Extreme concentration of marine biodiversity and exploitation of marine resources in the Coral Triangle pose challenges to biogeographers and resource managers. Comparative phylogeography provides a powerful tool to test biogeographic hypotheses evoked to explain species richness in the Coral Triangle. It can also be used to delineate management units for marine resources. After about a decade of phylogeographical studies, patterns for the Coral Triangle are emerging. Broad connectivity in some species support the notion that larvae have maintained gene flow among distant populations for long periods. Other phylogeographic patterns suggest vicariant events resulting from Pleistocene sea level fluctuations, which have, at least occasionally, resulted in speciation. Divergence dates ranging back to the Miocene suggest that changing land configurations may have precipitated an explosion of species diversification. A synthesis of the marine phylogeographic studies reveals repeated patterns that corroborate hypothesized biogeographic processes and suggest improved management schemes for marine resources.
Photobacterium damselae subsp. piscicida is a bacterial fish pathogen that causes a disease known as pasteurellosis. Two transferable multiple-drug resistance (R) plasmids, pP99-018 (carrying resistance to kanamycin, chloramphenicol, tetracycline, and sulfonamide) and pP91278 (carrying resistance to tetracycline, trimethoprim, and sulfonamide), isolated from P. damselae subsp. piscicida strains from Japan (P99-018) and the United States (P91278), respectively, were completely sequenced and analyzed, along with the multipledrug resistance regions of three other R plasmids also from P. damselae subsp. piscicida strains from Japan. The sequence structures of pP99-018 (150,057 bp) and pP91278 (131,520 bp) were highly conserved, with differences due to variation in the drug resistance and conjugative transfer regions. These plasmids, shown to be closely related to the IncJ element R391 (a conjugative, self-transmitting, integrating element, or constin), were divided into the conjugative transfer, replication, partition, and multiple-drug resistance regions. Each of the five multiple-drug resistance regions sequenced exhibited unique drug resistance marker composition and arrangement.Antimicrobial drugs have historically been used to control bacterial and mycotic infections in fish farming (16). This practice has helped the industry improve production but at the same time allowed for the emergence of drug-resistant pathogens, which is known to be made possible by transferable R plasmids present in fish-pathogenic gram-positive and gramnegative bacteria (17). The R plasmids of Photobacterium damselae subsp. piscicida, a gram-negative pathogen, carry several drug resistance genes, also called drug resistance markers, that include a class A -lactamase gene for ampicillin resistance (Ap r ), catI and catII for chloramphenicol resistance (Cp r ), ppflo for florfenicol resistance (Ff r ), aphA7 for kanamycin resistance (Km r ), sul2 for sulfonamide resistance (Sa r ), and tet(A) for tetracycline resistance (Tc r ). Some of these drugs (ampicillin, florfenicol, sulfonamide, and tetracycline) are used in aquaculture in Japan, while others (chloramphenicol and kanamycin) are not (7).P. damselae subsp. piscicida is the causative agent of pasteurellosis, a disease responsible for serious economic losses in fish farms across the world (17). However, even though the drug resistance patterns and genes contained in R plasmids from P. damselae subsp. piscicida strains in Japan, the United States, and Europe have been identified, the complete sequences of these R plasmids from P. damselae subsp. piscicida and the molecular mechanism responsible for the formation of resistance determinants in this species have not been well characterized.In this study, we determined and analyzed the complete nucleotide sequences of R plasmids pP99-018 (Japan) and pP91278 (United States) from P. damselae subsp. piscicida, as well as the multiple-drug resistance regions of three other R plasmids (pSP98048, pSP98026, and pP9014) also collected in Japan. ...
The emerging field of next-generation sequencing (NGs) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. This is particularly true in southeast Asia. The first Pan-Pacific Advanced studies Institute (PacAsI) entitled "Genomic Applications to Marine science and resource Management in southeast Asia" was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGs in helping address the aforementioned challenges. Here we synthesize discussions held during the PacAsI to provide perspectives and guidance to help scientists new to NGs choose among the variety of available advanced genomic methodologies specifically for marine science questions.
Granulocyte colony-stimulating factor (CSF3) is a glycoprotein cytokine, which influences the hematopoiesis of the phagocytic neutrophils and its precursors and was used extensively in cancer therapy and for the treatment of neutropenia in mammals. However, CSF3 is yet to be identified in nonmammalian species mainly because of its rapid mutation. Here, we report the first CSF3 genes from three teleost fishes: Japanese flounder (Paralichthys olivaceus), fugu (Takifugu rubripes), and green-spotted pufferfish (Tetraodon nigroviridis) and present evidence that the chicken (Gallus gallus) myelomonocytic growth factor is in fact the chicken CSF3 orthologue. We support this by showing significant conservation of the CSF3 genes' structure, domains, regulatory motifs, and synteny across species and by phylogenetic analysis. CSF3 orthologues are indeed evolving rapidly and appears to be undergoing purifying selection in mammals but positive selection in fish and chicken. Furthermore, the paralogous fugu and pufferfish CSF3-1s and CSF3-2s are shown to be the ancestral and duplicate genes, respectively. Finally, we demonstrate that the Japanese flounder CSF3 gene is at least involved in immunity based on its basal expression in immune-related tissues and its upregulation in kidney and peripheral blood leukocytes after in vitro stimulation with lipopolysaccharide and a combination of concanavalin A/phorbol myristate acetate.
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