scholarly journals Yet Another Mitochondrial Genome of the Pacific Cupped Oyster: The Published Mitogenome of Alectryonella plicatula (Ostreinae) Is Based on a Misidentified Magallana gigas (Crassostreinae)

2021 ◽  
Vol 8 ◽  
Author(s):  
Daniele Salvi ◽  
Emanuele Berrilli ◽  
Matteo Garzia ◽  
Paolo Mariottini
Keyword(s):  
Mitochondrial Genome ◽  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
Molecular Data ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Terminal Branch ◽  
The Pacific ◽  
Cupped Oyster

The recently published mitochondrial genome of the fingerprint oyster Alectryonella plicatula (Gmelin, 1791) with GenBank accession number MW143047 was resolved in an unexpected phylogenetic position, as sister to the Pacific cupped oyster Magallana gigas (Thunberg, 1793) and share with this species three typical gene duplications that represent robust synapomorphies of the Magallana clade. In this study, we verified the identity of MW143047 using direct comparisons of single gene sequences, DNA barcoding and phylogenetic analyses. BLAST searches using as query each of the 12 protein coding genes (PCGs) and rRNA genes extracted from MW143047 retrieved M. gigas as best hit with 100% sequence identity for all genes. MW143047 is nested within the clade formed by M. gigas sequences, with virtually zero-length terminal branch, both in the cox1 gene tree (based on 3639 sequences) and in the 16S gene tree (based on 1839 sequences), as well as in the Maximum Likelihood mitogenomic tree based on concatenated sequence of 12 PCGs. Our findings suggest that the original specimen used for mitogenome sequencing was misidentified and represents an individual of M. gigas. This study reinforces the notion that morphological shell analysis alone is not sufficient for oyster identification, not even at high taxonomic ranks such as subfamilies. While it is well established that morphological identification of oysters should be validated by molecular data, this study emphasizes that also molecular data should be taxonomically verified by means of DNA barcoding and phylogenetic analyses. The implications of the publication of taxonomically misidentified sequences and mitogenomes are discussed.

scholarly journals Yet another mitochondrial genome of the Pacific cupped oyster: the published mitogenome of Alectryonella plicatula (Ostreinae) is based on a misidentified Magallana gigas (Crassostreinae)

2021 ◽  
Author(s):  
Daniele Salvi ◽  
Emanuele Berrilli ◽  
Matteo Garzia ◽  
Paolo Mariottini
Keyword(s):  
Mitochondrial Genome ◽  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
Molecular Data ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Cox1 Gene ◽  
The Pacific ◽  
Cupped Oyster

The recently published mitochondrial genome of the fingerprint oyster Alectryonella plicatula (Gmelin, 1791) with GenBank accession number MW143047 was resolved in an unexpected phylogenetic position, as sister to the Pacific cupped oyster Magallana gigas (Thunberg, 1793) and share with this species three typical gene duplications that represent robust synapomorphies of the Magallana clade. In this study, we verified the identity of MW143047 using direct comparisons of single gene sequences, DNA barcoding and phylogenetic analyses. BLAST searches using each of the 12 protein coding genes and rRNA genes extracted from MW143047 as query retrieved M. gigas as best hit with 100% sequence identity. MW143047 is nested within the clade formed by M. gigas sequences, with virtually no difference between their terminal branch lengths, both in the cox1 gene tree (based on 3639 sequences) and in the 16S gene tree (based on 1839 sequences), as well as in the Maximum Likelihood mitogenomic tree based on concatenated sequence of 12 PCGs. Our findings suggest that the original specimen used for mitogenome sequencing was misidentified and represents an individual of M. gigas. This study reinforces the notion that morphological shell analysis alone is not sufficient for oyster identification, not even at high taxonomic ranks such as subfamilies. While it is well established that morphological identification of oysters should be validated by molecular data, this study emphasizes that also molecular data should be taxonomically validated by means of DNA barcoding and phylogenetic analyses. The implications of the publication of taxonomically misidentified sequences and mitogenomes are discussed

scholarly journals The first complete mitochondrial genome of Cheyletus malaccensis (Acari: Cheyletidae): gene rearrangement

2020 ◽  
Vol 25 (8) ◽  
pp. 1433-1443
Author(s):  
Yang-ming Lan ◽  
Shi-qian Feng ◽  
Li-yuan Xia ◽  
Zhi-hong Li ◽  
Yang Cao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mite Species ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Trna Genes ◽  
Protein Coding ◽  
Food Commodities ◽  
Cheyletus Malaccensis

The predatory mite Cheyletus malaccensis (Acari: Cheyletidae), commonly occurring in stores of various food commodities, is an important natural enemy of stored product pests. Disentangling the mt genome sequence of C. malaccensis at molecular level can decrease uncertainties during morphological identification and is useful in reconstructing the phylogeny of Acariformes group. In this study, the complete mitogenome of C. malaccensis was sequenced by the next-generation sequencing. After assembly and annotation, we found the circular 14,732 bp mitogenome of C. malaccensis, containing 13 protein coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Compared with the ancestral mitogenome organization of arthropods, most of tRNA were truncated without D-arm or/and TψC-arm. Rearrangement was found in 12 mitogenome genes. Phylogenetic analyses based on the mitogenome data from other 29 mite species were inferred by Bayesian and maximum likelihood methods, which strongly supported the closer relationship between C. malaccensis and Tetranychidae than other mites. The obtained results represent the first complete mitochondrial genome record for Cheyletidae group. It may help improve molecular phylogenetic relationship and population genetics of the Cheyletidae.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

scholarly journals Phylogenetic placement of enigmatic Astianthus (Bignoniaceae) based on molecular data, wood and bark anatomy

2021 ◽  
Vol 99 (2) ◽  
pp. 398-412
Author(s):  
Marcelo R. Pace ◽  
Brenda Hernández-Hernández ◽  
Esteban M. Martínez Salas ◽  
Lúcia G. Lohmann ◽  
N. Ivalu Cacho
Keyword(s):  
Pacific Coast ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Placement ◽  
The Pacific ◽  
Molecular Phylogenetic ◽  
Phloem Fibers ◽  
Plastid Markers ◽  
Bark Anatomy

Background: Astianthus is a monospecific arborescent genus of Bignoniaceae that occur in the Pacific Coast of central Mexico and northern Central America, where it grows in dense populations along riversides. Its phylogenetic placement has remained controversial since Astianthus has unusual morphological characters such as a four-loculed ovary, and simple, pulvinate, verticillate leaves. Methods: Here we used three plastid markers ndhF, rbcL, and trnL-F, wood, and bark anatomical data to investigate the phylogenetic placement of Astianthus and assign it to one of Bignoniaceae’s main clades. Results: Our molecular phylogenetic analyses indicated that Astianthus belongs in tribe Tecomeae s.s., where other charismatic Neotropical Bignoniaceae genera such as Campsis and Tecoma are currently placed. Wood and bark anatomy support this placement, as Astianthus reunites a unique combination of features only known from members of Tecomeae s.s., such as storied axial parenchyma, the co-occurrence of homo- and heterocellular rays, septate fibers, and scattered phloem fibers in the bark. Conclusions: The placement of Astianthus within Tecomeae s.s. provides further support to previous proposals for the Neotropical origin of this Pantropical tribe.

A curious nematode, Diploscapteroides persicus n. sp. (Nematoda: Rhabditida: Rhabditomorpha), from Iran with a note on the status of the male genital papillae

Nematology ◽  
2015 ◽  
Vol 17 (9) ◽  
pp. 1045-1056 ◽  
Author(s):  
Razieh Ghaemi ◽  
Ebrahim Pourjam ◽  
Sergio Álvarez-Ortega ◽  
Majid Pedram ◽  
Mohammad Reza Atighi
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Tail Length ◽  
Molecular Data ◽  
Rrna Genes ◽  
Valid Species ◽  
Female Tail ◽  
The Status ◽  
Species Being ◽  
Male Genital

Diploscapteroides persicus n. sp. is described and illustrated based on morphological, morphometric and molecular data. The new species is mainly characterised by female body length of 469-673 μm, female tail length of 51-99 μm, shape of gubernaculum and spicules and arrangement of male genital papillae. Also, the arrangement of male genital papillae of the new species shows the presence of precloacal papillae, a feature that has not been previously described for the genus. The new species is comparable with all valid species of the genus, namely D. boettgeri, D. brevicauda, D. chitinolabiatus, D. coroniger, D. dacchensis and D. flexuosus, from which the morphological comparisons of the new species with aforementioned species are discussed. Phylogenetic analyses using partial sequences of SSU and LSU rRNA genes were performed for the new species, being the first representative of the genus to be phylogenetically studied using both Bayesian inference (BI) and maximum likelihood (ML) methods, and revealed that D. persicus n. sp. formed a clade with a species of Cephaloboides.

scholarly journals Characterization and Analysis of the Mitochondrial Genome of Common Bean (Phaseolus vulgaris) by Comparative Genomic Approaches

2020 ◽  
Vol 21 (11) ◽  
pp. 3778
Author(s):  
Changwei Bi ◽  
Na Lu ◽  
Yiqing Xu ◽  
Chunpeng He ◽  
Zuhong Lu
Keyword(s):  
Phaseolus Vulgaris ◽  
Mitochondrial Genome ◽  
Common Bean ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Leguminous Plants ◽  
The Common

The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmFC gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmFC, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.

scholarly journals Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 461 ◽  
Author(s):  
Carina Carneiro de Melo Moura ◽  
Fabian Brambach ◽  
Kevin Jair Hernandez Bado ◽  
Konstantin V. Krutovsky ◽  
Holger Kreft ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Evolutionary Rate ◽  
Molecular Data ◽  
Morphological Identification ◽  
Chloroplast Gene ◽  
Taxonomic Level ◽  
Morphological Taxonomy ◽  
Traditional Taxonomy ◽  
Lowland Forests ◽  
Interspecific Genetic Distance

DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.

Characterization of the mitochondrial genome of Diphyllobothrium latum (Cestoda: Pseudophyllidea) – implications for the phylogeny of eucestodes

Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 749-759 ◽  
Author(s):  
J.-K. PARK ◽  
K.-H. KIM ◽  
S. KANG ◽  
H. K. JEON ◽  
J.-H. KIM ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Amino Acid Sequences ◽  
Hymenolepis Diminuta ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Diphyllobothrium Latum

SUMMARYThe complete nucleotide sequence of the mitochondrial genome was determined for the fish tapeworm Diphyllobothrium latum. This genome is 13 608 bp in length and encodes 12 protein-coding genes (but lacks the atp8), 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes, corresponding to the gene complement found thus far in other flatworm mitochondrial (mt) DNAs. The gene arrangement of this pseudophyllidean cestode is the same as the 6 cyclophyllidean cestodes characterized to date, with only minor variation in structure among these other genomes; the relative position of trnS2 and trnL1 is switched in Hymenolepis diminuta. Phylogenetic analyses of the concatenated amino acid sequences for 12 protein-coding genes of all complete cestode mtDNAs confirmed taxonomic and previous phylogenetic assessments, with D. latum being a sister taxon to the cyclophyllideans. High nodal support and phylogenetic congruence between different methods suggest that mt genomes may be of utility in resolving ordinal relationships within the cestodes. All species of Diphyllobothrium infect fish-eating vertebrates, and D. latum commonly infects humans through the ingestion of raw, poorly cooked or pickled fish. The complete mitochondrial genome provides a wealth of genetic markers which could be useful for identifying different life-cycle stages and for investigating their population genetics, ecology and epidemiology.

scholarly journals Amplification and Analysis of Cytocrome Oxidase I of Polypedates leucomystax from Bogor Agricultural University Area

2017 ◽  
Vol 3 (1) ◽  
pp. 13-19
Author(s):  
Perkasa Arian ◽  
I Made Artika ◽  
Syamsul Falah
Keyword(s):  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Genetic Identification ◽  
Coi Gene ◽  
Morphological Identification ◽  
Amphibian Species ◽  
Bufo Melanostictus ◽  
Polypedates Leucomystax

DNA barcoding has become a useful tool for identifying and confirming of species within a known taxonomic framework. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I (COI). This study was aimed to use DNA barcoding technique to identify and confirm species of Polypedates leucomystax and to analyze their phylogenetic relationship. Samples of Polypedates leucomystax were collected from Campus Area of Bogor Agricultural University. The cytochrome oxidase I gene of 600-700 nucleotides were amplified and observed in agarose gel electrophoresis. Forward sequence (604 base pairs) of COI gene was used for phylogenetic analyses. BLAST analysis against BOLD System database showed 95.75% identity with sequences of Polypedates leucomystax. The pairwise genetic distances of Polypedates leucomystax with Rhacophorus schlegelii, Limnonectes fujianensis, Fejervarya cancrivora, and Bufo melanostictus were 0.274, 0.352, 0.339, 0.339, 0.393, respectively. These results illustrated that the genetic identification is congruence with the morphological identification. Phylogenetic tree analysis showed that the samples were in one clade with other tree frogs. The DNA barcoding technique based on the sequence of COI gene can therefore be used to identify and confirm species of Polypedates leucomystax.

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