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PloS One 2021The present study aims to apply a DNA barcoding tool through amplifying two mitochondrial candidate genes i.e., COI and 16S rRNA for accurate identification of fish,...
The present study aims to apply a DNA barcoding tool through amplifying two mitochondrial candidate genes i.e., COI and 16S rRNA for accurate identification of fish, aquatic molluscs and crustaceans of Sundarbans mangrove wetland, to build a reference library of fish and shellfishes of this unique ecosystems. A total of 185 mitochondrial COI barcode sequences and 59 partial sequences of the 16S rRNA gene were obtained from 120 genera, 65 families and 21 orders of fish, crustaceans and molluscs. The collected samples were first identified by examining morphometric characteristics and then assessed by DNA barcoding. The COI and 16S rRNA sequences of fishes and crustaceans were clearly discriminated among genera in their phylogenies. The average Kimura two-parameter (K2P) distances of COI barcode sequences within species, genera, and families of fishes are 1.57±0.06%, 15.16±0.23%, and 17.79±0.02%, respectively, and for 16S rRNA sequences, these values are 1.74±.8%, 0.97±.8%, and 4.29±1.3%, respectively. The minimum and maximum K2P distance based divergences in COI sequences of fishes are 0.19% and 36.27%, respectively. In crustaceans, the K2P distances within genera, families, and orders are 1.4±0.03%, 17.73±0.15%, and 22.81±0.02%, respectively and the minimum and maximum divergences are 0.2% and 33.93%, respectively. Additionally, the present study resolves the misidentification of the mud crab species of the Sundarbans as Scylla olivacea which was previously stated as Scylla serrata. In case of molluscs, values of interspecific divergence ranges from 17.43% to 66.3% in the barcoded species. The present study describes the development of a molecular and morphometric cross-referenced inventory of fish and shellfish of the Sundarbans. This inventory will be useful in future biodiversity studies and in forming future conservation plan.
Topics: Animals; Avicennia; Base Sequence; DNA Barcoding, Taxonomic; Ecosystem; Electron Transport Complex IV; Fishes; Genetic Variation; Geography; Mollusca; Phylogeny; RNA, Ribosomal, 16S; Seawater; Shellfish
PubMed: 34339426
DOI: 10.1371/journal.pone.0255110 -
PeerJ 2023Unionid mussels are among the most imperiled group of organisms in North America, and is a freshwater species with a relatively wide latitudinal distribution that...
Unionid mussels are among the most imperiled group of organisms in North America, and is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus (formerly ) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing , , , and with (currently ). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise Φ measures based on ND1 data suggested there may be up to five major geographic groups present within . Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels the system.
Topics: Humans; Animals; Phylogeny; Mitochondria; Bivalvia; Unionidae; Texas; Ontario
PubMed: 37810794
DOI: 10.7717/peerj.15974 -
Scientific Reports Jul 2022Organisms with limited dispersal capabilities should show phenotypic plasticity in situ to keep pace with environmental changes. Therefore, to study the influence of...
Organisms with limited dispersal capabilities should show phenotypic plasticity in situ to keep pace with environmental changes. Therefore, to study the influence of environmental variation on the phenotypic diversity, we chose land snails, Trochulus hispidus and T. sericeus, characterized by high population variability. We performed long-term field studies as well as laboratory and common garden experiments, which revealed that temporal environmental changes generate visible variation in shell size and shape of these snails. Many shell measurements of T. hispidus varied significantly with temperature and humidity in individual years. According to this, the first generation of T. hispidus, bred in controlled laboratory conditions, became significantly different in higher spire and narrower umbilicus from its wild parents. Interestingly, offspring produced by this generation and transplanted to wild conditions returned to the 'wild' flat and wide-umbilicated shell shape. Moreover, initially different species T. hispidus and T. sericeus transferred into common environment conditions revealed rapid and convergent shell modifications within one generation. Such morphological flexibility and high genetic variation can be evolutionarily favored, when the environment is heterogeneous in time. The impact of climate change on the shell morphometry can lead to incorrect taxonomic classification or delimitation of artificial taxa in land snails. These findings have also important implications in the context of changing climate and environment.
Topics: Adaptation, Physiological; Animal Shells; Animals; Humidity; Plant Breeding; Snails
PubMed: 35853920
DOI: 10.1038/s41598-022-16638-w -
Environmental Monitoring and Assessment Aug 2023The present work is aimed at investigating the effects of seasonal changes and habitat conditions on reproductive state and gonadal development of two macrobenthic...
Influences of habitat and seasonal changes on gonadal maturation of Echinometra mathaei (Echinodermata: Echinoidea) and Tridacna squamosa (Mollusca: Bivalvia) in the Red Sea, Egypt.
The present work is aimed at investigating the effects of seasonal changes and habitat conditions on reproductive state and gonadal development of two macrobenthic fauna. Echinometra mathaei and Tridacna squamosa were collected seasonally (summer and winter) in July 2019 and January 2020 from three sites along the Red Sea coast, Egypt: Hamraween, Sedy Malek, and Porto Ghalb. Sexual differences and gonadal maturation in the two species were determined by performing biopsies of their gonads followed by morphologic analyses. Hematoxylin and eosin-stained gonadal sections were examined and analyzed. In E. mathaei, reproductive behavior was more active in the summer than in the winter; in T. squamosa, reproductive behavior was active almost all the year, especially during the winter. The reproductive activity and gonadal maturation of both species were affected by environmental factors. The results indicated that temperature is a vital factor affecting the reproductive activity of both species. This study concluded that temperature fluctuations may pose significant challenges to coastal marine ecosystems.
Topics: Animals; Echinodermata; Ecosystem; Egypt; Indian Ocean; Seasons; Environmental Monitoring; Bivalvia; Sea Urchins; Gonads
PubMed: 37615753
DOI: 10.1007/s10661-023-11713-9 -
BMC Genomics Jul 2022The immune repertoires of mollusks beyond commercially important organisms such as the pacific oyster Crassostrea gigas or vectors for human pathogens like the...
The immune repertoires of mollusks beyond commercially important organisms such as the pacific oyster Crassostrea gigas or vectors for human pathogens like the bloodfluke planorb Biomphalaria glabrata are understudied. Despite being an important model for neural aging and the role of inflammation in neuropathic pain, the immune repertoire of Aplysia californica is poorly understood. Recent discovery of a neurotropic nidovirus in Aplysia has highlighted the need for a better understanding of the Aplysia immunome. To address this gap in the literature, the Aplysia reference genome was mined using InterProScan and OrthoFinder for putative immune genes. The Aplysia genome encodes orthologs of all critical components of the classical Toll-like receptor (TLR) signaling pathway. The presence of many more TLRs and TLR associated adapters than known from vertebrates suggest yet uncharacterized, novel TLR associated signaling pathways. Aplysia also retains many nucleotide receptors and antiviral effectors known to play a key role in viral defense in vertebrates. However, the absence of key antiviral signaling adapters MAVS and STING in the Aplysia genome suggests divergence from vertebrates and bivalves in these pathways. The resulting immune gene set of this in silico study provides a basis for interpretation of future immune studies in this important model organism.
Topics: Animals; Aplysia; Biomphalaria; Crassostrea; Genome; Humans; Immunity, Innate; Signal Transduction
PubMed: 35906538
DOI: 10.1186/s12864-022-08780-6 -
Communications Biology Jul 2022Some marine organisms can resist to aqueous tidal environments and adhere tightly on wet surface. This behavior has raised increasing attention for potential...
Some marine organisms can resist to aqueous tidal environments and adhere tightly on wet surface. This behavior has raised increasing attention for potential applications in medicine, biomaterials, and tissue engineering. In mussels, adhesive forces to the rock are the resultant of proteinic fibrous formations called byssus. We present the solution structure of Pvfp-5β, one of the three byssal plaque proteins secreted by the Asian green mussel Perna viridis, and the component responsible for initiating interactions with the substrate. We demonstrate that Pvfp-5β has a stably folded structure in agreement with the presence in the sequence of two EGF motifs. The structure is highly rigid except for a few residues affected by slow local motions in the µs-ms time scale, and differs from the model calculated by artificial intelligence methods for the relative orientation of the EGF modules, which is something where computational methods still underperform. We also show that Pvfp-5β is able to coacervate even with no DOPA modification, giving thus insights both for understanding the adhesion mechanism of adhesive mussel proteins, and developing of biomaterials.
Topics: Adhesives; Animals; Artificial Intelligence; Biocompatible Materials; Epidermal Growth Factor; Perna; Tissue Engineering
PubMed: 35879391
DOI: 10.1038/s42003-022-03699-w -
Developmental Dynamics : An Official... Dec 2021The dwarf cuttlefish Sepia bandensis, a camouflaging cephalopod from the Indo-Pacific, is a promising new model organism for neuroscience, developmental biology, and...
BACKGROUND
The dwarf cuttlefish Sepia bandensis, a camouflaging cephalopod from the Indo-Pacific, is a promising new model organism for neuroscience, developmental biology, and evolutionary studies. Cuttlefish dynamically camouflage to their surroundings by altering the color, pattern, and texture of their skin. The skin's "pixels" (chromatophores) are controlled by motor neurons projecting from the brain. Thus, camouflage is a visible representation of neural activity. In addition to camouflage, the dwarf cuttlefish uses dynamic skin patterns for social communication. Despite more than 500 million years of evolutionary separation, cuttlefish and vertebrates converged to form limbs, camera-type eyes and a closed circulatory system. Moreover, cuttlefish have a striking ability to regenerate their limbs. Interrogation of these unique biological features will benefit from the development of a new set of tools. Dwarf cuttlefish reach sexual maturity in 4 months, they lay dozens of eggs over their 9-month lifespan, and the embryos develop to hatching in 1 month.
RESULTS
Here, we describe methods to culture dwarf cuttlefish embryos in vitro and define 25 stages of cuttlefish development.
CONCLUSION
This staging series serves as a foundation for future technologies that can be used to address a myriad of developmental, neurobiological, and evolutionary questions.
Topics: Adaptation, Physiological; Animals; Behavior, Animal; Biological Mimicry; Cells, Cultured; Decapodiformes; Embryo Culture Techniques; Embryo, Nonmammalian; Embryonic Development; Life Cycle Stages; Phylogeny; Sepia
PubMed: 34028136
DOI: 10.1002/dvdy.375 -
ELife Jan 2023Cephalopods are set apart from other mollusks by their advanced behavioral abilities and the complexity of their nervous systems. Because of the great evolutionary...
Cephalopods are set apart from other mollusks by their advanced behavioral abilities and the complexity of their nervous systems. Because of the great evolutionary distance that separates vertebrates from cephalopods, it is evident that higher cognitive features have evolved separately in these clades despite the similarities that they share. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Despite significant progress in genome and transcriptome sequencing, the molecular identities of cell types in cephalopods remain largely unknown. We here combine single-cell transcriptomics with in situ gene expression analysis to uncover cell type diversity in the European squid . We describe cell types that are conserved with other phyla such as neurons, muscles, or connective tissues but also cephalopod-specific cells, such as chromatophores or sucker cells. Moreover, we investigate major components of the squid nervous system including progenitor and developing cells, differentiated cells of the brain and optic lobes, as well as sensory systems of the head. Our study provides a molecular assessment for conserved and novel cell types in cephalopods and a framework for mapping the nervous system of .
Topics: Animals; Decapodiformes; Loligo; Mollusca; Cephalopoda; Chromatophores
PubMed: 36594460
DOI: 10.7554/eLife.80670 -
Brazilian Journal of Biology = Revista... 2021Physids belong to Class Gastropoda; belong to Phylum Mollusca and being bioindicators, intermediate hosts of parasites and pests hold a key position in the ecosystem....
Physids belong to Class Gastropoda; belong to Phylum Mollusca and being bioindicators, intermediate hosts of parasites and pests hold a key position in the ecosystem. There are three species of Genus Physa i.e. P. fontinalis, Physa acuta and P. gyrina water bodies of Central Punjab and were characterized on the basis of molecular markers High level of genetic diversity was revealed by polymorphic RAPD, however SSR markers were not amplified. The multivariate analysis revealed polymorphism ranging from 9.09 percent to 50 percent among the three Physid species. Total number of 79 loci were observed for the three species under study and 24 loci were observed to be polymorphic. These RAPD fragment(s) can be developed into co dominant markers (SCAR) by cloning and can be further sequenced for the development of the Physa species specific markers to identify the introduced and native species in Pakistan.
Topics: Animals; Ecosystem; Gastropoda; Introduced Species; Pakistan; Phylogeny; Random Amplified Polymorphic DNA Technique
PubMed: 34431913
DOI: 10.1590/1519-6984.246984 -
International Journal of Biological... Mar 2024Crustaceans and mollusks are widely consumed around the world due to their delicacy and nutritious value. During the processing, only 30-40 % of these shellfish are... (Review)
Review
Crustaceans and mollusks are widely consumed around the world due to their delicacy and nutritious value. During the processing, only 30-40 % of these shellfish are considered edible, while 70-60 % of portions are thrown away as waste or byproduct. These byproducts harbor valuable constituents, notably chitin. This chitin can be extracted from shellfish byproducts through chemical, microbial, enzymatic, and green technologies. However, chitin is insoluble in water and most of the organic solvents, hampering its wide application. Hence, chitin is de-acetylated into chitosan, which possesses various functional applications. Recently, nanotechnology has proven to improve the surface area and numerous functional properties of metals and molecules. Further, the nanotechnology principle can be extended to nanochitosan formation. Therefore, this review article centers on crustaceans and mollusks byproduct utilization for chitosan, its nano-formation, and their food industry applications. The extensive discussion has been focused on nanochitosan formation, characterization, and active site modification. Lastly, nanochitosan applications in various food industries, including biodegradable food packaging, fat replacer, bioactive compound carrier, and antimicrobial agent have been reported.
Topics: Animals; Chitosan; Chitin; Crustacea; Mollusca; Food Industry
PubMed: 38331073
DOI: 10.1016/j.ijbiomac.2024.130008