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Shi Q.,Shenzhen Key Laboratory of Marine Genomics | Chung J.S.,University of Maryland, Baltimore
Gene | Year: 2014

Adult blue crab Callinectes sapidus exhibit behavioral and ecological dimorphisms: females migrating from the low salinity water to the high salinity area vs. males remaining in the same areas. The flesh basal muscle of the swimming paddle shows a dimorphic color pattern in that levator (Lev) and depressor (Dep) of females tend to be much darker than those of males, while both genders have the same light colored remoter (Rem) and promoter (Pro). The full-length cDNA sequence of four structural isoforms of trehalose-6-phosphate synthase (TPS) is isolated from chela muscles of an adult female, C. sapidus. Two isoforms of the C. sapidus TPS encode functional domains of TPS and trehalose-6-phosphorylase (TPP) in tandem as a fused gene product of Escherichia coli Ost A and Ost B. The other two isoforms contain only a single TPS domain. In both males and females, the darker (Lev. +. Dep) muscles exhibit greater amounts of trehalose, TPS and trehalase activities than the light colored (Rem. +. Pro). The fact that adult females show higher levels of trehalase activity in the basal muscles and of glucose in Lev. +. Dep than those of adult males suggests that there may be a metabolic dimorphism. Moreover, the involvement of trehalose in energy metabolism that was examined under the condition of strenuous swimming activity mimicked in adult females demonstrates the intrinsic trehalose metabolism in Lev. +. Dep, which subsequently results in hemolymphatic hyperglycemia and hyperlactemia. Our data support that trehalose serves as an additional carbohydrate source of hemolymphatic hyperglycemia in this species. Behavioral and ecological dimorphisms of C. sapidus adults may be supported by a functional dimorphism in energy metabolism. © 2013 Elsevier B.V. Source

He S.,University of Chinese Academy of Sciences | Lu J.,University of Chinese Academy of Sciences | Jiang W.,CAS Kunming Institute of Zoology | Yang S.,BGI Shenzhen | And 4 more authors.
Mitochondrial DNA | Year: 2015

Sinocyclocheilus anshuiensis is a special cavefish that lives in the Southwestern China with many specific regressive features, such as rudimentary eyes and scales, and loss of pigmentation. In this study, we performed sequencing and assembly of its complete mitochondrial genome. We confirmed that total length of the mitochondrion is 16 618 bp with an AT ratio of 55.4%. The complete mitochondrial genome contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a 963 bp control region. Our current data provide important resources for the research of cavefish mitochondrial evolution and energy metabolism. © 2015 Taylor & Francis. Source

You X.,Shenzhen Key Laboratory of Marine Genomics | Bian C.,Shenzhen Key Laboratory of Marine Genomics | Zan Q.,Shenzhen Wild Animal Rescue Center | Xu X.,BGI Shenzhen | And 45 more authors.
Nature Communications | Year: 2014

Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers' tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates. © 2014 Macmillan Publishers Limited. Source

Yang J.,CAS Kunming Institute of Zoology | Chen X.,BGI Shenzhen | Bai J.,BGI Shenzhen | Bai J.,Shenzhen Key Laboratory of Marine Genomics | And 59 more authors.
BMC Biology | Year: 2016

Background: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. Results: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. Conclusion: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology. © 2016 Yang et al. Source

Li J.,University of Chinese Academy of Sciences | Li J.,Shenzhen Key Laboratory of Marine Genomics | You X.,Shenzhen Key Laboratory of Marine Genomics | Bian C.,Shenzhen Key Laboratory of Marine Genomics | And 7 more authors.
International Journal of Molecular Sciences | Year: 2015

All living organisms synchronize biological functions with environmental changes; melatonin plays a vital role in regulating daily and seasonal variations. Due to rhythmic activity of the timezyme aralkylamine N-acetyltransferase (AANAT), the blood level of melatonin increases at night and decreases during daytime. Whereas other vertebrates have a single form of AANAT, bony fishes possess various isoforms of aanat genes, though the reasons are still unclear. Here, we have taken advantage of multiple unpublished teleost aanat sequences to explore and expand our understanding of the molecular evolution of aanat in fish. Our results confirm that two rounds of whole-genome duplication (WGD) led to the existence of three fish isoforms of aanat, i.e., aanat1a, aanat1b, and aanat2; in addition, gene loss led to the absence of some forms from certain special fish species. Furthermore, we suggest the different roles of two aanat1s in amphibious mudskippers, and speculate that the loss of aanat1a, may be related to terrestrial vision change. Several important sites of AANAT proteins and regulatory elements of aanat genes were analyzed for structural comparison and functional forecasting, respectively, which provides insights into the molecular evolution of the differences between AANAT1 and AANAT2. © 2015 by the authors; licensee MDPI, Basel, Switzerland. Source

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