scholarly journals A New Genus of Terrestrial-Breeding Frogs (Holoadeninae, Strabomantidae, Terrarana) from Southern Peru

Diversity ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 184 ◽  
Author(s):  
Alessandro Catenazzi ◽  
Luis Mamani ◽  
Edgar Lehr ◽  
Rudolf von May
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Nuclear Protein ◽  
High Elevation ◽  
Rrna Genes ◽  
12S Rrna ◽  
Gene Recombination ◽  
Tropical Andes ◽  
Protein Coding ◽  
Molecular Analyses

We propose to erect a new genus of terrestrial-breeding frogs of the Terrarana clade to accommodate three species from the Province La Convención, Department of Cusco, Peru previously assigned to Bryophryne: B. flammiventris, B. gymnotis, and B. mancoinca. We examined types and specimens of most species, reviewed morphological and bioacoustic characteristics, and performed molecular analyses on the largest phylogeny of Bryophryne species to date. We performed phylogenetic analysis of a dataset of concatenated sequences from fragments of the 16S rRNA and 12S rRNA genes, the protein-coding gene cytochrome c oxidase subunit I (COI), the nuclear protein-coding gene recombination-activating protein 1 (RAG1), and the tyrosinase precursor (Tyr). The three species are immediately distinguishable from all other species of Bryophryne by the presence of a tympanic membrane and annulus, and by males having median subgular vocal sacs and emitting advertisement calls. Our molecular phylogeny confirms that the three species belong to a new, distinct clade, which we name Qosqophryne, and that they are reciprocally monophyletic with species of Microkayla. These two genera (Qosqophryne and Microkayla) are more closely related to species of Noblella and Psychrophrynella than to species of Bryophryne. Although there are no known morphological synapomorphies for either Microkayla or Qosqophryne, the high endemism of their species, and the disjoint geographic distribution of the two genera, with a gap region of ~310 km by airline where both genera are absent, provide further support for Qosqophryne having long diverged from Microkayla. The exploration of high elevation moss and leaf litter habitats in the tropical Andes will contribute to increase knowledge of the diversity and phylogenetic relationships within Terrarana.

The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

2022 ◽  
Author(s):  
Tianhong Wang ◽  
Zihao Wang ◽  
Ruwei Bai ◽  
Zhijun Yu ◽  
Jingze Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Haemaphysalis Qinghaiensis ◽  
Mitogenome Sequence ◽  
Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

scholarly journals Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

2020 ◽  
Vol 21 (13) ◽  
pp. 4685
Author(s):  
Zhenhai Li ◽  
Min Li ◽  
Shannan Xu ◽  
Li Liu ◽  
Zuozhi Chen ◽  
...  
Keyword(s):  
Divergence Time ◽  
Rrna Genes ◽  
12S Rrna ◽  
Trna Genes ◽  
Coding Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Gc Skew ◽  
The Family ◽  
Conserved Genes

Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.

scholarly journals Phylogenetic analysis of Myriapoda using three nuclear protein-coding genes

2005 ◽  
Vol 34 (1) ◽  
pp. 147-158 ◽  
Author(s):  
Jerome C. Regier ◽  
Heather M. Wilson ◽  
Jeffrey W. Shultz
Keyword(s):  
Phylogenetic Analysis ◽  
Nuclear Protein ◽  
Protein Coding ◽  
Protein Coding Genes

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

Diversity ◽  
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.

scholarly journals Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Dong Liu ◽  
Yuanyuan Zhang ◽  
Ming Zhang ◽  
Jinquan Yang ◽  
Wenqiao Tang
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Morphological Evolution ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
12S Rrna ◽  
Trna Genes ◽  
Protein Coding ◽  
Jaw Apparatus ◽  
Intergenic Regions

Abstract Background The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species. Results We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments. Conclusions This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.

scholarly journals Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis

ZooKeys ◽  
2020 ◽  
Vol 1005 ◽  
pp. 57-72
Author(s):  
I-Chen Wang ◽  
Hung-Du Lin ◽  
Chih-Ming Liang ◽  
Chi-Chun Huang ◽  
Rong-Da Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Genomic Variation ◽  
Rrna Genes ◽  
Valid Species ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes

The cyprinid genus Onychostoma Günther, 1896 consists of 24 valid species distributed in Southeast Asia, including Taiwan, Hainan, mainland China and the Indochina region. In the present study, we determined the complete mitochondrial genome of O. lepturum, which is 16,598 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region (D-loop). To verify the molecular phylogeny of the subfamily Acrossocheilinae, we provide new insights to better understand the taxonomic status of Acrossocheilus, Onychostoma and Folifer brevifilis. The phylogenetic trees presented three major clades based on the 13 protein-coding genes from 28 Acrossocheilinae species. Clades I and II represent the Onychostoma and Acrossocheilus groups, respectively. Species of Acrossocheilus, Onychostoma and F. brevifilis are included in Clade III, which is considered as an ancestral group. This work provides genomic variation information and improves our understanding of the Acrossocheilinae mitogenome, which will be most valuable in providing new insights for phylogenetic analysis and population genetics research.

scholarly journals Discovery of a New Virus of the Family Tymoviridae Isolated from Mosquitoes of the Genus Mansonia in Brazil

2021 ◽  
Author(s):  
Keissy Karoline Pinheiro Miranda ◽  
Glennda Juscely Pereira Galvão ◽  
Pedro Arthur da Silva Araújo ◽  
Ana Claudia da Silva Ribeiro ◽  
Poliana da Silva Lemos ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Genomic Organization ◽  
Protein Coding ◽  
A Genome ◽  
The Family ◽  
Complete Sequencing ◽  
Ek Balam

Abstract A new virus, named Mutum virus, of the Family Tymoviridae was isolated from mosquitoes (Mansonia spp.). This virus was isolated in clone C6/36 cells. After complete sequencing, it presented a genome with 6,494 nt. The isolated virus is phylogenetically more related to two viruses isolated from Culex spp. mosquitoes: Ek Balam virus, isolated from Mexico, and Culex-originated Tymoviridae-like virus, isolated from China. Owing to the similarity of the protein coding domains, genomic organization, and phylogenetic analysis, we suggest that this virus belongs to a new genus, family Tymoviridae

scholarly journals A new genus and species of tachinid flies from Iran (Diptera, Tachinidae, Goniini)

2021 ◽  
Vol 746 ◽  
pp. 162-185
Author(s):  
Ebrahim Gilasian ◽  
Joachim Ziegler ◽  
Andrea Tóthová ◽  
Mehrdad Parchami-Araghi
Keyword(s):  
Phylogenetic Analysis ◽  
National Park ◽  
Type Species ◽  
New Genus ◽  
Systematic Position ◽  
Ribosomal Genes ◽  
Identification Key ◽  
New Genus And Species ◽  
Molecular Analyses

Susamyia Ziegler & Gilasian gen. nov. and its type species Susamyia mira Ziegler & Gilasian gen. et sp. nov. are described from southwestern Karkheh National Park and southeastern Jazmourian Wetland of Iran. Drawings of terminalia and head of the male as well as images of habitus, head and egg are provided. Susamyia gen. nov. is incorporated into the identification key to the Palearctic tachinid genera of Tschorsnig & Richter (1998). The systematic position of Susamyia gen. nov. in the tribe Goniini (Exoristinae) is discussed in light of molecular analyses based on the ribosomal genes 16S, 18S and 28S, and the egg type of females. The morphology of the microtype eggs was studied and compared with that of other Goniini, but proved too unreliable to be included in the phylogenetic analysis. Susamyia gen. nov. is believed to be most closely related to the goniine genera Gymnophryxe Villeneuve, 1922, Palesisa Villeneuve, 1929 and Prosopodopsis Townsend, 1926.

Loculosulcatispora thailandica gen. et sp. nov. (Sulcatisporaceae), saprobic on woody litter in Thailand

Phytotaxa ◽  
2020 ◽  
Vol 475 (2) ◽  
pp. 67-78
Author(s):  
GUANG-CONG REN ◽  
DHANUSHKA N. WANASINGHE ◽  
DE-PING WEI ◽  
JUTAMART MONKAI ◽  
ERANDI YASANTHIKA ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
New Genus ◽  
New Genus And Species ◽  
Protein Coding ◽  
Coding Regions ◽  
The Family ◽  
Distinct Lineage ◽  
Woody Litter

A new monotypic coelomycetous genus, Loculosulcatispora (type species L. thailandica) is introduced in Pleosporales from woody litter in Thailand. Phylogenetic analysis of combined non-translated loci (SSU, LSU, ITS) and protein-coding regions (tef1-α, rpb2) shows the genus is a distinct lineage in Sulcatisporaceae. Loculosulcatispora is distinguished from other genera in the family, by having 1-celled, oblong, hyaline, smooth-walled conidia with guttules. Comprehensive morphological descriptions and illustrations are provided for the new genus and species.

scholarly journals Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae)

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 109
Author(s):  
Kuan Liu ◽  
Rong Wang ◽  
Xiu-Xiu Guo ◽  
Xue-Jie Zhang ◽  
Xiao-Jian Qu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Structure ◽  
Single Copy ◽  
Rrna Genes ◽  
Molecular Evidence ◽  
Trna Genes ◽  
Protein Coding ◽  
Hypervariable Regions ◽  
Chloroplast Genomes ◽  
Small Single Copy

Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed. The length of these chloroplast genomes varied from 130,773 bp to 135,322 bp. These chloroplast genomes showed a typical quadripartite structure, including a large single-copy region (77,993–80,643 bp), a small single-copy region (12,410–12,668 bp), and a pair of inverted repeats region (19,394–21,074 bp). There were, in total, 129–133 genes annotated in the genome, including 83–87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Forward and palindromic repeats were the most common repeat types. In total, 10 hypervariable regions (rpl22, rpoA, ndhF, matK, trnG–UCC-trnT–GGU, ndhF–rpl32, ycf4–cemA, rpl32–trnL–UAG, trnG–GCC–trnfM–CAU, and ccsA–ndhD) were found, which can be used as candidate molecular markers for Eragrostideae. Phylogenomic studies concluded that Enneapogon diverged first, and Eragrostis including Harpachne is the sister to Uniola. Furthermore, Harpachne harpachnoides is considered as a species of Eragrostis based on morphological and molecular evidence. In addition, the interspecies relationships within Eragrostis are resolved based on complete chloroplast genomes. This study provides useful chloroplast genomic information for further phylogenetic analysis of Eragrostideae.

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