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

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.

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

Insects ◽

10.3390/insects11040232 ◽

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.

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

Insects ◽

10.3390/insects12121049 ◽

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.

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Comparative Mitogenomic Analysis of Two Longhorn Beetles (Coleoptera: Cerambycidae: Lamiinae) with Preliminary Investigation into Phylogenetic Relationships of Tribes of Lamiinae

Insects ◽

10.3390/insects12090820 ◽

2021 ◽

Vol 12 (9) ◽

pp. 820

Author(s):

Yifang Ren ◽

Huanhuan Lu ◽

Longyan Chen ◽

Simone Sabatelli ◽

Chaojie Wang ◽

...

Keyword(s):

Ribosomal Rna ◽

Phylogenetic Relationships ◽

Stop Codon ◽

Preliminary Investigation ◽

Mitochondrial Genes ◽

Start Codon ◽

Rich Region ◽

Protein Coding ◽

Longhorn Beetles ◽

Rna Genes

The subfamily Lamiinae is the most taxonomically diverse subfamily of Cerambycidae, but relationships between tribes of Lamiinae are still unresolved. In order to study the characteristics of the mitogenomes of Lamiinae and the tribal-level phylogenetic relationships, we sequenced the mitogenomes of two species representing two tribes, Agapanthia amurensis (Agapanthiini) and Moechotypa diphysis (Ceroplesini), with a total length of 15,512 bp and 15,493 bp, respectively. The gene arrangements of these two new mitogenomes were consistent with the inferred ancestral insect mitogenomes. Each species contained 37 typical mitochondrial genes and a control region (A + T-rich region), including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). All PCGs initiated with the standard start codon ATN, and terminated with the complete stop codons of TAA and TAG, or incomplete stop codon T. All tRNAs could be folded into a clover-leaf secondary structure except for trnS1, in which the dihydrouridine (DHU) arm was reduced. Moreover, we studied the phylogenetic relationships between some tribes of Lamiinae based in mitochondrial PCGs in nucleotides; our results show that the relationships were as follows: (Onciderini + ((Apomecynini + Acanthocinini) + ((Ceroplesini + Agapanthiini) + ((Mesosini + Pteropliini) + ((Dorcaschematini + (Saperdini 1 + (Phytoeciini + Saperdini 2))) + (Batocerini + Lamiini)))))).

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Characterization of Two Complete Mitochondrial Genomes of Atkinsoniella (Hemiptera: Cicadellidae: Cicadellinae) and the Phylogenetic Implications

Insects ◽

10.3390/insects12040338 ◽

2021 ◽

Vol 12 (4) ◽

pp. 338

Author(s):

Yan Jiang ◽

Hao-Xi Li ◽

Xiao-Fei Yu ◽

Mao-Fa Yang

Keyword(s):

Stop Codon ◽

Phylogenetic Analyses ◽

Initiation Site ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Phylogenetic Implications ◽

Rna Genes ◽

Complete Mitochondrial Genomes

The complete mitochondrial genomes of Atkinsoniella grahami and Atkinsoniella xanthonota were sequenced. The results showed that the mitogenomes of these two species are 15,621 and 15,895 bp in length, with A+T contents of 78.6% and 78.4%, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (CR). For all PCGs, a standard start ATN codon (ATT, ATG, or ATA) was found at the initiation site, except for ATP8, for which translation is initiated with a TTG codon. All PCGs terminate with a complete TAA or TAG stop codon, except for COX2, which terminates with an incomplete stop codon T. All tRNAs have the typical cloverleaf secondary structure, except for trnS, which has a reduced dihydrouridine arm. Furthermore, these phylogenetic analyses were reconstructed based on 13 PCGs and two rRNA genes of 73 mitochondrial genome sequences, with both the maximum likelihood (ML) and Bayesian inference (BI) methods. The obtained mitogenome sequences in this study will promote research into the classification, population genetics, and evolution of Cicadellinae insects in the future.

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Complete mitogenome of Parum colligata (Lepidoptera: Sphingidae) and its phylogenetic position within the Sphingidae

Zootaxa ◽

10.11646/zootaxa.4652.1.6 ◽

2019 ◽

Vol 4652 (1) ◽

pp. 126-134 ◽

Cited By ~ 2

Author(s):

JUN LI ◽

KUNJIE HU ◽

YAQI ZHAO ◽

RUIRUI LIN ◽

YAOYAO ZHANG ◽

...

Keyword(s):

Mitochondrial Dna ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Transfer Rna ◽

Phylogenetic Position ◽

Rich Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Complete Mitogenome ◽

Rna Genes

In this study, the complete mitochondrial DNA sequence of Parum colligata (Lepidoptera: Sphingidae: Smerinthinae) was sequenced firstly. The mitogenome is 15,288 bp in size, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and an A+T-rich region. In the mitogenome, Ile, Leu2, and Phe are the most frequently used codon families, while codons GCG, TGC, GGC, CTG, AGG, and ACG are absent. The A+T-rich region is 358 bp in length including a motif ‘ATAGA’, an 18 bp poly-T stretch, three copies of a 12 bp ‘TATATATATATA’, and a short poly-A element. The nucleotides sequence of A+T-rich region is closer to Sphinginae than Macroglossinae. Phylogenetic analyses, based on the PCGs by using Maximum Likelihood (ML) and Bayesian Inference (BI) methods, generated consistent results that Smerinthinae was clustered together with Sphinginae to be the sister groups rather than Macroglossinae.

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Characterization of the Complete Mitochondrial Genomes of Two Species with Preliminary Investigation on Phylogenetic Status of Zyginellini (Hemiptera: Cicadellidae: Typhlocybinae)

Insects ◽

10.3390/insects11100684 ◽

2020 ◽

Vol 11 (10) ◽

pp. 684

Author(s):

Xian Zhou ◽

Christopher H. H. Dietrich ◽

Min Huang

Keyword(s):

Tandem Repeats ◽

Stop Codon ◽

Phylogenetic Analyses ◽

Preliminary Investigation ◽

Start Codon ◽

Coding Region ◽

Rich Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Rna Genes

To explore the characteristics of mitogenomes and reveal phylogenetic relationships of the tribes of Zyginellini and Typhlocybini in Typhlocybinae, mitogenomes of two species of the Zyginellini, Parazyginella tiani and Limassolla sp., were sequenced. Mitogenomes of both species contain 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a large non-coding region (A + T-rich region). These characteristics are similar to other Membracoidea mitogenomes. All PCGs initiate with the standard start codon of ATN and terminate with the complete stop codon of TAA/G or with an incomplete T codon. All tRNAs have the typical clover-leaf structure, except trnS1 which has a reduced DHU arm and the acceptor stem of trnR is 5 or 6 bp in some species, an unusual feature here reported for the first time in Typhlocybinae. The A + T-rich region is highly variable in length and in numbers of tandem repeats present. Our analyses indicate that nad6 and atp6 exhibit higher evolutionary rates compared to other PCGs. Phylogenetic analyses by both maximum likelihood and Bayesian methods based on 13 protein-coding genes of 12 species of Typhlocybinae suggest that Zyginellini are paraphyletic with respect to Typhlocybini.

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The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications

ZooKeys ◽

10.3897/zookeys.1061.70176 ◽

2021 ◽

Vol 1061 ◽

pp. 57-73

Author(s):

Renyi Zhang ◽

Qian Tang ◽

Lei Deng

Keyword(s):

Complete Mitochondrial Genome ◽

Genetic Material ◽

Start Codon ◽

Trna Genes ◽

Protein Coding ◽

Simple Loop ◽

Stop Codons ◽

Phylogenetic Implications ◽

Complete Mitogenome ◽

Rna Genes

Mitochondria are important organelles with independent genetic material of eukaryotic organisms. In this study, we sequenced and analyzed the complete mitogenome of a small cyprinid fish, Microphysogobio elongatus (Yao & Yang, 1977). The mitogenome of M. elongatus is a typical circular molecule of 16,612 bp in length containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 930 bp control region. The base composition of the M. elongatus mitogenome is 30.8% A, 26.1% T, 16.7% G, and 26.4% C. All PCGs used the standard ATG start codon with the exception of COI. Six PCGs terminate with complete stop codons, whereas seven PCGs (ND2, COII, ATPase 6, COIII, ND3, ND4, and Cyt b) terminate with incomplete (T or TA) stop codons. All tRNA genes exhibited typical cloverleaf secondary structures with the exception of tRNASer(AGY), for which the dihydrouridine arm forms a simple loop. The phylogenetic analysis divided the subfamily Gobioninae in three clades with relatively robust support, and that Microphysogobio is not a monophyletic group. The complete mitogenome of M. elongatus provides a valuable resource for future studies about molecular phylogeny and/or population genetics of Microphysogobio.

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The complete chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses

Scientific Reports ◽

10.1038/s41598-020-77661-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Wenbin Xu ◽

Boshun Xia ◽

Xinwei Li

Keyword(s):

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Distinct Species ◽

The Other ◽

Trna Genes ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Noncoding Sequences ◽

Chloroplast Genomes ◽

Rna Genes

AbstractThe six pinnate-leaved species are a very particular group in the genus Primula. In the present paper, we sequenced, assembled and annotated the chloroplast genomes of five of them (P. cicutarrifolia, P. hubeiensis, P. jiugongshanensis, P. merrilliana, P. ranunculoides). The five chloroplast genomes ranged from ~ 150 to 152 kb, containing 113 genes (four ribosomal RNA genes, 29 tRNA genes and 80 protein-coding genes). The six pinnate-leaved species exhibited synteny of gene order and possessed similar IR boundary regions in chloroplast genomes. The gene accD was pseudogenized in P. filchnerae. In the chloroplast genomes of the six pinnate-leaved Primula species, SSRs, repeating sequences and divergence hotspots were identified; ycf1 and trnH-psbA were the most variable markers among CDSs and noncoding sequences, respectively. Phylogenetic analyses showed that the six Primula species were separated into two distant clades: one was formed by P. filchnerae and P. sinensis and the other clade was consisting of two subclades, one formed by P. hubeiensis and P. ranunculoides, the other by P. merrilliana, P. cicutarrifolia and P. jiugongshanensis. P. hubeiensis was closely related with P. ranunculoides and therefore it should be placed into Sect. Ranunculoides. P. cicutarrifolia did not group first with P. ranunculoides but with P. merrilliana, although the former two were once united in one species, our results supported the separation of P. ranunculoides from P. cicutarrifolia as one distinct species.

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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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Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

ZooKeys ◽

10.3897/zookeys.1070.72742 ◽

2021 ◽

Vol 1070 ◽

pp. 13-30

Author(s):

Wanqing Zhao ◽

Dajun Liu ◽

Qian Jia ◽

Xin Wu ◽

Hufang Zhang

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Purifying Selection ◽

Sister Group ◽

Start Codon ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Inference Methods

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

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