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Shen Y.,Texas State University | Shen Y.,Key Laboratory of Coastal and Wetland Ecosystems | Chalopin D.,CNRS Lyon Institute of Functional Genomics | Garcia T.,Texas State University | And 10 more authors.
BMC Genomics | Year: 2016

Background: Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species. Results: We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus. Conclusions: Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development. © 2016 Shen et al. Source


Liu X.,Key Laboratory of Coastal and Wetland Ecosystems | Liu X.,National Taiwan Ocean University | Liu X.,Xiamen University | Chiang K.-P.,National Taiwan Ocean University | And 5 more authors.
Deep-Sea Research Part I: Oceanographic Research Papers | Year: 2015

In early spring, a hydrological front emerges in the central Yellow Sea, resulting from the intrusion of the high temperature and salinity Yellow Sea Warm Current (YSWC). The present study, applying phytoplankton pigments and flow cytometry measurements in March of 2007 and 2009, focuses on the biogeochemical effects of the YSWC. The nutrients fronts were coincident with the hydrological front, and a positive linear relationship between nitrate and salinity was found in the frontal area. This contrast with the common situation of coastal waters where high salinity values usually correlate with poor nutrients. We suggested nutrient concentrations of the YSWC waters might have been enhanced by mixing with the local nutrient-rich waters when it invaded the Yellow Sea from the north of the Changjiang estuary. In addition, our results indicate that the relative abundance of diatoms ranged from 26% to 90%, showing a higher value in the YSCC than in YSWC waters. Similar distributions were found between diatoms and dinoflagellates, however the cyanobacteria and prasinophytes showed an opposite distribution pattern. Good correlations were found between the pigments and flow cytometry observations on the picophytoplankton groups. Prasinophytes might be the major contributor to pico-eukaryotes in the central Yellow Sea as similar distributional patterns and significant correlations between them. It seems that the front separates the YSWC from the coastal water, and different phytoplankton groups are transported in these water masses and follow their movement. These results imply that the YSWC plays important roles in the distribution of nutrients, phytoplankton biomass and also in the community structure of the central Yellow Sea. © 2015 Elsevier Ltd. Source


Huang X.,Key Laboratory of Coastal and Wetland Ecosystems | Huang X.,Xiamen University | Huang X.,Zhangzhou Normal University | Zeng Y.,Key Laboratory of Coastal and Wetland Ecosystems | And 4 more authors.
Journal of Plankton Research | Year: 2014

Coincidence of dinoflagellate and Aurelia ephyrae blooms can occur in coastal waters in spring or early summer. We examined the behavior and growth of ephyrae of Aurelia sp. feeding at different concentrations of the dinoflagellate Alexandrium catenella. The results showed that the behavior and growth of Aurelia sp. ephyra could be significantly inhibited by high concentrations of A. catenella, suggesting that A. catenella blooms potentially depress the mass occurrence of Aurelia medusa. © The Author 2013. Published by Oxford University Press. All rights reserved. Source

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