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

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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A description of the second species of the genus Bleptus Eaton, 1885 (Ephemeroptera: Heptageniidae) from Japan, and phylogenetic relationships of two Bleptus mayflies inferred from mitochondrial and nuclear gene sequences

Zootaxa ◽

10.11646/zootaxa.4974.2.5 ◽

2021 ◽

Vol 4974 (2) ◽

pp. 333-360

Author(s):

KOJI TOJO ◽

KEN MIYAIRI ◽

YUTO KATO ◽

AYANA SAKANO ◽

TOMOYA SUZUKI

Keyword(s):

Phylogenetic Analyses ◽

Ribosomal Subunit ◽

Nuclear Gene ◽

Taxonomic Status ◽

16S Rrna Genes ◽

Rrna Genes ◽

Gene Sequences ◽

Molecular Phylogenetic ◽

Black Band ◽

Relationship Of

A new mayfly species, Bleptus michinokuensis sp. nov. (Ephemeroptera: Heptageniidae) is described on the basis of specimens of male and female adults and mature nymphs collected at a seepage zone of a small freshwater branch of the ‘Tachiya-zawa-gawa’ River located amongst the northern foothills of Mt. Gassan (Shonai-machi Town, Yamagata Prefecture, Japan). This new Bleptus species is characterized by its clear fore and hind wings. That is, they neither exhibit the distinct black band on the fore wings, nor the characteristic darkened margins along the edges of both the fore and hind wings. Rather it has a blackish colored terminal half of its fore legs (i.e., tibial, tarsal and pretarsal segments). These features differ clearly when comparing them to the other known species, Bleptus fasciatus Eaton. The information and data describing the habitat and distribution range of this new species are also noted. We also examined and discussed the genetic relationship of two Bleptus mayflies to settle the taxonomic status, inferred from the partially sequenced cytochrome c oxidase subunit I (COI) and large mitochondrial ribosomal subunit (16S rRNA) genes, and also the nuclear internal transcribed spacer 2 (ITS2) gene sequences. Consequently, phenetic and molecular phylogenetic analyses agreed well in terms of clustering.

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Mitogenomics and the Phylogeny of Mantis Shrimps (Crustacea: Stomatopoda)

Diversity ◽

10.3390/d13120647 ◽

2021 ◽

Vol 13 (12) ◽

pp. 647

Author(s):

Cassandra Koga ◽

Greg W. Rouse

Keyword(s):

Sister Group ◽

18S Rrna Gene ◽

16S Rrna Genes ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

12S Rrna ◽

Rrna Gene ◽

Slight Variation ◽

Ancestral State ◽

Protein Coding

Stomatopoda, commonly known as mantis shrimps, are notable for their enlarged second maxillipeds encompassing the raptorial claw. The form of the claw can be used to divide them into two basic groups: smashers and spearers. Previous phylogenetic studies of Stomatopoda have focused on morphology or a few genes, though there have been whole mitochondrial genomes published for 15 members of Stomatopoda. However, the sampling has been somewhat limited with key taxa not included. Here, nine additional stomatopod mitochondrial genomes were generated and combined with the other available mitogenomes for a phylogenetic analysis. We used the 13 protein coding genes, as well as 12S rRNA, 16S rRNA genes, and included nuclear 18S rRNA gene sequences. Different rooting options were used for the analyses: (1) single and multiple outgroups from various eumalocostracan relatives and (2) a stomatopod-only dataset, with Hemisquilla californiensis used to root the topologies, based on the current hypothesis that Hemisquilla is the sister group to the rest of Stomatopoda. The eumalocostracan-rooted analyses all showed H. californiensis nested within Stomatopoda, raising doubts as to previous hypotheses as to its placement. Allowing for the rooting difference, the H. californiensis outgroup datasets had the same tree topology as the eumalocostracan outgroup datasets with slight variation at poorly supported nodes. Of the major taxonomic groupings sampled to date, Squilloidea was generally found to be monophyletic while Gonodactyloidea was not. The position of H. californiensis was found inside its superfamily, Gonodactyloidea, and grouped in a weakly supported clade containing Odontodactylus havanensis and Lysiosquillina maculata for the eumalocostracan-rooted datasets. An ancestral state reconstruction was performed on the raptorial claw form and provides support that spearing is the ancestral state for extant Stomatopoda, with smashing evolving subsequently one or more times.

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Review of the systematics, morphology and distribution of Asian Clawed Salamanders, genus Onychodactylus (Amphibia, Caudata: Hynobiidae), with the description of four new species

Zootaxa ◽

10.11646/zootaxa.3465.1.1 ◽

2012 ◽

Vol 3465 (1) ◽

pp. 1 ◽

Cited By ~ 16

Author(s):

NIKOLAY A. POYARKOV, JR. ◽

JING CHE ◽

MI-SOOK MIN ◽

MASAKI KURO-O ◽

FANG YAN ◽

...

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Russian Far East ◽

Far East ◽

Molecular Data ◽

16S Rrna Genes ◽

Rrna Genes ◽

Mitochondrial Coi ◽

Threat Status ◽

Molecular Phylogenetic

We describe four new species of Asian Clawed salamanders of the genus Onychodactylus (Caudata: Hynobiidae), basedon fresh material collected during fieldwork in Japan, Korea, the Russian Far East and northeastern China between 2003and 2010, as well as older voucher specimens deposited in several museums. Our analyses comprise all species currentlyrecognized within this genus across its entire distribution range. We follow an integrative taxonomic approach bycombining detailed morphological comparative analyses with molecular phylogenetic analyses. We find significantdifferences among species in this genus, based on morphological and molecular data, which resulted in the recognitionand description of four new species within this genus. The new species have uncorrected molecular divergences of over4.5–7.4% and 1.9–4.1% to their closest relatives in the mitochondrial COI and 16S rRNA genes respectively. In themolecular analyses, we found two very divergent lineages in Korea and Japan that need further investigation, as detailedmorphological data are not available for them. We also discuss our approach to delimit species on salamanders. For thenew species described in this group we evaluate their threat status according to IUCN criteria: O. koreanus sp. nov. Min,Poyarkov & Vieites and O. nipponoborealis sp. nov. Kuro-o, Poyarkov & Vieites are classified as Least Concern, whileO. zhaoermii sp. nov. Che, Poyarkov & Yan and O. zhangyapingi sp. nov. Che, Poyarkov, Li & Yan are classified as Vulnerable (Vu2a).

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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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A new species of the genus Pseudocrangonyx (Crustacea: Amphipoda: Pseudocrangonyctidae) from Simbok Cave, Korea

Zootaxa ◽

10.11646/zootaxa.4731.3.2 ◽

2020 ◽

Vol 4731 (3) ◽

pp. 321-334 ◽

Cited By ~ 4

Author(s):

CHI-WOO LEE ◽

KO TOMIKAWA ◽

TAKAFUMI NAKANO ◽

GI-SIK MIN

Keyword(s):

Phylogenetic Analyses ◽

Histone H3 ◽

16S Rrna Genes ◽

Rrna Genes ◽

28S Rrna ◽

Mitochondrial Cytochrome ◽

Molecular Phylogenetic ◽

Subterranean Species ◽

A New Species ◽

Honshu Island

A new subterranean species of pseudocrangonyctid amphipod, Pseudocrangonyx joolaei, is described from the groundwater of a cave in South Korea. Pseudocrangonyx joolaei sp. nov. can be distinguished from its congeners by the number of sternal gills as well as a combination of the antennal sinus, the accessory flagellum of antenna 1, and the terminal article of uropod 3. Molecular phylogenetic analyses based on nuclear 28S rRNA and histone H3, and mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes revealed that P. joolaei sp. nov. formed a clade with P. akatsukai Tomikawa & Nakano, 2018 that inhabits limestone caves in the western Honshu island, Japan.

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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 mitochondrial genome of Whitmania laevis (Annelida, Hirudinea) and comparative analyses within Whitmania mitochondrial genomes

Belgian Journal of Zoology ◽

10.26496/bjz.2015.52 ◽

2020 ◽

Vol 145 (2) ◽

Author(s):

Fei Ye ◽

Ting Liu ◽

Wenbo Zhu ◽

Ping You

Keyword(s):

Mitochondrial Genome ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Nucleotide Composition ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Close Relationship

The complete mitochondrial genome of Whitmania laevis is 14,442 bp in length and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The almost-complete mitochondrial genome of Whitmania acranulata, consisting of 13,494 bp, contains 35 genes including 13 PCGs, 20 tRNA genes, and two rRNA genes. COI phylogenetic analyses showed that the samples reported in GenBank and analysed as Hirudo nipponia KC667144, Hirudinaria manillensis KC688268 and Erpobdella octoculata KC688270 are not the named species and they should belong to Whitmania. We compared and analyzed the characteristics of nucleotide composition, codon usage, and secondary structures of 22 tRNAs and two rRNAs from Whitmania taxa. Moreover, we analyzed phylogenetic relationships of Annelida using maximum likelihood (ML) and Bayesian inference (BI) methods, based on 11 mitochondrial genes. Our results reveal that W. laevis has a close relationship with W. pigra.

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Comparative Mitogenomes of Two Coreamachilis Species (Microcoryphia: Machilidae) along with Phylogenetic Analyses of Microcoryphia

Insects ◽

10.3390/insects12090795 ◽

2021 ◽

Vol 12 (9) ◽

pp. 795

Author(s):

Jia-Yin Guan ◽

Shi-Qi Shen ◽

Zi-Yi Zhang ◽

Xiao-Dong Xu ◽

Kenneth B. Storey ◽

...

Keyword(s):

16S Rrna ◽

Positive Selection ◽

Adaptive Evolution ◽

Reproductive Strategies ◽

Phylogenetic Analyses ◽

16S Rrna Genes ◽

Rrna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Sister Clade

The order Microcoryphia, commonly known as bristletails, is considered as the most primitive one among living insects. Within this order, two species, Coreamachilis coreanus and C. songi (Machilidae: Machilinae), display the following contrasting reproductive strategies: parthenogenesis occurs in C. coreanus, whereas sexual reproduction is found in C. songi. In the present study, the complete mitogenomes of C. coreanus and C. songi were sequenced to compare their mitogenome structure, analyze relationships within the Microcoryphia, and assess adaptive evolution. The length of the mitogenomes of C. coreanus and C. songi were 15,578 bp and 15,570 bp, respectively, and the gene orders were those of typical insects. A long hairpin structure was found between the ND1 and 16S rRNA genes of both species that seem to be characteristic of Machilinae and Petrobiinae species. Phylogenetic assessment of Coreamachilis was conducted using BI and ML analyses with concatenated nucleotide sequences of the 13 protein-coding genes. The results showed that the monophyly of Machilidae, Machilinae, and Petrobiinae was not supported. The genus Coreamachilis (C. coreanus and C. songi) was a sister clade to Allopsontus helanensis, and then the clade of ((C. coreanus + C. songi) + A. helanensis) was a sister clade to A. baii, which suggests that the monophyly of Allopsontus was not supported. Positive selection analysis of the 13 protein-coding genes failed to reveal any positive selection in C. coreanus or C. songi. The long hairpin structures found in Machilinae and Petrobiinae were highly consistent with the phylogenetic results and could potentially be used as an additional molecular characteristic to further discuss relationships within the Microcoryphia.

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Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling

Applied and Environmental Microbiology ◽

10.1128/aem.01382-15 ◽

2015 ◽

Vol 81 (19) ◽

pp. 6901-6914 ◽

Cited By ~ 35

Author(s):

Feifei Sun ◽

Xiaoli Zhang ◽

Qianqian Zhang ◽

Fanghua Liu ◽

Jianping Zhang ◽

...

Keyword(s):

Bacterial Community ◽

Zostera Marina ◽

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

Coastal Sediments ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sulfur Cycling ◽

Polymorphism Analysis ◽

Content Type

ABSTRACTSeagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of aZostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. ThenifHphylotypes detected were mostly affiliated with theGeobacteraceae,Desulfobulbus,Desulfocapsa, andPseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution ofnifHgenotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence ofGeobacteraceaeandDesulfobulbaceaephylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducingGeobacteraceaeand sulfate-reducingDesulfobulbaceaediazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches,Desulfococcus(Deltaproteobacteria) andAnaerolineae(Chloroflexi) presented with much higher proportions in the vegetated sediments, andFlavobacteriaceae(Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favorDesulfococcusandAnaerolineaelineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem.

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Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽

10.1186/s12864-021-07394-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yiheng Wang ◽

Sheng Wang ◽

Yanlei Liu ◽

Qingjun Yuan ◽

Jiahui Sun ◽

...

Keyword(s):

Chloroplast Genome ◽

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

Herbal Medicines ◽

Structural Genomic ◽

Protein Coding ◽

Chloroplast Genomes ◽

Original Plant ◽

Morphological Differences ◽

Rna Genes

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

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