scholarly journals DNA barcoding Australia's fish species

2005 ◽  
Vol 360 (1462) ◽  
pp. 1847-1857 ◽  
Author(s):  
Robert D Ward ◽  
Tyler S Zemlak ◽  
Bronwyn H Innes ◽  
Peter R Last ◽  
Paul D.N Hebert
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Codon Position ◽  
Phylogenetic Signal ◽  
Gc Content ◽  
Morphological Evidence ◽  
Separate Species ◽  
Operational Taxonomic Units ◽  
The Family ◽  
Taxonomic Groups

Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene ( cox1 ). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus , flatheads of the family Platycephalidae, and tunas of the genus Thunnus —were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species.

DNA barcoding reflects the diversity and variety of brooding traits of fish species in the family Syngnathidae along China’s coast

2017 ◽  
Vol 185 ◽  
pp. 137-144 ◽  
Author(s):  
Yan-Hong Zhang ◽  
Geng Qin ◽  
Hui-Xian Zhang ◽  
Xin Wang ◽  
Qiang Lin
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
The Family

scholarly journals Molecular Identification of Mudskipper Fish (Periophthalmus spp.) from Baros Beach, Bantul, Yogyakarta

2021 ◽  
Vol 6 (3) ◽  
pp. 66391
Author(s):  
Katon Waskito Aji ◽  
Tuty Arisuryanti
Keyword(s):  
Genetic Distance ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Universal Primers ◽  
Molecular Approaches ◽  
Morphological Studies ◽  
The Family ◽  
Pcr Method

Mudskipper fish is amphibious fish belonging to the family Gobiidae. Coastal communities widely consume mudskipper to meet their animal protein needs. Mudskipper is primarily cryptic species that are morphologically difficult to identify and distinguish from other mudskipper fish species. Consequently, it can be confused with the naming of mudskipper fish species and can affect the conservation efforts of the fish in their habitat. One of the molecular approaches that can be used to identify the fish species quickly and accurately is DNA barcoding using the COI mitochondrial gene. However, the research on the identification of mudskipper fish in Indonesia is still very limited. Therefore, this study aimed to identify 26 mudskipper fish from Baros Beach, Bantul, Yogyakarta, using COI mitochondrial gene as a molecular marker for DNA barcoding. The method used in this study was a PCR method with universal primers, FishF2 and FishR2. The data obtained were then analyzed using GeneStudio, DNASTAR, BLAST, Identification Engine, Mesquite, MEGAX, and BEAST. The analysis was conducted to obtain similarity, genetic distance and reconstruct a phylogenetic tree. The result revealed that all 26 samples of mudskippers collected from Baros Beach were identified in one genus, namely Periophthalmus, and consisted of 3 species, namely P. kalolo (16 samples), P. argentilineatus (9 samples), and P. novemradiatus (1 sample). Furthermore, this study also discovered a suspected cryptic species in P. argentilineatus with a genetic distance of 5.46-5.96% between clade E, F compared with clade G. Further morphological studies are needed to confirm the species status of these three clades before solidly proclaim that they are cryptic species. 

scholarly journals DNA barcoding of marine fish species from Rongcheng Bay, China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5013 ◽  
Author(s):  
Lijuan Wang ◽  
Zhihao Wu ◽  
Mengxia Liu ◽  
Wei Liu ◽  
Wenxi Zhao ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Dna Barcode ◽  
Gc Content ◽  
Genetic Distances ◽  
Dna Barcodes ◽  
Reference Library ◽  
Fish Species Identification ◽  
Northern Yellow Sea ◽  
Coastal Bay

Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.

Efficacy of DNA barcoding for the identification of larval fish species in the Upper and Middle Ing River, Thailand

Gene Reports ◽  
2021 ◽  
Vol 23 ◽  
pp. 101057
Author(s):  
Dutrudi Panprommin ◽  
Kanyanat Soontornprasit ◽  
Siriluck Tuncharoen ◽  
Niti Iamchuen
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Larval Fish

scholarly journals Metabolomics and DNA-Based Authentication of Two Traditional Asian Medicinal and Aromatic Species of Salvia subg. Perovskia

Cells ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 112
Author(s):  
Monika Bielecka ◽  
Bartosz Pencakowski ◽  
Marta Stafiniak ◽  
Klemens Jakubowski ◽  
Mehdi Rahimmalek ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Performance ◽  
Carnosic Acid ◽  
Limited Information ◽  
Metabolomic Analysis ◽  
Separate Species ◽  
Flight Mass Spectrometry ◽  
Aerial Parts ◽  
Central Asian ◽  
Aromatic Species

Subgenus Perovskia of the extended genus of Salvia comprises several Central Asian medicinal and aromatic species, of which S. yangii and S. abrotanoides are the most widespread. These plants are cultivated in Europe as robust ornamentals, and several cultivars are available. However, their medicinal potential remains underutilized because of limited information about their phytochemical and genetic diversity. Thus, we combined an ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) based metabolomics with DNA barcoding approach based on trnH-psbA and ITS2 barcodes to clarify the relationships between these two taxa. Metabolomic analysis demonstrated that aerial parts are more similar than roots and none of the major compounds stand out as distinct. Sugiol in S. yangii leaves and carnosic acid quinone in S. abrotanoides were mostly responsible for their chemical differentiation, whereas in roots the distinction was supported by the presence of five norditerpenoids in S. yangii and two flavonoids and one norditerpenoid in S. abrotanoides. To verify the metabolomics-based differentiation, we performed DNA authentication that revealed S. yangii and S. abrotanoides to be very closely related but separate species. We demonstrated that DNA barcoding coupled with parallel LC-MS profiling constitutes a powerful tool in identification of taxonomically close Salvia species.

Biodiversity of the Simuliidae family

2022 ◽  
Vol 4 (1) ◽  
pp. 001-012
Author(s):  
Carlos Henrique Marchiori
Keyword(s):  
World Wide ◽  
Economic Importance ◽  
Academic Science ◽  
Scientific Journals ◽  
Black Flies ◽  
Study Objective ◽  
The Family ◽  
English Speaking ◽  
Biological Aspects ◽  
Taxonomic Groups

Simuliidae belong to the order Diptera, suborder Nematocera, Infraorder Culicomorpha, Superfamily Chironomoidea, and Family Simuliidae. They are known as “borrachudo” or “pium” in Brazil and as “black flies” in English-speaking countries. This study objective to report the characteristics of the Family Simuliidae. The research was carried out in studies related to quantitative aspects of the Family, Subfamily and Species (taxonomic groups) and conceptual aspects such as: biology, geographical distribution, species, life cycle, damage, economic importance, medicinal importance, biological aspects, and reproduction. A literature search was carried out containing articles published from 1950 to 2021. The mini-review was prepared in Goiânia, Goiás, from September to October 2021, through the Portal of Scientific Journals in Health Sciences, Pubmed, Online Scientific Library (Scielo), internet, ResearchGate, Academia.edu, Frontiers, Biological Abstract, Publons, Qeios, Dialnet, World, Wide Science, Springer, RefSeek, Microsoft Academic, Science, ERIC, Science Research.com, SEEK education, Periodicals CAPES, Google Academic, Bioline International and VADLO.

Mimaporia, a new genus of Epicopeiidae (Lepidoptera), with description of a new species from Vietnam

Zootaxa ◽  
2017 ◽  
Vol 4254 (5) ◽  
pp. 537 ◽  
Author(s):  
CHIA-HSUAN WEI ◽  
SHEN-HORN YEN
Keyword(s):  
New Species ◽  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Sister Group ◽  
Morphological Evidence ◽  
New Taxon ◽  
The Family ◽  
A New Species

The Epicopeiidae is a small geometroid family distributed in the East Palaearctic and Oriental regions. It exhibits high morphological diversity in body size and wing shape, while their wing patterns involve in various complex mimicry rings. In the present study, we attempted to describe a new genus, and a new species from Vietnam, with comments on two assumed congeneric novel species from China and India. To address its phylogenetic affinity, we reconstructed the phylogeny of the family by using sequence data of COI, EF-1α, and 28S gene regions obtained from seven genera of Epicopeiidae with Pseudobiston pinratanai as the outgroup. We also compared the morphology of the new taxon to other epicopeiid genera to affirm its taxonomic status. The results suggest that the undescribed taxon deserve a new genus, namely Mimaporia gen. n. The species from Vietnam, Mimaporia hmong sp. n., is described as new to science. Under different tree building strategies, the new genus is the sister group of either Chatamla Moore, 1881 or Parabraxas Leech, 1897. The morphological evidence, which was not included in phylogenetic analyses, however, suggests its potential affinity with Burmeia Minet, 2003. This study also provides the first, although preliminary, molecular phylogeny of the family on which the revised systematics and interpretation of character evolution can be based. 

scholarly journals GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring

2022 ◽  
Vol 12 ◽  
Author(s):  
Ilona A. Ruhl ◽  
Andriy Sheremet ◽  
Chantel C. Furgason ◽  
Susanne Krause ◽  
Robert M. Bowers ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Hot Spring ◽  
Gc Content ◽  
Gene Copy ◽  
Marker Genes ◽  
Rrna Gene ◽  
Separate Species ◽  
Distinct Subgroup

GAL08 are bacteria belonging to an uncultivated phylogenetic cluster within the phylum Acidobacteria. We detected a natural population of the GAL08 clade in sediment from a pH-neutral hot spring located in British Columbia, Canada. To shed light on the abundance and genomic potential of this clade, we collected and analyzed hot spring sediment samples over a temperature range of 24.2–79.8°C. Illumina sequencing of 16S rRNA gene amplicons and qPCR using a primer set developed specifically to detect the GAL08 16S rRNA gene revealed that absolute and relative abundances of GAL08 peaked at 65°C along three temperature gradients. Analysis of sediment collected over multiple years and locations revealed that the GAL08 group was consistently a dominant clade, comprising up to 29.2% of the microbial community based on relative read abundance and up to 4.7 × 105 16S rRNA gene copy numbers per gram of sediment based on qPCR. Using a medium quality threshold, 25 single amplified genomes (SAGs) representing these bacteria were generated from samples taken at 65 and 77°C, and seven metagenome-assembled genomes (MAGs) were reconstructed from samples collected at 45–77°C. Based on average nucleotide identity (ANI), these SAGs and MAGs represented three separate species, with an estimated average genome size of 3.17 Mb and GC content of 62.8%. Phylogenetic trees constructed from 16S rRNA gene sequences and a set of 56 concatenated phylogenetic marker genes both placed the three GAL08 bacteria as a distinct subgroup of the phylum Acidobacteria, representing a candidate order (Ca. Frugalibacteriales) within the class Blastocatellia. Metabolic reconstructions from genome data predicted a heterotrophic metabolism, with potential capability for aerobic respiration, as well as incomplete denitrification and fermentation. In laboratory cultivation efforts, GAL08 counts based on qPCR declined rapidly under atmospheric levels of oxygen but increased slightly at 1% (v/v) O2, suggesting a microaerophilic lifestyle.

scholarly journals Importance of the postcranial skeleton in eusuchian phylogeny: Reassessing the systematics of allodaposuchid crocodylians

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251900
Author(s):  
Alejandro Blanco
Keyword(s):  
Current Knowledge ◽  
Phylogenetic Signal ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Postcranial Skeleton ◽  
Skull Morphology ◽  
Taxonomic Descriptions ◽  
The Family ◽  
Phylogenetic Hypotheses ◽  
Internal Relationships

Our current knowledge on the crocodyliform evolution is strongly biased towards the skull morphology, and the postcranial skeleton is usually neglected in many taxonomic descriptions. However, it is logical to expect that it can contribute with its own phylogenetic signal. In this paper, the changes in the tree topology caused by the addition of the postcranial information are analysed for the family Allodaposuchidae, the most representative eusuchians in the latest Cretaceous of Europe. At present, different phylogenetic hypotheses have been proposed for this group without reaching a consensus. The results of this paper evidence a shift in the phylogenetic position when the postcranium is included in the dataset, pointing to a relevant phylogenetic signal in the postcranial elements. Finally, the phylogenetic relationships of allodaposuchids within Eusuchia are reassessed; and the internal relationships within Allodaposuchidae are also reconsidered after an exhaustive revision of the morphological data. New and improved diagnoses for each species are here provided.

scholarly journals The Draft Genome Sequence of The Endophytic Streptomyces Strain VITGV156

2021 ◽  
Author(s):  
Veilumuthu P ◽  
Nagarajan T ◽  
Sasikumar S ◽  
Siva R ◽  
J Godwin Christopher
Keyword(s):  
Secondary Metabolites ◽  
Draft Genome ◽  
Gc Content ◽  
Gene Clusters ◽  
Dominant Group ◽  
Protein Coding ◽  
Peptide Synthetase ◽  
The Family ◽  
Modified Peptides ◽  
Endophytic Streptomyces

Abstract Streptomyces species is one among the dominant group of bacteria in the family Actinobacteria with a rich repertoire of secondary metabolites. Secondary metabolites with antimicrobial activity and plant growth promotor have been isolated from various Streptomyces sp. Here in this investigation, we present the draft genome of a new species, Streptomyces sp. VITGV156 isolated from healthy tomato plant (Lycopersicon esculentum) which has some rare antimicrobial secondary metabolites, like coelichelin, fluostatins, vicenistatin, nystatin, sipanmycin, and informatipeptin. The genome is 8.18 Mb in size with 6,259 protein coding genes. The average GC content of the genome is 72.61 %. Preliminary analysis with antiSMASH 6.0 revealed the presence of 29 biosynthetic gene clusters for the synthesis of potential secondary metabolites. These includes 4 NRPS (non – ribosomal peptide synthetase), 7 PKS (Polyketide Synthases), 2 RiPP (Ribosomally synthesized and post-translationally modified peptides) clusters. When we look into genes associated with secondary metabolites, 406 genes are present which includes 184 genes for cofactor and vitamins, 72 genes for terpenoids and polyketides, 70 genes for xenobiotics and 80 genes for other metabolites are present. Comparative genome analysis of VITGV156 with its closest neighbor Streptomyces luteus strain TRM45540 revealed ANI 91.22% and dDDH value 44.00%.

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