Transcriptional profiling of pigmentation-regulated long non-coding RNAs in the mantle of Manila clam (Ruditapes philippinarum)

[1]  Yanming Zhang,et al.  MiRNA-mRNA Integration Analysis Reveals the Regulatory Roles of MiRNAs in Shell Pigmentation of the Manila clam (Ruditapes philippinarum) , 2021, Marine Biotechnology.

[2]  Yinghui Dong,et al.  Characterization and Function Analysis of β, β-carotene-9′, 10′-oxygenase 2 (BCDO2) Gene in Carotenoid Metabolism of the Red Shell Hard Clam (Meretrix meretrix) , 2021, Frontiers in Marine Science.

[3]  Shikai Liu,et al.  Shell Biosynthesis and Pigmentation as Revealed by the Expression of Tyrosinase and Tyrosinase-like Protein Genes in Pacific Oyster (Crassostrea gigas) with Different Shell Colors , 2021, Marine Biotechnology.

[4]  D. Tong,et al.  LncRNA-42060 Regulates Tamoxifen Sensitivity and Tumor Development via Regulating the miR-204-5p/SOX4 Axis in Canine Mammary Gland Tumor Cells , 2021, Frontiers in Veterinary Science.

[5]  Qi Li,et al.  Identification and characterization of key haem pathway genes associated with the synthesis of porphyrin in Pacific oyster (Crassostrea gigas). , 2021, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[6]  Wu Jin,et al.  Integrated proteomic and transcriptomic analysis reveals that polymorphic shell colors vary with melanin synthesis in Bellamya purificata snail. , 2020, Journal of proteomics.

[7]  Z. Huo,et al.  Physiological and gene expression analysis of the Manila clam Ruditapes philippinarum in response to cold acclimation. , 2020, The Science of the total environment.

[8]  Z. Huo,et al.  Molecular cloning and expression analysis of tyrosinases (tyr) in four shell-color strains of Manila clam Ruditapes philippinarum , 2020, PeerJ.

[9]  Ning Li,et al.  Transcriptome analysis reveals the pigmentation-related genes in two shell color strains of the Manila clam Ruditapes philippinarum , 2020, Animal biotechnology.

[10]  Qingheng Wang,et al.  LncMSEN1, a mantle-specific LncRNA participating in nacre formation and response to polyI:C stimulation in pearl oyster Pinctada fucata martensii. , 2019, Fish & shellfish immunology.

[11]  Z. Huo,et al.  Transcriptome analysis reveals the pigmentation related genes in four different shell color strains of the Manila clam Ruditapes philippinarum. , 2019, Genomics.

[12]  Yaqing Chang,et al.  Histological and Expression Differences Among Different Mantle Regions of the Yesso Scallop (Patinopecten yessoensis) Provide Insights into the Molecular Mechanisms of Biomineralization and Pigmentation , 2019, Marine Biotechnology.

[13]  Jianjun Fu,et al.  Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp , 2019, BMC Genomics.

[14]  Jia-Le Li,et al.  A Kunitz proteinase inhibitor (HcKuPI) participated in antimicrobial process during pearl sac formation and induced the overgrowth of calcium carbonate in Hyriopsis cumingii , 2019, Fish & shellfish immunology.

[15]  Hao Song,et al.  Transcriptome analysis of shell color-related genes in the hard clam Mercenaria mercenaria. , 2019, Comparative biochemistry and physiology. Part D, Genomics & proteomics.

[16]  Jiale Li,et al.  Cloning of a microphthalmia-associated transcription factor gene and its functional analysis in nacre formation and melanin synthesis in Hyriopsis cumingii , 2018, Aquaculture and Fisheries.

[17]  Jixing Feng,et al.  Differential lncRNA expression profiles reveal the potential roles of lncRNAs in antiviral immune response of Crassostrea gigas , 2018, Fish & shellfish immunology.

[18]  Qi Li,et al.  Gonad Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Identifies Potential Genes Regulating the Sex Determination and Differentiation Process , 2018, Marine Biotechnology.

[19]  Qi Li,et al.  Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation , 2018, Scientific Reports.

[20]  Zhao Yuming,et al.  Selection of a new scallop strain, the Bohai Red, from the hybrid between the bay scallop and the Peruvian scallop , 2017 .

[21]  Guangzheng Wen,et al.  A Simple Process of RNA-Sequence Analyses by Hisat2, Htseq and DESeq2 , 2017, ICBEB 2017.

[22]  P. Sunnucks,et al.  De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read , 2017, GigaScience.

[23]  R. Rae.  The gastropod shell has been co-opted to kill parasitic nematodes , 2017, Scientific Reports.

[24]  Fabián J. Tapia,et al.  Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra. , 2017, Marine genomics.

[25]  S. Williams,et al.  Molluscan shell colour , 2017, Biological reviews of the Cambridge Philosophical Society.

[26]  Qi Li,et al.  Identification of conserved proteins from diverse shell matrix proteome in Crassostrea gigas: characterization of genetic bases regulating shell formation , 2017, Scientific Reports.

[27]  Z. Huo,et al.  The HSP70 gene expression responses to thermal and salinity stress in wild and cultivated Manila clam Ruditapes philippinarum , 2017 .

[28]  Jiale Li,et al.  HcTyr and HcTyp-1 of Hyriopsis cumingii, novel tyrosinase and tyrosinase-related protein genes involved in nacre color formation. , 2017, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[29]  K. Lindblad-Toh,et al.  FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome , 2017, Nucleic acids research.

[30]  A. Chinnaiyan,et al.  TACO produces robust multi-sample transcriptome assemblies from RNA-seq , 2016, Nature Methods.

[31]  Ling-Ling Chen,et al.  Research progress of long noncoding RNA in China , 2016, IUBMB life.

[32]  Benjamin Marie,et al.  Insights from the Shell Proteome: Biomineralization to Adaptation , 2016, Molecular biology and evolution.

[33]  Yinghui Dong,et al.  Integration of Next Generation Sequencing and EPR Analysis to Uncover Molecular Mechanism Underlying Shell Color Variation in Scallops , 2016, PloS one.

[34]  Shuai Zhang,et al.  Systematic Analysis of Long Noncoding RNAs in the Senescence-accelerated Mouse Prone 8 Brain Using RNA Sequencing , 2016, Molecular therapy. Nucleic acids.

[35]  B. Degnan,et al.  Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization , 2016, Frontiers in Zoology.

[36]  Xuelin Zhao,et al.  Genome-wide identification and characterization of long intergenic noncoding RNAs and their potential association with larval development in the Pacific oyster , 2016, Scientific Reports.

[37]  Xuelin Zhao,et al.  Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation , 2015, PloS one.

[38]  Howard Y. Chang,et al.  Unique features of long non-coding RNA biogenesis and function , 2015, Nature Reviews Genetics.

[39]  Selene L. Fernandez-Valverde,et al.  Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity , 2015, Molecular biology and evolution.

[40]  P. Kapranov,et al.  The Landscape of long noncoding RNA classification. , 2015, Trends in genetics : TIG.

[41]  D. Moazed,et al.  RNA-mediated epigenetic regulation of gene expression , 2015, Nature Reviews Genetics.

[42]  P. de Knijff,et al.  De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes , 2014, BMC Genomics.

[43]  Saakshi Jalali,et al.  Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs , 2012, Biology Direct.

[44]  L. Xie,et al.  The role of matrix proteins in the control of nacreous layer deposition during pearl formation , 2012, Proceedings of the Royal Society B: Biological Sciences.

[45]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[46]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[47]  Benjamin Marie,et al.  Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization , 2010, BMC Genomics.

[48]  Wenhua Liu,et al.  Total carotenoid differences in scallop tissues of Chlamys nobilis (Bivalve: Pectinidae) with regard to gender and shell colour , 2010 .

[49]  Michael Kube,et al.  Parallel evolution of nacre building gene sets in molluscs. , 2010, Molecular biology and evolution.

[50]  J. Hirabayashi,et al.  Isolation, characterization and molecular evolution of a novel pearl shell lectin from a marine bivalve, Pteria penguin. , 2006, Molecular diversity.

[51]  A. Nappi,et al.  Melanization immune responses in mosquito vectors. , 2005, Trends in parasitology.

[52]  M. Hediger,et al.  Modulation of DMT1 Activity by Redox Compounds , 2004, The Journal of Membrane Biology.

[53]  J. Buggy.  Binding of alpha-melanocyte-stimulating hormone to its G-protein-coupled receptor on B-lymphocytes activates the Jak/STAT pathway. , 1998, The Biochemical journal.

[54]  B. Charlesworth,et al.  INBREEDING DEPRESSION WITH HETEROZYGOTE ADVANTAGE AND ITS EFFECT ON SELECTION FOR MODIFIERS CHANGING THE OUTCROSSING RATE , 1990, Evolution; international journal of organic evolution.

[55]  L. Pratt,et al.  Molecular and isotopic compositions of lipids in bivalve shells: A new prospect for molecular paleontology , 1995 .

[56]  T. Wright.  The genetics of biogenic amine metabolism, sclerotization, and melanization in Drosophila melanogaster. , 1987, Advances in genetics.

[57]  A. Comfort.  Acid-soluble pigments of shells. 1. The distribution of porphyrin fluorescence in molluscan shells. , 1949, The Biochemical journal.

[58]  A. Comfort.  Acid-soluble pigments of molluscan shells. 2. Pigments other than porphyrins. , 1949, The Biochemical journal.