Australia's marine fishes DNA barcode reference library for integrated taxonomy, metabarcoding & eDNA research.

Over 15 000 species of fishes are found globally in the marine environment and DNA barcodes are used extensively to describe, catalogue, understand and manage this diversity. The dataset outlined here represents a DNA barcode reference library of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) from 9767 voucher specimens (representing at least 2220 species and 288 families) of marine fishes. This publicly available dataset in the Barcode of Life Data System (BOLD) represents 17 years (2005-2022) of barcoding of marine fishes identified from Australian territorial waters.

A two-step DNA barcoding approach for delimiting moth species: moths of Dongling Mountain (Beijing, China) as a case study.

DNA barcoding, based on a fragment of cytochrome c oxidase I (COI) mtDNA, is as an effective molecular tool for identification, discovery, and biodiversity assessment for most animals. However, multiple gene markers coupled with more sophisticated analytical approaches may be necessary to clarify species boundaries in cases of cryptic diversity or morphological plasticity. Using 339 moths collected from mountains surrounding Beijing, China, we tested a pipeline consisting of two steps: (1) rapid morphospecies sorting and screening of the investigated fauna with standard COI barcoding approaches; (2) additional analyses with multiple molecular markers for those specimens whose morphospecies and COI barcode grouping were incongruent.

FuzzyID2: A software package for large data set species identification via barcoding and metabarcoding using hidden Markov models and fuzzy set methods.

Species identification through DNA barcoding or metabarcoding has become a key approach for biodiversity evaluation and ecological studies. However, the rapid accumulation of barcoding data has created some difficulties: for instance, global enquiries to a large reference library can take a very long time. We here devise a two-step searching strategy to speed identification procedures of such queries.

DNA barcoding reveals species composition of sharks and rays in the Indian commercial fishery.

DNA barcoding was successfully used for the accurate identification of chondrichthyans in the Indian commercial marine fishery. About 528 specimens of 111 chondrichthyan species and 34 families, collected from the Indian EEZ, were barcoded for a 655 bp region of the mitochondrial gene cytochrome c oxidase subunit 1 (COI). Generally, five specimens per species were barcoded, but numbers ranged from 2 to 13.

Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes.

Background: Pine moths (Lepidoptera; Bombycoidea; Lasiocampidae: Dendrolimus spp.) are among the most serious insect pests of forests, especially in southern China. Although COI barcodes (a standardized portion of the mitochondrial cytochrome c oxidase subunit I gene) can distinguish some members of this genus, the evolutionary relationships of the three morphospecies Dendrolimus punctatus, D.

Identifying species of moths (Lepidoptera) from Baihua Mountain, Beijing, China, using DNA barcodes.

DNA barcoding has become a promising means for the identification of organisms of all life-history stages. Currently, distance-based and tree-based methods are most widely used to define species boundaries and uncover cryptic species. However, there is no universal threshold of genetic distance values that can be used to distinguish taxonomic groups.

A role for site-specific phosphorylation of mouse progesterone receptor at serine 191 in vivo.

Progesterone receptors (PRs) are phosphorylated on multiple sites, and a variety of roles for phosphorylation have been suggested by cell-based studies. Previous studies using PR-null mice have shown that PR plays an important role in female fertility, regulation of uterine growth, the uterine decidualization response, and proliferation as well as ductal side-branching and alveologenesis in the mammary gland. To study the role of PR phosphorylation in vivo, a mouse was engineered with homozygous replacement of PR with a PR serine-to-alanine mutation at amino acid 191.

Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae) on the Qinghai-Tibetan Plateau.

With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity.

Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding.

Identification of taxonomical units underpins most biological endeavours ranging from accurate biodiversity estimates to the effective management of sustainably harvested, protected or endangered species. Successful species identification is now frequently based on a combination of approaches including morphometrics and DNA markers. Sequencing of the mitochondrial COI gene is an established methodology with an international campaign directed at barcoding all fishes.

FISH-BOL, a case study for DNA barcodes.

The FISH-BOL campaign was initiated in 2005, and currently has barcoded for the cytochrome c oxidase subunit I (COI) gene about 8,000 of the 31,000 fish species currently recognised. This includes the great majority of the world's most important commercial species. Results thus far show that about 98% and 93% of marine and freshwater species, respectively, are barcode distinguishable.

A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic.

Aged PROP1 deficient dwarf mice maintain ACTH production.

Humans with PROP1 mutations have multiple pituitary hormone deficiencies (MPHD) that typically advance from growth insufficiency diagnosed in infancy to include more severe growth hormone (GH) deficiency and progressive reduction in other anterior pituitary hormones, eventually including adrenocorticotropic hormone (ACTH) deficiency and hypocortisolism. Congenital deficiencies of GH, prolactin, and thyroid stimulating hormone have been reported in the Prop1(null) (Prop1(-/-)) and the Ames dwarf (Prop1(df/df)) mouse models, but corticotroph and pituitary adrenal axis function have not been thoroughly investigated. Here we report that the C57BL6 background sensitizes mutants to a wasting phenotype that causes approximately one third to die precipitously between weaning and adulthood, while remaining homozygotes live with no signs of illness.

DNA barcoding of morid cods reveals deep divergence in the antitropical Halargyreus johnsoni but little distinction between Antimora rostrata and Antimora microlepis.

Background And Aims: DNA barcoding strongly suggests that specimens of the slender codling (Halargyreus johnsonii) from New Zealand and Tasmania belong to a different species to H. johnsonii reported from other areas.

Results: Sequence divergence between the two groups averaged 3.

Tetracha hope 1838 of the Turks and Caicos Islands (coleoptera, carabidae, cicindelinae).

A new species, Tetracha (Neotetracha) naviauxi, and a new subspecies, Tetracha (Tetracha) sobrina caicosensis, are described from the Turks and Caicos Islands. The key to Tetracha species in Naviaux (2007) is adapted to accommodate Tetracha naviauxi. Tetracha sobrina caicosensis is compared to other Caribbean subspecies of Tetracha sobrina.

Synchronous saccular and fusiform extracranial internal carotid artery aneurysms with ipsilateral cerebral embolism.

We report the case of a 77-year-old woman with synchronous fusiform and saccular extracranial atherosclerotic internal carotid artery aneurysm treated by excisional surgery and external to internal carotid artery transposition.

Steroid receptor phosphorylation: Assigning function to site-specific phosphorylation.

Steroid receptors (SRs) are hormone-activated transcription factors important for a wide variety of cellular functions. Post-translational modifications of SRs, including phosphorylation, ubiquitination, acetylation, and sumoylation regulate their expression and function. The remarkable number of phosphorylation sites in these receptors and the wide variety of kinases shown to modulate phosphorylation influence the integration between cell-signaling pathways and SR action.

Importance of extranuclear estrogen receptor-alpha and membrane G protein-coupled estrogen receptor in pancreatic islet survival.

Objective: We showed that 17beta-estradiol (E(2)) favors pancreatic beta-cell survival via the estrogen receptor-alpha (ERalpha) in mice. E(2) activates nuclear estrogen receptors via an estrogen response element (ERE). E(2) also activates nongenomic signals via an extranuclear form of ERalpha and the G protein-coupled estrogen receptor (GPER).

DNA barcode divergence among species and genera of birds and fishes.

COI DNA barcoding is increasingly recognized as a significant new tool for the recognition and identification of animal species. Here, publicly available barcode data are compiled and analysed for birds (657 species) and fishes (1088 species). The proportion of species that cannot be barcode-distinguished by this marker is approximately 6.

DNA barcoding reveals overlooked marine fishes.

With more than 15 000 described marine species, fishes are a conspicuous, diverse and increasingly threatened component of marine life. It is generally accepted that most large-bodied fishes have been described, but this conclusion presumes that current taxonomic systems are robust. DNA barcoding, the analysis of a standardized region of the cytochrome c oxidase 1 gene (COI), was used to examine patterns of sequence divergence between populations of 35 fish species from opposite sides of the Indian Ocean, chosen to represent differing lifestyles from inshore to offshore.

DNA barcoding discriminates echinoderm species.

DNA barcode sequences (a 657-bp segment of the mtDNA cytochrome oxidase I gene, COI) were collected from 191 species (503 specimens) of Echinodermata. All five classes were represented: Ophiuroidea, Asteroidea, Echinoidea, Holothuroidea and Crinoidea. About 30% of sequences were collected specifically for this study, the remainder came from GenBank.

Rapid detection of oilfish and escolar in fish steaks: A tool to prevent keriorrhea episodes.

The outbreak of keriorrhea caused by the wax ester-rich oilfish and escolar has become a frequent and worldwide concern. To help prevent such episodes, rapid detection of these fishes in the supply chain of the seafood industry and by food and health inspection agencies is essential. Through a combination of DNA, GC-MS and TLC analyses with reference to authentic samples, fish steaks of oilfish and escolar mislabeled as other species could be accurately identified.

Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene.

Mutations in PROP1 are a common genetic cause of multiple pituitary hormone deficiency (MPHD). We used a comparative genomics approach to predict the transcriptional regulatory domains of Prop1 and tested them in cell culture and mice. A BAC transgene containing Prop1 completely rescues the Prop1 mutant phenotype, demonstrating that the regulatory elements necessary for proper PROP1 transcription are contained within the BAC.

Cell proliferation and vascularization in mouse models of pituitary hormone deficiency.

Mutations in the transcription factors PIT1 (pituitary transcription factor 1) and PROP1 (prophet of Pit1) lead to pituitary hormone deficiency and hypopituitarism in mice and humans. To determine the basis for this, we performed histological analysis of Pit1- and Prop1-deficient dwarf mouse pituitaries throughout fetal and postnatal development. Pit1-deficient mice first exhibit pituitary hypoplasia after birth, primarily caused by reduced cell proliferation, although there is some apoptosis.