One Hundred Mitochondrial Genomes of Cicadas

Abstract Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.

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Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

International Journal of Molecular Sciences ◽

10.3390/ijms21051874 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1874 ◽

Cited By ~ 1

Author(s):

Huiting Ruan ◽

Min Li ◽

Zhenhai Li ◽

Jiajie Huang ◽

Weiyuan Chen ◽

...

Keyword(s):

Purifying Selection ◽

Living Environment ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Marine Fishery ◽

Gc Skew ◽

The Difference ◽

Early Paleogene ◽

Complete Mitochondrial Genomes

Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.

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Mitochondrial genomes of the stoneflies Mesonemoura metafiligera and Mesonemoura tritaenia (Plecoptera, Nemouridae), with a phylogenetic analysis of Nemouroidea

ZooKeys ◽

10.3897/zookeys.835.32470 ◽

2019 ◽

Vol 835 ◽

pp. 43-63 ◽

Cited By ~ 3

Author(s):

Jin–Jun Cao ◽

Ying Wang ◽

Yao–Rui Huang ◽

Wei–Hai Li

Keyword(s):

Tandem Repeats ◽

Phylogenetic Analyses ◽

Purifying Selection ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Rich Region ◽

Stem Loop ◽

Protein Coding ◽

The Family

In this study, two new mitochondrial genomes (mitogenomes) ofMesonemourametafiligeraandMesonemouratritaeniafrom the family Nemouridae (Insecta: Plecoptera) were sequenced. TheMesonemourametafiligeramitogenome was a 15,739 bp circular DNA molecule, which was smaller than that ofM.tritaenia(15,778 bp) due to differences in the size of the A+T-rich region. Results show that gene content, gene arrangement, base composition, and codon usage were highly conserved in two species. Ka/Ks ratios analyses of protein-coding genes revealed that the highest and lowest rates were found in ND6 and COI and that all these genes were evolving under purifying selection. All tRNA genes in nemourid mitogenomes had a typical cloverleaf secondary structure, except for tRNASer(AGN)which appeared to lack the dihydrouridine arm. The multiple alignments of nemourid lrRNA and srRNA genes showed that sequences of three species were highly conserved. All the A+T-rich region included tandem repeats regions and stem-loop structures. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) generated identical results. Amphinemurinae and Nemourinae were sister-groups and the family Nemouridae was placed as sister to Capniidae and Taeniopterygidae.

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Investigating diversity, evolution, development and physiology of red algal parasites from New Zealand

10.26686/wgtn.17132219.v1 ◽

2021 ◽

Author(s):

◽

Maren Preuss

Keyword(s):

Host Species ◽

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

Host Cells ◽

Gene Content ◽

Infected Host ◽

Parasite Development ◽

Future Research ◽

Mitochondrial Genomes ◽

Red Algal

<p>Red algal parasites have evolved independently over a 100 times and grow only on other red algal hosts. Most parasites are closely related to their host based on the similarity of their reproductive structures. Secondary pit connections between red algal parasites and their hosts are used to transfer parasite organelles and nuclei into host cells. Morphological and physiological changes in infected host cells have been observed in some species. Parasite mitochondrial genomes are similar in size and gene content to free-living red algae whereas parasite plastids are highly reduced. Overall, red algal parasites are poorly studied and thus the aim of this study was to increase the general knowledge of parasitic taxa with respect to their diversity, evolutionary origin, development, physiology, and organelle evolution. Investigation of the primary literature showed that most species descriptions of red algal parasites were poor and did not meet the criteria for defining a parasitic relationship. This literature study also revealed a lack of knowledge of many key parasitic processes including early parasite development, host cell “control”, and parasite origin. Many of these poorly studied research areas were addressed in this thesis. Phylogenetic analyses, using a range of markers from all three genomes (cpDNA: rbcL, nDNA: actin, LSU rRNA; mtDNA: cox1), showed different patterns of phylogenetic relationships for the four new red algal parasites and their hosts. The parasites Phycodrys novae-zelandiophila sp. nov. and Vertebrata aterrimophila sp. nov. closest relative is its host species. Cladhymenia oblongifoliophila sp. nov. closest relative is its host species based on nuclear and mitochondrial markers whereas the plastid markers group the parasite with Cladhymenia lyallii, suggesting that the parasite plastid was acquired when previously parasitizing C. lyallii. Judithia parasitica sp. nov. grows on two Blastophyllis species but the parasites’ closest relative is the non-host species Judithia delicatissima. Developmental studies of the parasite Vertebrata aterrimophila, showed a unique developmental structure (“trunk-like” cell) not known in other parasites, plus localised infection vi and few changes in infected host cells. High-throughput-sequencing revealed mitochondrial genomes of similar size, gene content and order in the parasite Pterocladiophila hemisphaerica to its host Pterocladia lucida, and a reduced non-photosynthetic plastid in the parasite. Mitochondrial (mt) and plastid (cp) genome phylogenies placed Pterocladiophila hemisphaerica on long branches, either as sister to Ceramiales (mt) or Gracilariales (cp). Further analyses, filtering non-elevated plastid genes grouped the parasite neither with the Gracilariales (mt) or Gelidiales (cp) on shorter branches but without support. Nuclear phylogeny grouped P. hemisphaerica as sister to the Gelidiales and other red algal orders and was the only phylogenetic relationship with support. Investigations of photosystem II capacity using PAM fluorometry, and quantifying chlorophyll a content in three pigmented parasites, showed different host nutrient dependencies. Rhodophyllis parasitica and Vertebrata aterrimophila are not able to photosynthesize and are fully dependent on host nutrients. Pterocladiophila hemisphaerica is able to photosynthesize independently, even though it has a reduced non-photosynthetic plastid genome, and therefore is only partially dependent on its host. This study advances our current understanding of red algal parasites and highlights many possibilities for future research including genome evolution and understanding parasite diversity.</p>

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Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

Molecular Biology and Evolution ◽

10.1093/molbev/msaa297 ◽

2020 ◽

Author(s):

Solomon T C Chak ◽

Juan Antonio Baeza ◽

Phillip Barden

Keyword(s):

Molecular Evolution ◽

Genome Evolution ◽

Purifying Selection ◽

Synonymous Substitution ◽

Mitochondrial Genomes ◽

Comparative Genomic ◽

Effective Population ◽

Protein Coding ◽

Marine Realm ◽

Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

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Mitochondrial Genomes of Hestina persimilis and Hestinalis nama (Lepidoptera, Nymphalidae): Genome Description and Phylogenetic Implications

Insects ◽

10.3390/insects12080754 ◽

2021 ◽

Vol 12 (8) ◽

pp. 754

Author(s):

Yupeng Wu ◽

Hui Fang ◽

Jiping Wen ◽

Juping Wang ◽

Tianwen Cao ◽

...

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Mitochondrial Genomes ◽

Comparative Genomic ◽

Trna Genes ◽

Cox1 Gene ◽

Protein Coding ◽

Phylogenetic Implications ◽

Typical Composition

In this study, the complete mitochondrial genomes (mitogenomes) of Hestina persimilis and Hestinalis nama (Nymphalidae: Apaturinae)were acquired. The mitogenomes of H. persimilis and H. nama are 15,252 bp and 15,208 bp in length, respectively. These two mitogenomes have the typical composition, including 37 genes and a control region. The start codons of the protein-coding genes (PCGs) in the two mitogenomes are the typical codon pattern ATN, exceptCGA in the cox1 gene. Twenty-one tRNA genes show a typical clover leaf structure, however, trnS1(AGN) lacks the dihydrouridine (DHU) stem. The secondary structures of rrnL and rrnS of two species were predicted, and there are several new stem loops near the 5’ of rrnL secondary structure. Based on comparative genomic analysis, four similar conservative structures can be found in the control regions of these two mitogenomes. The phylogenetic analyses were performed on mitogenomes of Nymphalidae. The phylogenetic trees show that the relationships among Nymphalidae are generally identical to previous studies, as follows: Libytheinae\Danainae + ((Calinaginae + Satyrinae) + Danainae\Libytheinae + ((Heliconiinae + Limenitidinae) + (Nymphalinae + (Apaturinae + Biblidinae)))). Hestinalisnama isapart fromHestina, andclosely related to Apatura, forming monophyly.

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Population genetics of Paramecium mitochondrial genomes: recombination, mutational spectrum, and efficacy of selection

10.1101/281865 ◽

2018 ◽

Author(s):

Parul Johri ◽

Georgi K. Marinov ◽

Thomas G. Doak ◽

Michael Lynch

Keyword(s):

Gc Content ◽

Purifying Selection ◽

Mitochondrial Genomes ◽

Unique Combination ◽

Protein Coding ◽

Unicellular Eukaryotes ◽

Population Genomic ◽

Outgroup Species ◽

Multiple Species ◽

Mutation Spectra

ABSTRACTThe evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate mitochondrial genomes exhibit a unique combination of characteristics, including a linear organization and the presence of multiple genes with no known function or detectable homologs in other eukaryotes. Here we study the variation of ciliate mitochondrial genomes both within and across thirteen highly diverged Paramecium species, including multiple species from the P. aurelia species complex, with four outgroup species: P. caudatum, P. multimicronucleatum, and two strains that may represent novel related species. We observe extraordinary conservation of gene order and protein-coding content in Paramecium mitochondria across species. In contrast, significant differences are observed in tRNA content and copy number, which is highly conserved in species belonging to the P. aurelia complex but variable among and even within the other Paramecium species. There is an increase in GC content from ~20% to ~40% on the branch leading to the P. aurelia complex. Patterns of polymorphism in population-genomic data and mutation-accumulation experiments suggest that the increase in GC content is primarily due to changes in the mutation spectra in the P. aurelia species. Finally, we find no evidence of recombination in Paramecium mitochondria and find that the mitochondrial genome appears to experience either similar or stronger efficacy of purifying selection than the nucleus.

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Morpho-Phylo Taxonomy of Novel Dothideomycetous Fungi Associated With Dead Woody Twigs in Yunnan Province, China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.654683 ◽

2021 ◽

Vol 12 ◽

Author(s):

Peter E. Mortimer ◽

Rajesh Jeewon ◽

Jian-Chu Xu ◽

Saisamorn Lumyong ◽

Dhanushka N. Wanasinghe

Keyword(s):

Yunnan Province ◽

Phylogenetic Analyses ◽

Protein Coding ◽

Research Attention ◽

Multiple Gene ◽

Asexual Morph ◽

Coding Regions ◽

Extant Species ◽

Ocular Chamber ◽

Taxonomic Novelties

Within the field of mycology, macrofungi have been relatively well-studied when compared to microfungi. However, the diversity and distribution of microfungi inhabiting woody material have not received the same degree of research attention, especially in relatively unexplored regions, such as Yunnan Province, China. To help address this knowledge gap, we collected and examined fungal specimens from different plants at various locations across Yunnan Province. Our investigation led to the discovery of four species that are clearly distinct from extant ones. These taxonomic novelties were recognized based on morphological comparisons coupled with phylogenetic analyses of multiple gene sequences (non-translated loci and protein-coding regions). The monotypic genus Neoheleiosa gen. nov. (type: N. lincangensis) is introduced in Monoblastiaceae (Monoblastiales) for a woody-based saprobic ascomycete that possesses globose to subglobose or obpyriform ascomata with centric or eccentric, papillate ostioles, an ascomatal wall with thin-walled cells of textura globulosa, cylindric, pedicellate asci with an ocular chamber, and 1-septate, brown, guttulate, longitudinally striated, bicellular ascospores. Neoheleiosa has a close phylogenetic affinity to Heleiosa, nevertheless, it is morphologically dissimilar by its peridium cells and ornamented ascospores. Acrocalymma hongheense and A. yuxiense are described and illustrated as new species in Acrocalymmaceae. Acrocalymma hongheense is introduced with sexual and asexual (coelomycetous) features. The sexual morph is characterized by globose to subglobose, ostiolate ascomata, a peridium with textura angularis cells, cylindric-clavate asci with a furcate to truncate pedicel and an ocular chamber, hyaline, fusiform, 1-septate ascospores which are surrounded by a thick, distinct sheath, and the asexual morph is featured by pycnidial conidiomata, subcylindrical, hyaline, smooth, annelledic, conidiogenous cells, hyaline, guttulate, subcylindrical, aseptate conidia with mucoid ooze at the apex and with a rounded hilum at the base. Acrocalymma yuxiense is phylogenetically distinct from other extant species of Acrocalymma and differs from other taxa in Acrocalymma in having conidia with three vertical eusepta. Magnibotryascoma kunmingense sp. nov. is accommodated in Teichosporaceae based on its coelomycetous asexual morph which is characterized by pycnidial, globose to subglobose, papillate conidiomata, enteroblastic, annelledic, discrete, cylindrical to oblong, hyaline conidiogenous cells arising from the inner layer of pycnidium wall, subglobose, oval, guttulate, pale brown and unicelled conidia.

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Sareomycetes cl. nov.: A new proposal for placement of the resinicolous genus Sarea (Ascomycota, Pezizomycotina)

Fungal Systematics and Evolution ◽

10.3114/fuse.2020.06.02 ◽

2020 ◽

Vol 6 (1) ◽

pp. 25-37 ◽

Cited By ~ 1

Author(s):

C. Beimforde ◽

A.R. Schmidt ◽

J. Rikkinen ◽

J.K. Mitchell

Keyword(s):

Bayesian Inference ◽

Genetic Variability ◽

Sequence Data ◽

Current Knowledge ◽

Phylogenetic Analyses ◽

Protein Coding ◽

Infrageneric Classification ◽

New Class ◽

Molecular Studies

Resinicolous fungi constitute a heterogeneous assemblage of fungi that live on fresh and solidified plant resins. The genus Sarea includes, according to current knowledge, two species, S. resinae and S. difformis. In contrast to other resinicolous discomycetes, which are placed in genera also including non-resinicolous species, Sarea species only ever fruit on resin. The taxonomic classification of Sarea has proven to be difficult and currently the genus, provisionally and based only on morphological features, has been assigned to the Trapeliales (Lecanoromycetes). In contrast, molecular studies have noted a possible affinity to the Leotiomycetes. Here we review the taxonomic placement of Sarea using sequence data from seven phylogenetically informative DNA regions including ribosomal (ITS, nucSSU, mtSSU, nucLSU) and protein-coding (rpb1, rpb2, mcm7) regions. We combined available and new sequence data with sequences from major Pezizomycotina classes, especially Lecanoromycetes and Leotiomycetes, and assembled three different taxon samplings in order to place the genus Sarea within the Pezizomycotina. Based on our data, none of the applied phylogenetic approaches (Bayesian Inference, Maximum Likelihood and Maximum Parsimony) supported the placement of Sarea in the Trapeliales or any other order in the Lecanoromycetes. A placement of Sarea within the Leotiomycetes is similarly unsupported. Based on our data, Sarea forms an isolated and highly supported phylogenetic lineage within the " Leotiomyceta". From the results of our multilocus phylogenetic analyses we propose here a new class, order, and family, Sareomycetes, Sareales and Sareaceae in the Ascomycota to accommodate the genus Sarea. The genetic variability within the newly proposed class suggests that it is a larger group that requires further infrageneric classification.

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A novel mitogenomic rearrangement for Odorrana schmackeri (Anura: Ranidae) and phylogeny of Ranidae inferred from thirteen mitochondrial protein-coding genes

Amphibia-Reptilia ◽

10.1163/15685381-00002958 ◽

2014 ◽

Vol 35 (3) ◽

pp. 331-343 ◽

Cited By ~ 5

Author(s):

Yongmin Li ◽

Huabin Zhang ◽

Xiaoyou Wu ◽

Hui Xue ◽

Peng Yan ◽

...

Keyword(s):

Nucleotide Sequence ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Mitochondrial Protein ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes

We determined the complete nucleotide sequence of the mitochondrial genome of Odorrana schmackeri (family Ranidae). The O. schmackeri mitogenome (18 302 bp) contained 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes and a single control region (CR). In the new mitogenome, the distinctive feature is the loss of tRNA-His, which could be explained by a hypothesis of gene substitution. The new sequence data was used to assess the phylogenetic relationships among 23 ranid species mostly from China using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses support two families (Ranidae, Dicroglossidae) for Chinese ranids. In Ranidae, we support the genus Amolops should be retained in the subfamily Raninae rather than in a distinct subfamily Amolopinae of its own. Meanwhile, the monophyly of the genus Odorrana was supported. Within Dicroglossidae, four tribes were well supported including Occidozygini, Dicroglossini, Limnonectini and Paini. More mitochondrial genomes and nuclear genes are required to decisively evaluate phylogenetic relationships of ranids.

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First mitochondrial genomes of five hoverfly species of the genus Eristalinus (Diptera: Syrphidae)

Genome ◽

10.1139/gen-2019-0009 ◽

2019 ◽

Vol 62 (10) ◽

pp. 677-687 ◽

Cited By ~ 2

Author(s):

Gontran Sonet ◽

Yannick De Smet ◽

Min Tang ◽

Massimiliano Virgilio ◽

Andrew Donovan Young ◽

...

Keyword(s):

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

16S Rrna Genes ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Base Pairs ◽

Protein Coding ◽

Phylogenetic Informativeness ◽

Molecular Phylogenetic ◽

Phylogenetic Hypotheses

The hoverfly genus Eristalinus (Diptera, Syrphidae) contains many widespread pollinators. The majority of the species of Eristalinus occur in the Afrotropics and their molecular systematics still needs to be investigated. This study presents the first complete and annotated mitochondrial genomes for five species of Eristalinus. They were obtained by high-throughput sequencing of total genomic DNA. The total length of the mitogenomes varied between 15 757 and 16 245 base pairs. Gene composition, positions, and orientation were shared across species, and were identical to those observed for other Diptera. Phylogenetic analyses (maximum likelihood and Bayesian inference) based on the 13 protein coding and both rRNA genes suggested that the subgenus Eristalinus was paraphyletic with respect to the subgenus Eristalodes. An analysis of the phylogenetic informativeness of all protein coding and rRNA genes suggested that NADH dehydrogenase subunit 5 (nad5), cytochrome c oxidase subunit 1, nad4, nad2, cytochrome b, and 16S rRNA genes are the most promising mitochondrial molecular markers to result in supported phylogenetic hypotheses of the genus. In addition to the five complete mitogenomes currently available for hoverflies, the five mitogenomes published here will be useful for broader molecular phylogenetic analyses among hoverflies.

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