Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications

The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.

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Mitochondrial genome of the sweet potato hornworm, Agrius convolvuli (Lepidoptera: Sphingidae), and comparison with other Lepidoptera species

Genome ◽

10.1139/gen-2016-0058 ◽

2017 ◽

Vol 60 (2) ◽

pp. 128-138 ◽

Cited By ~ 6

Author(s):

Li-Shang Dai ◽

Sheng Li ◽

Hui-min Yu ◽

Guo-Qing Wei ◽

Lei Wang ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Cox1 Gene ◽

Base Pairs ◽

Protein Coding ◽

Transfer Rnas ◽

The Family ◽

Circular Molecule ◽

Cloverleaf Structure

In the present study, we sequenced the complete mitochondrial genome (mitogenome) of Agrius convolvuli (Lepidoptera: Sphingidae) and compared it with previously sequenced mitogenomes of lepidopteran species. The mitogenome was a circular molecule, 15 349 base pairs (bp) long, containing 37 genes. The order and orientation of genes in the A. convolvuli mitogenome were similar to those in sequenced mitogenomes of other lepidopterans. All 13 protein-coding genes (PCGs) were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which seemed to be initiated by the codon CGA, as observed in other lepidopterans. Three of the 13 PCGs had the incomplete termination codon T, while the remainder terminated with TAA. Additionally, the codon distributions of the 13 PCGs revealed that Asn, Ile, Leu2, Lys, Phe, and Tyr were the most frequently used codon families. All transfer RNAs were folded into the expected cloverleaf structure except for tRNASer(AGN), which lacked a stable dihydrouridine arm. The length of the adenine (A) + thymine (T)-rich region was 331 bp. This region included the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)8 element next to the motif ATTTA. Phylogenetic analyses (maximum likelihood and Bayesian methods) showed that A. convolvuli belongs to the family Sphingidae.

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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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Notes, outline and divergence times of Basidiomycota

Fungal Diversity ◽

10.1007/s13225-019-00435-4 ◽

2019 ◽

Vol 99 (1) ◽

pp. 105-367 ◽

Cited By ~ 32

Author(s):

Mao-Qiang He ◽

Rui-Lin Zhao ◽

Kevin D. Hyde ◽

Dominik Begerow ◽

Martin Kemler ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Divergence Times ◽

Sequence Information ◽

Divergence Time Estimates ◽

Time Estimates ◽

The Family ◽

Life Mode ◽

Species Type ◽

Phylogeny And Evolution

AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

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Characterization of the Complete Mitochondrial Genome of Drabescus ineffectus and Roxasellana stellata (Hemiptera: Cicadellidae: Deltocephalinae: Drabescini) and Their Phylogenetic Implications

Insects ◽

10.3390/insects11080534 ◽

2020 ◽

Vol 11 (8) ◽

pp. 534 ◽

Cited By ~ 1

Author(s):

Deliang Xu ◽

Tinghao Yu ◽

Yalin Zhang

Keyword(s):

Mitochondrial Genome ◽

Stop Codon ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Strong Support ◽

Start Codon ◽

Protein Coding ◽

Simple Loop ◽

Repeat Units ◽

Phylogenetic Implications

To explore the mitogenome characteristics and shed light on the phylogenetic relationships and molecular evolution of Drabescini species, we sequenced and analyzed the complete mitochondrial genome of two species including Drabescus ineffectus and Roxasellana stellata. The complete mitogenomes of D. ineffectus and R. stellata are circular, closed and double-stranded molecules with a total length of 15744 bp and 15361 bp, respectively. These two newly sequenced mitogenomes contain the typical 37 genes. Most protein-coding genes (PCGs) began with the start codon ATN and terminated with the terminal codon TAA or TAG, with an exception of a special initiation codon of ND5, which started with TTG, and an incomplete stop codon T-- was found in the Cytb, COX2, ND1 and ND4. All tRNAs could be folded into the canonical cloverleaf secondary structure except for the trnS1, which lacks the DHU arm and is replaced by a simple loop. The multiple tandem repeat units were found in A + T-control region. The sliding window, Ka/Ks and genetic distance analyses indicated that the ATP8 presents a high variability and fast evolutionary rate compared to other PCGs. Phylogenetic analyses based on three different datasets (PCG123, PCG12R and AA) using both Bayesian inference (BI) and maximum likelihood (ML) methods showed strong support for the monophyly of Drabescini.

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

Insects ◽

10.3390/insects12020087 ◽

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.

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Novel gene rearrangement in the mitochondrial genome of Siliqua minima (Bivalvia, Adapedonta) and phylogenetic implications for Imparidentia

PLoS ONE ◽

10.1371/journal.pone.0249446 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0249446

Author(s):

Jiantong Feng ◽

Yahong Guo ◽

Chengrui Yan ◽

Yingying Ye ◽

Xiaojun Yan ◽

...

Keyword(s):

Mitochondrial Genome ◽

Gene Rearrangement ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Protein Coding ◽

Sinonovacula Constricta ◽

Phylogenetic Implications ◽

The Family ◽

Phylogenetic Resolution ◽

Rna Genes

Siliqua minima (Gmelin, 1791) is an important economic shellfish species belonging to the family Pharidae. To date, the complete mitochondrial genome of only one species in this family (Sinonovacula constricta) has been sequenced. Research on the Pharidae family is very limited; to improve the evolution of this bivalve family, we sequenced the complete mitochondrial genome of S. minima by next-generation sequencing. The genome is 17,064 bp in length, consisting of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA). From the rearrangement analysis of bivalves, we found that the gene sequences of bivalves greatly variable among species, and with closer genetic relationship, the more consistent of the gene arrangement is higher among the species. Moreover, according to the gene arrangement of seven species from Adapedonta, we found that gene rearrangement among families is particularly obvious, while the gene order within families is relatively conservative. The phylogenetic analysis between species of the superorder Imparidentia using 12 conserved PCGs. The S. minima mitogenome was provided and will improve the phylogenetic resolution of Pharidae species.

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The complete mitochondrial genome of Amphinemura claviloba (Wu, 1973) (Plecoptera: Nemouridae)

Zootaxa ◽

10.11646/zootaxa.4732.3.8 ◽

2020 ◽

Vol 4732 (3) ◽

pp. 461-473

Author(s):

JIAJIA CHEN ◽

JINJUN CAO ◽

MENGDAN CHEN ◽

SIJIN CHEN ◽

WEIHAI LI ◽

...

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Trna Genes ◽

Structural Elements ◽

Protein Coding ◽

Simple Loop ◽

The Family ◽

Secondary Structure Models

We sequenced the complete mitochondrial genome (mitogenome) of a stonefly, Amphinemura claviloba (Wu, 1973), of the family Nemouridae (Insecta: Plecoptera). The mitogenome was 15,707 bp long and contained typical 37 genes with an A+T content of 68.5%. All protein-coding genes (PCGs) use standard initiation codons (methionine and isoleucine), except ND1 and ND5 which starts with TTG and GTG, respectively. Two of the 13 PCGs harbor the incomplete termination codon. All tRNA genes have typical clover secondary structures, except the dihydrouridine (DHU) arm of tRNASer(AGN) forms a simple loop. Secondary structure models of the ribosomal RNA genes of A. claviloba are similar to those proposed for other insects. We also found some structural elements in the control region, such as tandem repeats, poly-C stretch and microsatellite-like elements, etc. Phylogenetic analyses showed the clades for the Nemoura, Amphinemura, and (Mesonemoura + Sphaeronemoura + Indonemoura + Protonemura) are well supported in a polytomy.

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Structural Features and Phylogenetic Implications of Two New Mitogenomes of Erythroneurine Leafhoppers (Hemiptera: Cicadellidae: Typhlocybinae)

10.21203/rs.3.rs-74836/v1 ◽

2020 ◽

Author(s):

Xiaoxiao Chen ◽

Zhouwei Yuan ◽

Can Li ◽

Christopher H Dietrich ◽

Yuehua Song

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Divergence Time ◽

Structural Features ◽

Rrna Genes ◽

Genome Sequences ◽

Protein Coding ◽

Trna Secondary Structure ◽

Phylogenetic Implications ◽

Evolutionary Event

Abstract Background: Complete mitochondrial genome sequences facilitate species identification and analyses of phylogenetic relationships. However, the available data are limited for the diverse and widespread insect familiy Cicadellidae. In this study, we sequenced complete mitochondrial genomes of two species of Erythroneurini. Results: The mitogenomes of Empoascanara wengangensis and E. gracilis were 14,830 and 14,627 bp in length, respectively, and similar to other published leafhopper mitogenomes in terms of gene size, base composition, gene order, PCGs codon usage, and tRNA secondary structure. Most protein coding genes start with ATN and end with TAA or TAG. Two rRNA genes are highly conserved and encoded on the minority strand, and the AT content in 16S is higher than that of 12S. The control regions in the genus Empoascanara are highly variable and contain various numbers of repeat sequences. Conclusions: The mitogenomes of these two species closely resemble those of most other sequenced leafhoppers in various structural and compositional aspects. Phylogenetic analysis of 13 PCGs yielded a well-supported topology with most branches receiving maximum support and most relationships agreeing with those of other recent phylogenetic studies. Nucleotide diversity analysis show that nad4 and nad5 can be evaluated as potential DNA markers that define the Cicadellidae insect species. Like other studies, the main evolutionary event of leafhoppers occurred in the Tertiary, and its divergence time is estimated to be 10.03~122.48 Ma. This study confirms results of previous studies indicating that mitochondrial genome sequences are informative of leafhopper phylogeny.

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Integrating Different Lines of Evidence to Establish a Novel Ascomycete Genus and Family (Anastomitrabeculia, Anastomitrabeculiaceae) in Pleosporales

Journal of Fungi ◽

10.3390/jof7020094 ◽

2021 ◽

Vol 7 (2) ◽

pp. 94

Author(s):

Chitrabhanu S. Bhunjun ◽

Chayanard Phukhamsakda ◽

Rajesh Jeewon ◽

Itthayakorn Promputtha ◽

Kevin D. Hyde

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Distinct Species ◽

Divergence Time Estimates ◽

New Family ◽

Time Estimates ◽

The Family ◽

Freshwater Stream ◽

Cretaceous Period ◽

Lines Of Evidence

A novel genus, Anastomitrabeculia, is introduced herein for a distinct species, Anastomitrabeculia didymospora, collected as a saprobe on dead bamboo culms from a freshwater stream in Thailand. Anastomitrabeculia is distinct in its trabeculate pseudoparaphyses and ascospores with longitudinally striate wall ornamentation. A new family, Anastomitrabeculiaceae, is introduced to accommodate Anastomitrabeculia. Anastomitrabeculiaceae forms an independent lineage basal to Halojulellaceae in Pleosporales and it is closely related to Neohendersoniaceae based on phylogenetic analyses of a combined LSU, SSU and TEF1α dataset. In addition, divergence time estimates provide further support for the establishment of Anastomitrabeculiaceae. The family diverged around 84 million years ago (MYA) during the Cretaceous period, which supports the establishment of the new family. The crown and stem age of Anastomitrabeculiaceae was also compared to morphologically similar pleosporalean families.

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Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

Zootaxa ◽

10.11646/zootaxa.2107.1.2 ◽

2009 ◽

Vol 2107 (1) ◽

pp. 41-52 ◽

Cited By ~ 5

Author(s):

CAROLINA M VOLOCH ◽

PABLO R FREIRE ◽

CLAUDIA A M RUSSO

Keyword(s):

Fossil Record ◽

Divergence Time ◽

Penaeid Shrimp ◽

Divergence Time Estimates ◽

Time Estimates ◽

Global Clock ◽

Late Tertiary ◽

The Family ◽

Molecular Studies ◽

Triassic Period

Fossil record of penaeids indicates that the family exists since the Triassic period, but extant genera appeared only recently in Tertiary strata. Molecular based divergence time estimates on the matter of penaeid radiation were never properly addressed, due to shortcomings of the global molecular clock assumptions. Here, we studied the diversification patterns of the family, uncovering, more specifically, a correlation between fossil and extant Penaeid fauna. For this, we have used a Bayesian framework that does not assume a global clock. Our results suggest that Penaeid genera originated between 20 million years ago and 43 million years ago, much earlier than expected by previous molecular studies. Altogether, these results promptly discard late Tertiary or even Quaternary hypotheses that presumed a major glaciations influence on the diversification patterns of the family.

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