scholarly journals Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11086
Author(s):  
Xianyi Wang ◽  
Jiajia Wang ◽  
Ren-Huai Dai
Keyword(s):  
Phylogenetic Tree ◽  
Control Region ◽  
Strong Support ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Nucleotide Composition ◽  
Protein Coding ◽  
Approval Ratings ◽  
Phylogenetic Implications ◽  
Paraphyletic Group

Similar morphological characteristics and limited molecular data of Olidiana resulted in their unknown phylogenetic statuses and equivocal relationships. To further understand the genus Olidiana, we sequenced and annotated five Olidiana complete mitochondrial genomes (mitogenomes). Our results show that Olidiana mitogenomes range from 15,205 bp to 15,993 bp in length and include 37 typical genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region. Their nucleotide composition, codon usage, features of control region, and tRNA secondary structures are similar to other members of Cicadellidae. We constructed the phylogenetic tree of Cicadellidae using the maximum likelihood (ML) and Bayesian inference (BI) methods based on all valid mitogenome sequences. The most topological structure of the obtained phylogenetic tree is consistent. Our results support the monophyletic relationships among 10 subfamilies within Cicadellidae and confirm Iassinae and Coelidiinae to be sister groups with high approval ratings. Interestingly, Olidiana was inferred as a paraphyletic group with strong support via both ML and BI analyses. These complete mitogenomes of five Olidiana species could be useful in further studies for species diagnosis, evolution, and phylogeny research within Cicadellidae.

scholarly journals Two Complete Mitogenomes of Chalcididae (Hymenoptera: Chalcidoidea): Genome Description and Phylogenetic Implications

Insects ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1049
Author(s):  
Huifeng Zhao ◽  
Ye Chen ◽  
Zitong Wang ◽  
Haifeng Chen ◽  
Yaoguang Qin
Keyword(s):  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sister Group ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Molecular Phylogenetic ◽  
Rna Genes

The complete mitochondrial genomes of two species of Chalcididae were newly sequenced: Brachymeria lasus and Haltichella nipponensis. Both circular mitogenomes are 15,147 and 15,334 bp in total length, respectively, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A+T-rich region. The nucleotide composition indicated a strong A/T bias. All PCGs of B. lasus and H. nipponensis began with the start codon ATD, except for B. lasus, which had an abnormal initiation codon TTG in ND1. Most PCGs of the two mitogenomes are terminated by a codon of TAR, and the remaining PCGs by the incomplete stop codon T or TA (ATP6, COX3, and ND4 in both species, with an extra CYTB in B. lasus). Except for trnS1 and trnF, all tRNAs can be folded into a typical clover structure. Both mitogenomes had similar control regions, and two repeat units of 135 bp were found in H. nipponensis. Phylogenetic analyses based on two datasets (PCG123 and PCG12) covering Chalcididae and nine families of Chalcidoidea were conducted using two methods (maximum likelihood and Bayesian inference); all the results support Mymaridae as the sister group of the remaining Chalcidoidea, with Chalcididae as the next successive group. Only analyses of PCG123 generated similar topologies of Mymaridae + (Chalcididae + (Agaonidae + remaining Chalcidoidea)) and provided one relative stable clade as Eulophidae + (Torymidae + (Aphelinidae + Trichogrammatidae)). Our mitogenomic phylogenetic results share one important similarity with earlier molecular phylogenetic efforts: strong support for the monophyly of many families, but a largely unresolved or unstable “backbone” of relationships among families.

The Complete Mitogenome of Curculio Chinensis (Coleoptera: Curculionidae: Curculioninae): Structural Characterization and Phylogenetic Implication

2021 ◽  
Author(s):  
Zaihua Yang ◽  
Kai Hu ◽  
Niannian Zhang
Keyword(s):  
Control Region ◽  
Tandem Repeats ◽  
Strong Support ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Protein Coding ◽  
Region Length ◽  
Complete Mitogenome

Abstract To explore the phylogenetic position of Curculio chinensis Chevrolat, 1878 and phylogenetic relationships among major lineages of the family Curculionidae, we sequenced and annotated this mitogenome. The mitogenome is 18,680 bp in length, and includes the 37 typical mitochondrial genes and a large control region (length: 1,997 bp). Mitogenome organization, nucleotide composition, and codon usage are similar to most of the previously sequenced Curculioninae mitogenomes. All 13 protein-coding genes use ATN or TTG as start codon, and end with TAA/G or incomplete stop codons (single T-). Twenty-one transfer RNA genes have the typical clover-leaf structures, while the dihydrouridine (DHU) arm of trnS1 is missing. In Curculioninae mitogenomes, the size and number of tandem repeats in the control region are highly variable. Both ML and BI analyses based on the 13 PCGs and two rRNAs from 91 species of Coleoptera strongly supported the monophyly of Curculionidae and three of the included subfamilies (Platypodinae, Dryophthorinae, and Cryptorhynchinae) plus the sister relationship between Platypodinae and Dryophthorinae. Additionally, the monophyly of the genus Curculio was recovered with strong support.

scholarly journals Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1185
Author(s):  
Wenqian Wang ◽  
Huan Zhang ◽  
Jérôme Constant ◽  
Charles R. Bartlett ◽  
Daozheng Qin
Keyword(s):  
Control Region ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Start Codon ◽  
Rrna Genes ◽  
Rich Region ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Rna Genes ◽  
Unpaired Base

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

scholarly journals Complete Mitogenomic Structure and Phylogenetic Implications of the Genus Ostrinia (Lepidoptera: Crambidae)

Insects ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 232
Author(s):  
Nan Zhou ◽  
Yanling Dong ◽  
Pingping Qiao ◽  
Zhaofu Yang
Keyword(s):  
Control Region ◽  
Ostrinia Nubilalis ◽  
Phylogenetic Analyses ◽  
Structural Elements ◽  
Ostrinia Furnacalis ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Ostrinia Scapulalis ◽  
The Relationship ◽  
Rna Genes

To understand mitogenome characteristics and reveal phylogenetic relationships of the genus Ostrinia, including several notorious pests of great importance for crops, we sequenced the complete mitogenomes of four species: Ostrinia furnacalis (Guenée, 1854), Ostrinia nubilalis (Hübner, 1796), Ostrinia scapulalis (Walker, 1859) and Ostrinia zealis (Guenée, 1854). Results indicate that the four mitogenomes—O. furnacalis, O. nubilalis, O. scapulalis, and O. zealis—are 15,245, 15,248, 15,311, and 15,208 bp in size, respectively. All four mitogenomes are comprised of 37 encoded genes and a control region. All 13 protein-coding genes (PCGs) initiate with ATN and terminate with TAN, with the exception of cox1 that starts with CGA, and cox1, cox2, and nad5 that terminate with an incomplete codon T. All transfer RNA genes (tRNAs) present the typical clover-leaf secondary structure except for the trnS1 (AGN) gene. There are some conserved structural elements in the control region. Our analyses indicate that nad6 and atp6 exhibit higher evolution rates compared to other PCGs. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods revealed the relationship (O. palustralis + (O. penitalis + (O. zealis + (O. furnacalis + (O. nubilalis + O. scapulalis))))) within Ostrinia.

Diversity of Auricularia (Auriculariaceae, Auriculariales) in Thailand

Phytotaxa ◽  
2017 ◽  
Vol 292 (1) ◽  
pp. 19 ◽  
Author(s):  
ASANKA R. BANDARA ◽  
SAMANTHA C. KARUNARATHNA ◽  
ALAN J.L. PHILLIPS ◽  
PETER E. MORTIMER ◽  
JIANCHU XU ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Tree ◽  
New Records ◽  
Light Exposure ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Full Description ◽  
Fruiting Bodies ◽  
A New Species

The identification of Auricularia species has previously relied on the examination of macroscopic features of mushroom samples collected in Thailand. These features may vary with age, light exposure, moisture and other factors, making such identification prone to error. This study uses morphological characteristics and molecular data to improve upon previous classifications of Auricularia species. Fruiting bodies collected during recent field excursions and previous collections from herbaria were examined and sequenced for two loci, viz. ITS and rpb2. Auricularia asiatica is described as a new species based on both morphological characteristics and molecular data, and is introduced with a full description, illustrations and colour photographs. Auricularia cornea and A. villosula are described as new records from Thailand. A combined ITS and rpb2 phylogenetic tree is provided, showing the placement of five Auricularia species found in Thailand.

Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae)

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 188-202 ◽  
Author(s):  
Stephen L. Cameron ◽  
Michael F. Whiting
Keyword(s):  
Control Region ◽  
Repeat Unit ◽  
General Characteristic ◽  
Nucleotide Composition ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Stem Loop ◽  
Protein Coding ◽  
Repeat Units ◽  
Mt Genome

Termites of the genus Reticulitermes are some of the most significant pests of structural timber and tree farming in the northern hemisphere, causing losses in the billions of dollars annually because of direct damage and termite control costs. This group has been frequently targeted for population genetic, phylogenetic, and species limit studies, most of which use mitochondrial (mt) genes; however, only a small fraction of the genome has been sequenced. The entire mt genome was sequenced for the eastern North American members of Reticulitermes: R. flavipes, R. santonensis, R. virginicus, and R. hageni. The mt genome has the same gene content and organization as that found in most insect species; however, the nucleotide composition and skew are highly biased (AT% low, strong A- and C-skew). Both the protein-coding and transfer RNA genes show high absolute levels of nucleotide substitution, suggesting that the high rates of mutation within Reticulitermes inferred from analyses of single mt genes are a general characteristic of the entire mt genome. The AT-rich or control region has a remarkable structure not previously observed in insect mt genomes. The majority of the control region is made up of 2 sets of repeat units, typically with 2 full and 1 partial copies of both the A (or small; 186 bp) and B (or large; 552 bp) repeats. The partial repeat units overlap by 36 bp. The size, location, and degree of overlap for the partial repeat units correspond to highly conserved stem/loop structures within the repeat units, suggesting that these structures are involved in the replication-mediated processes that govern repeat-unit evolution within mt genomes. Finally, molecular variation within the mt gene regions was compared with previous regions used in molecular diagnostics or phylogenetics of Reticulitermes. High numbers of single nucleotide polymorphisms were found in each of the mt genes, and some of the highest variability was found in gene regions that have not previously been investigated in this group. The whole mt genome sequence can thus be used to predict useful regions for future investigation.

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

Insects ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 534 ◽  
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.

Trechispora yunnanensis sp. nov. (Hydnodontaceae, Basidiomycota) from China

Phytotaxa ◽  
2019 ◽  
Vol 424 (4) ◽  
pp. 253-261 ◽  
Author(s):  
TAI-MIN XU ◽  
YU-HUI CHEN ◽  
CHANG-LIN ZHAO
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Strong Support ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Fungal Species ◽  
Monophyletic Lineage ◽  
Molecular Phylogenetic ◽  
Inference Methods

A new wood-inhabiting fungal species, Trechispora yunnanensis sp. nov., is proposed based on morphological characteristics and molecular phylogenetic analyses. The species is characterized by resupinate basidiomata, rigid and fragile up on drying, cream to pale greyish hymenial surface; a monomitic hyphal system with generative hyphae bearing clamp connections, IKI-, CB-; ellipsoid, hyaline, thick-walled, ornamented, IKI-, CB- basidiospores measuring as 7–8.5 × 5–5.5 µm. The internal transcribed spacer (ITS) and the large subunit (LSU) regions of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood (ML), maximum parsimony (MP) and bayesian inference methods (BPP). The phylogenetic analyses based on molecular data of ITS+nLSU sequences showed that T. yunnanensis formed a monophyletic lineage with a strong support (100% ML, 100% MP, 1.00 BPP) and was closely related to T. byssinella and T. laevis. Both morphological characteristics and results of molecular phylogenetic analyses confirmed the placement of the new species in Trechispora.

scholarly journals Plastid phylogenomic insights into relationships of all flowering plant families

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Hong-Tao Li ◽  
Yang Luo ◽  
Lu Gan ◽  
Peng-Fei Ma ◽  
Lian-Ming Gao ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Strong Support ◽  
Terrestrial Ecosystems ◽  
Nuclear Data ◽  
Molecular Data ◽  
Flowering Plants ◽  
Flowering Plant ◽  
Bootstrap Support ◽  
Plant Phylogeny ◽  
Phylogenomic Analyses

Abstract Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. Results Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. Conclusions We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.

Morpho-phylogenetic evidence reveals Lasiodiplodia chiangraiensis sp. nov. (Botryosphaeriaceae) associated with woody hosts in northern Thailand

Phytotaxa ◽  
2021 ◽  
Vol 508 (2) ◽  
Author(s):  
NA WU ◽  
ASHA J. DISSANAYAKE ◽  
K.W. THILINI CHETHANA ◽  
KEVIN D. HYDE ◽  
JIAN-KUI LIU
Keyword(s):  
New Species ◽  
Phylogenetic Tree ◽  
Sequence Data ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Northern Thailand ◽  
Data Support ◽  
Distinct Lineage

Lasiodiplodia species are commonly as endophytes, saprobes and pathogens in tropics and subtropics. During an investigation of Botryosphaeriaceae in Thailand, two Lasiodiplodia taxa were isolated. Morphological characteristics and phylogenetic analyses based on combined ITS, tef and tub2 sequence data support the establishment of a novel species, Lasiodiplodia chiangraiensis, isolated from woody hosts. Lasiodiplodia chiangraiensis is phylogenetically close to L. iraniensis and L. thailandica, but represents a distinct lineage. The new species could be distinguished from extant Lasiodiplodia species by its mature conidial dimensions. A detailed description and illustration are provided, as well as an updated phylogenetic tree (ITS, tef and tub2) including all species (with available molecular data) of Lasiodiplodia. In addition, the accepted genera in Botryosphaeriaceae based on recent studies are given.

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