna Genes ◽

Trna Genes ◽

Sister Relationship ◽

Protein Coding ◽

Variable Regions ◽

Chloroplast Genomes ◽

Distinct Genus ◽

Relationship Of

Taxonomic and phylogenetic relationships of Christia, Urariopsis, Uraria and related genera within the tribe Desmodieae (Fabaceae: Papilionoideae) have long been controversial. Here, we report the complete chloroplast (cp) genomes of Christia vespertilionis and Urariopsis brevissima and perform comparative and phylogenetic analyses with Uraria lagopodioides and other relatives in the Desmodieae. The cp genomes of C. vespertilionis and U. brevissima are 149,656 and 149,930 bp long, with 128 unique genes (83 protein-coding genes, 37 tRNA genes and 8 rRNA genes), respectively. Comparative analyses revealed 95-129 simple sequence repeats (SSRs) and eleven highly variable regions (trnK-rbcL, rbcL-atpB, ndhJ-trnF, trnL-trnT, psbD-rpoB, accD-cemA, petA-psbL, psbE-petL, rps11-rps19, ndhF-ccsA, and rps15-ycf1) among six Desmodieae species. Phylogenetic analyses clearly resolved two subtribes (Desmodiinae and Lespedezinae) of Desmodieae as monophyletic, and the newly reported C. vespertilionis and U. brevissima clustered in subtribe Desmodiinae. A sister relationship of C. vespertilionis to U. lagopodioides was supported. Evidence was presented to support the treatment of Urariopsis as a distinct genus rather than in synonymy with Uraria. The results provide valuable information for further studies on species delimitation, phylogenetics, population genetics, and the evolutionary process of speciation in the Desmodieae.

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Highly rearranged mitochondrial genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from endangered eagles

Parasites & Vectors ◽

10.1186/s13071-021-04776-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Yu Nie ◽

Yi-Tian Fu ◽

Yu Zhang ◽

Yuan-Ping Deng ◽

Wei Wang ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Gene Rearrangements ◽

Posterior Probabilities ◽

Protein Coding ◽

Protein Coding Genes ◽

The Family ◽

Louse Species ◽

Mt Genome ◽

Rna Genes

Abstract Background Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is known about the mt genomes from the family Philopteridae, the most species-rich family within the suborder Ischnocera. Methods Herein, we use next-generation sequencing to decode the mt genome of Falcolipeurus suturalis and compare it with the mt genome of F. quadripustulatus. Phylogenetic relationships within the family Philopteridae were inferred from the concatenated 13 protein-coding genes of the two Falcolipeurus lice and members of the family Philopteridae using Bayesian inference (BI) and maximum likelihood (ML) methods. Results The complete mt genome of F. suturalis is a circular, double-stranded DNA molecule 16,659 bp in size that contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and three non-coding regions. The gene order of the F. suturalis mt genome is rearranged relative to that of F. quadripustulatus, and is radically different from both other louse species and the putative ancestral insect. Phylogenetic analyses revealed clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities = 1.0 and bootstrapping frequencies = 100), and that the genus Falcolipeurus is sister to the genus Ibidoecus (Bayesian posterior probabilities = 1.0 and bootstrapping frequencies = 100). Conclusions These datasets help to better understand gene rearrangements in lice and the phylogenetic position of Falcolipeurus and provide useful genetic markers for systematic studies of bird lice. Graphic abstract

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Highly Rearranged Mitochondrial Genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from Endangered Eagles

10.21203/rs.3.rs-249932/v1 ◽

2021 ◽

Author(s):

Yu Nie ◽

Yi-Tian Fu ◽

Yu Zhang ◽

Yuan-Ping Deng ◽

Ya Tu ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Gene Rearrangements ◽

Posterior Probabilities ◽

Genome Sequences ◽

Protein Coding ◽

Protein Coding Genes ◽

The Family ◽

Mt Genome ◽

Rna Genes

Abstract Background: Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is available about the mt genomes from the family Philopteridae that is the most species-rich family within the suborder Ischnocera. Methods: Herein, we use next-generation sequencing to decode the mt genome sequences of Falcolipeurus suturalis and compared it with the mt genome sequences of F. quadripustulatus. Phylogenetic relationship of the concatenated amino acid sequence data for 13 protein-coding genes of the two Falcolipeurus lice and selected members of the family Philopteridae was evaluated using Bayesian inference (BI).Results: The complete mt genome of F. suturalis is a circular double-stranded DNA molecule of 16,659 bp, and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, as well as three putative non-coding regions. The gene order in F. suturalis mt genome was rearranged compared with that of F. quadripustulatus, and they were radical different from other louse species and the ancestral insect. Phylogenetic analyses revealed that the clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities=1.0), and the genus Falcolipeurus is more closely related to the genus Ibidoecus than to other genera (Bayesian posterior probabilities=1.0). Conclusions: These novel datasets will help to better understand the gene rearrangements and phylogenetic position of Falcolipeurus and provide useful genetic markers for systematics and phylogenetic studies of bird lice.

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Mitogenomics, Phylogeny and Morphology Reveal Ophiocordyceps pingbianensis Sp. Nov., an Entomopathogenic Fungus from China

Life ◽

10.3390/life11070686 ◽

2021 ◽

Vol 11 (7) ◽

pp. 686

Author(s):

Siqi Chen ◽

Yuanbing Wang ◽

Kongfu Zhu ◽

Hong Yu

Keyword(s):

Entomopathogenic Fungus ◽

Evolutionary Biology ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Mitochondrial Protein ◽

Nuclear Gene ◽

Systematic Position ◽

Open Reading Frames ◽

Protein Coding ◽

Rna Genes

The new entomopathogenic fungus Ophiocordyceps pingbianensis, collected from Southeast China, was described by mitogenomic, morphological, and phylogenetic evidence. The systematic position of O. pingbianensis was determined by phylogenetic analyses based on six nuclear gene (ITS, tef1-α, nrSSU, nrLSU, rpb1 and rpb2) and 14 mitochondrial protein-coding gene (PCGs) (cox1, cox2, cox3, atp6, atp8, atp9, cob, nad1, nad2, nad3, nad4, nad5, nad6 and nad4L) data. Phylogenetic analyses reveal that O. pingbianensis was belonged to the Hirsutella nodulosa clade in the genus Ophiocordyceps of Ophiocordycipiaceae. This fungus exhibits distinctive characteristics which differed from other related Ophiocordyceps species with slender and geminate stromata, monophialidic conidiogenous cells with an inflated awl-shaped base, a twisty and warty phialide neck and a fusiform or oval conidia, as well as being found on a tiger beetle of Coleoptera buried in moss at the cave. The complete mitochondrial genome of O. pingbianensis was a circular DNA molecule 80,359 bp in length, containing 15 PCGs, 24 open reading frames genes (ORFs), 25 transfer RNA genes (tRNAs) and 27 introns. Ophiocordyceps pingbianensis, containing 27 introns, has the second largest mitogenome in Ophiocordycipiaceae and was next to O. sinensis. To our knowledge, this is the first report of the mitogenome from a new entomopathogenic fungus, and thus provides an important foundation for future studies on taxonomy, genetics and evolutionary biology of Ophiocordycipiaceae.

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The mitochondrial genomes of two walnut pests, Gastrolina depressa depressa and G. depressa thoracica (Coleoptera: Chrysomelidae), and phylogenetic analyses

PeerJ ◽

10.7717/peerj.4919 ◽

2018 ◽

Vol 6 ◽

pp. e4919 ◽

Cited By ~ 6

Author(s):

Qiqi Wang ◽

Guanghui Tang

Keyword(s):

Sanger Sequencing ◽

Insect Pests ◽

Phylogenetic Analyses ◽

Mitochondrial Genomes ◽

Sequencing Technology ◽

Sister Relationship ◽

Protein Coding ◽

Protein Coding Genes ◽

Genomic Analyses ◽

Relationship Of

In this study, the mitochondrial genomes (mitogenomes) of two walnut leaf insect pests, Gastrolina depressa depressa and G. depressa thoracica, were sequenced by Sanger sequencing technology. The mitogenome of G. depressa thoracica was complete at 16,109 bp in length, while the mitogenome of G. depressa depressa (14,277 bp) was partial. The genomic analyses indicated that both mitogenomes have the typical gene content and arrangement. The formerly identified elements, ‘TAGTA’ between trnSer(UCN) and nad2, and ‘ATGATAA’ between atp8 and atp6, were more conserved than that between nad4L and nad4, which was ‘ATGTTAA’ in Coleoptera excluding Polyphaga. Phylogenetic analyses of the 13 protein-coding genes from 36 coleopteran species well supported a close affinity between the subfamily Chrysomelinae including G. depressa thoracica and G. depressa depressa and Galerucinae, as well as a sister relationship of ((Eumolpinae + Cryptocephalinae) + Cassidinae) within Chrysomelidae.

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Schroeteria Decaisneana, S. Poeltii, and Ciboria Ploettneriana (Sclerotiniaceae, Helotiales, Ascomycota), Three Parasites on Veronica Seeds: First Report of Teleomorphs in Schroeteria

10.21203/rs.3.rs-578062/v1 ◽

2021 ◽

Author(s):

Hans-Otto Baral ◽

Peter Rönsch ◽

Udo Richter ◽

Alexander Urban ◽

Julia Kruse ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Similar Species ◽

Protein Coding ◽

Ultrastructural Studies ◽

The Core ◽

Rdna Sequences ◽

False Smut ◽

Relationship Of ◽

First Time ◽

The Relationship

Abstract Three little known, morphologically similar species of Sclerotiniaceae which form their apothecia on fallen stromatized Veronica seeds are described and illustrated in detail based on fresh collections or moist chamber cultures of infected seeds: Ciboria ploettneriana, Schroeteria decaisneana, and Schroeteria poeltii. The former two were found on Veronica hederifolia agg. at different sites of temperate central Europe, the latter on V. cymbalaria in a mediterranean region of Spain. The latter two are anamorph-typified and here reported for the first time with their teleomorph.Ciboria ploettneriana was described by Kirschstein as Sclerotiniaploettneriana on seeds of V. hederifolia agg. but is currently treated in Ciboria. Based on the reexamination of four syntype specimens in B it became evident that Kirschstein confused the two species on V. hederifolia. A lectotype is therefore designated for S. ploettneriana.Members of Schroeteria are specific plant parasites infecting fruits of different Veronica spp. Schroeteria has earlier been referred to the Ustilaginales (Basidiomycota) based on its smut-like chlamydospores, but later light-microscopic and ultrastructural studies suggested that it represents a false smut fungus belonging to the Sclerotiniaceae (Helotiales).rDNA sequences were obtained from chlamydospores of Schroeteria bornmuelleri (on V. rubrifolia), S. delastrina (generic type, on Veronica arvensis), S. decaisneana, and S. poeltii, and from apothecia on V. hederifolia agg. and V. cymbalaria seeds. As a result, the anamorph-teleomorph connection could be verified for Schroeteria decaisneana and S. poeltii based on a 100% ITS similarity between both morphs, whereas Ciboria ploettneriana in the here redefined sense could not be connected to an anamorph.Our phylogenetic analyses show that Ciboria ploettneriana belongs in the relationship of Sclerotinia, Stromatinia, and Grovesinia rather than Ciboria, but its placement was not supported. Also Schroeteria poeltii clustered unresolved in this relationship but has a much higher molecular distance to those. The remaining three Schroeteria spp. formed a supported monophyletic group, the Schroeteria core clade, which clustered with medium to low support distantly to a member of the Monilinia alpina group of section Disjunctoriae (M. jezoensis). ITS distances of 5–6.3% were found among members of the Schroeteria core clade, and 13.8–14.7% between the core clade and S. poeltii. The high distance of S. poeltii reflects its deviating chlamydospore morphology.Despite the high heterogeneity in the available ITS and LSU data, Schroeteria is accepted here under inclusion of S. poeltii as a genus distinct from Monilinia, particularly because of its very special anamorphs. A similar heterogeneity in rDNA analyses was observed in Monilinia and other genera of Sclerotiniaceae. Protein-coding genes should be investigated in order to obtain a more natural phylogeny within the Sclerotiniaceae.

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The complete mitochondrial genome of Orthocoelium streptocoelium (Digenea: Paramphistomidae) for comparison with other digeneans

Journal of Helminthology ◽

10.1017/s0022149x16000183 ◽

2016 ◽

Vol 91 (2) ◽

pp. 255-261 ◽

Cited By ~ 1

Author(s):

Y.Y. Zhao ◽

X. Yang ◽

H.M. Chen ◽

L.X. Wang ◽

H.L. Feng ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Small Ruminants ◽

Amino Acid Sequences ◽

Population Variation ◽

Protein Coding ◽

Protein Coding Genes ◽

Mt Genome ◽

Rna Genes

AbstractOrthocoelium streptocoelium is a common paramphistome species parasitizing the rumen and/or reticulum of small ruminants, leading to significant losses. This study first determined the complete mitochondrial (mt) genome of O. streptocoelium. The complete mt genome of O. streptocoelium was amplified, sequenced, assembled, analysed and then compared with those of other digeneans. The entire mt genome of O. streptocoelium is 13,800 bp in length, which is smaller than those of other digeneans except for Opisthorchis viverrini. This mt genome contains 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. The arrangement of the O. streptocoelium mt genome is the same as those of other digeneans except for Schistosoma haematobium and Schistosoma spindale. Phylogenetic analyses based on concatenated amino acid sequences of the 12 protein-coding genes representing 16 digeneans were conducted to assess the relationship of O. streptocoelium with other digeneans. The result indicated that O. streptocoelium is closely related to Paramphistomum cervi and Fischoederius elongates, which is in accordance with their relationships by taxonomy. This complete mt genome of O. streptocoelium enriched the mitochondrial genome data of paramphistomes and provided important molecular markers for diagnostics and studies of population variation, epidemiology, ecology and evolution of O. streptocoelium and other digeneans.

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