Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Mar Biotechnol (NY)
2018 Apr 01;202:193-205. doi: 10.1007/s10126-018-9796-6.
Show Gene links
Show Anatomy links
Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids.
Wang Z
,
Cui J
,
Song J
,
Wang H
,
Gao K
,
Qiu X
,
Gou M
,
Li X
,
Hu Z
,
Wang X
,
Chang Y
.
???displayArticle.abstract???
Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.
Abdelrahman,
Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.
2017, Pubmed
Abdelrahman,
Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.
2017,
Pubmed
Ashpole,
Growth hormone, insulin-like growth factor-1 and the aging brain.
2015,
Pubmed
Barbacid,
ras genes.
1987,
Pubmed
Birchler,
In search of the molecular basis of heterosis.
2003,
Pubmed
Bustin,
The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.
2009,
Pubmed
Casar,
Ras subcellular localization defines extracellular signal-regulated kinase 1 and 2 substrate specificity through distinct utilization of scaffold proteins.
2009,
Pubmed
Chatchaiphan,
De Novo Transcriptome Characterization and Growth-Related Gene Expression Profiling of Diploid and Triploid Bighead Catfish (Clarias macrocephalus Günther, 1864).
2017,
Pubmed
Cheng,
EGF-mediated EGFR/ERK signaling pathway promotes germinative cell proliferation in Echinococcus multilocularis that contributes to larval growth and development.
2017,
Pubmed
Citri,
EGF-ERBB signalling: towards the systems level.
2006,
Pubmed
de la Torre-Ubieta,
A FOXO-Pak1 transcriptional pathway controls neuronal polarity.
2010,
Pubmed
Dhillon,
MAP kinase signalling pathways in cancer.
2007,
Pubmed
Djebali,
Landscape of transcription in human cells.
2012,
Pubmed
Dobin,
STAR: ultrafast universal RNA-seq aligner.
2013,
Pubmed
Drew,
HSP72 is a mitochondrial stress sensor critical for Parkin action, oxidative metabolism, and insulin sensitivity in skeletal muscle.
2014,
Pubmed
Fan,
Characterization of Embryo Transcriptome of Gynogenetic Olive Flounder Paralichthys olivaceus.
2016,
Pubmed
Gao,
Transcriptome analysis of artificial hybrid pufferfish Jiyan-1 and its parental species: implications for pufferfish heterosis.
2013,
Pubmed
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Holbro,
ErbB receptors: directing key signaling networks throughout life.
2004,
Pubmed
Holloway,
A novel role for MAPKAPK2 in morphogenesis during zebrafish development.
2009,
Pubmed
Holmberg,
Laminin-211 in skeletal muscle function.
2013,
Pubmed
Hua,
Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid.
2003,
Pubmed
Huang,
Transcriptomic Analysis of Compromise Between Air-Breathing and Nutrient Uptake of Posterior Intestine in Loach (Misgurnus anguillicaudatus), an Air-Breathing Fish.
2016,
Pubmed
Huang,
Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster.
2016,
Pubmed
Im,
Transcriptome-Based Identification of the Desiccation Response Genes in Marine Red Algae Pyropia tenera (Rhodophyta) and Enhancement of Abiotic Stress Tolerance by PtDRG2 in Chlamydomonas.
2017,
Pubmed
Kanehisa,
The KEGG resource for deciphering the genome.
2004,
Pubmed
Khatri,
Ten years of pathway analysis: current approaches and outstanding challenges.
2012,
Pubmed
Kholodenko,
Signalling ballet in space and time.
2010,
Pubmed
Kim,
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
2013,
Pubmed
Klee,
Calmodulin.
1982,
Pubmed
Koyama,
Nutritional control of body size through FoxO-Ultraspiracle mediated ecdysone biosynthesis.
2014,
Pubmed
Leicht,
Raf kinases: function, regulation and role in human cancer.
2007,
Pubmed
Leithner,
PCK2 activation mediates an adaptive response to glucose depletion in lung cancer.
2015,
Pubmed
Li,
RNA-Seq Analysis of the Antioxidant Status and Immune Response of Portunus trituberculatus Following Aerial Exposure.
2017,
Pubmed
Li,
Identification and Differential Expression of Biomineralization Genes in the Mantle of Pearl Oyster Pinctada fucata.
2017,
Pubmed
Li,
Transcriptome Sequencing and Comparative Analysis of Ovary and Testis Identifies Potential Key Sex-Related Genes and Pathways in Scallop Patinopecten yessoensis.
2016,
Pubmed
Lippman,
The making of a compound inflorescence in tomato and related nightshades.
2008,
Pubmed
Liu,
Mice carrying null mutations of the genes encoding insulin-like growth factor I (Igf-1) and type 1 IGF receptor (Igf1r).
1993,
Pubmed
Liu,
A Novel ω3-Desaturase in the Deep Sea Giant Tubeworm Riftia pachyptila.
2017,
Pubmed
Lombardi,
NGF-dependent axon growth and regeneration are altered in sympathetic neurons of dystrophic mdx mice.
2017,
Pubmed
Lui,
Mechanisms limiting body growth in mammals.
2011,
Pubmed
Martins,
Long live FOXO: unraveling the role of FOXO proteins in aging and longevity.
2016,
Pubmed
Matallanas,
Raf family kinases: old dogs have learned new tricks.
2011,
Pubmed
McKenna,
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
2010,
Pubmed
Méndez-Lucas,
Mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M) is a pro-survival, endoplasmic reticulum (ER) stress response gene involved in tumor cell adaptation to nutrient availability.
2014,
Pubmed
Mungunsukh,
Hepatocyte Growth Factor Isoforms in Tissue Repair, Cancer, and Fibrotic Remodeling.
2014,
Pubmed
Mutter,
Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays.
2004,
Pubmed
Niu,
Developmental Transcriptome Analysis and Identification of Genes Involved in Larval Metamorphosis of the Razor Clam, Sinonovacula constricta.
2016,
Pubmed
Núñez-Acuña,
Functional Diets Modulate lncRNA-Coding RNAs and Gene Interactions in the Intestine of Rainbow Trout Oncorhynchus mykiss.
2017,
Pubmed
Pang,
Local delivery of a collagen-binding FGF-1 chimera to smooth muscle cells in collagen scaffolds for vascular tissue engineering.
2010,
Pubmed
Pir,
The genetic control of growth rate: a systems biology study in yeast.
2012,
Pubmed
Powell-Braxton,
IGF-I is required for normal embryonic growth in mice.
1993,
Pubmed
Rao,
Processing and transfer of epidermal growth factor in developing rat jejunum and ileum.
1990,
Pubmed
Rohner,
Duplication of fgfr1 permits Fgf signaling to serve as a target for selection during domestication.
2009,
Pubmed
Rousselle,
Laminin 332 processing impacts cellular behavior.
2013,
Pubmed
Rushworth,
Regulation and role of Raf-1/B-Raf heterodimerization.
2006,
Pubmed
Sahai,
RHO-GTPases and cancer.
2002,
Pubmed
Schenk,
Properties and functions of the thiamin diphosphate dependent enzyme transketolase.
1998,
Pubmed
Schubbert,
Hyperactive Ras in developmental disorders and cancer.
2007,
Pubmed
Schulze,
SERE: single-parameter quality control and sample comparison for RNA-Seq.
2012,
Pubmed
Shuaib,
Multi-Compartmentalisation in the MAPK Signalling Pathway Contributes to the Emergence of Oscillatory Behaviour and to Ultrasensitivity.
2016,
Pubmed
Song,
Bias and Correction in RNA-seq Data for Marine Species.
2017,
Pubmed
Sun,
Transcriptome analysis reveals the molecular mechanisms underlying growth superiority in a novel grouper hybrid (Epinephelus fuscogutatus♀ × E. lanceolatus♂).
2016,
Pubmed
Tank,
Spontaneous age-related neurite branching in Caenorhabditis elegans.
2011,
Pubmed
Varshavsky,
The ubiquitin system, an immense realm.
2012,
Pubmed
Vuylsteke,
Genetic analysis of variation in gene expression in Arabidopsis thaliana.
2005,
Pubmed
Wang,
AMP-activated protein kinase, stress responses and cardiovascular diseases.
2012,
Pubmed
Wang,
Identification and Characterization of MicroRNAs from Longitudinal Muscle and Respiratory Tree in Sea Cucumber (Apostichopus japonicus) Using High-Throughput Sequencing.
2015,
Pubmed
,
Echinobase
Wang,
Identification and characterization of a novel Foxo transcription factors in Apostichopus japonicus.
2015,
Pubmed
,
Echinobase
Wang,
Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss).
2016,
Pubmed
Wei,
A transcriptomic analysis of superhybrid rice LYP9 and its parents.
2009,
Pubmed
Wellbrock,
The RAF proteins take centre stage.
2004,
Pubmed
Winick,
Quantitative changes in DNA, RNA, and protein during prenatal and postnatal growth in the rat.
1965,
Pubmed
Wolf,
What are maternal effects (and what are they not)?
2009,
Pubmed
Xie,
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.
2011,
Pubmed
Yang,
Comparative Transcriptome Analysis Provides Insights into Differentially Expressed Genes and Long Non-Coding RNAs between Ovary and Testis of the Mud Crab (Scylla paramamosain).
2018,
Pubmed
Yang,
RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus.
2016,
Pubmed
,
Echinobase
Yao,
Identification of differentially expressed genes in leaf and root between wheat hybrid and its parental inbreds using PCR-based cDNA subtraction.
2005,
Pubmed
Żarski,
Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation.
2017,
Pubmed
Zebisch,
Signaling through RAS-RAF-MEK-ERK: from basics to bedside.
2007,
Pubmed
Zhao,
Gene Co-Expression Network Analysis Reveals the Correlation Patterns Among Genes in Euryhaline Adaptation of Crassostrea gigas.
2016,
Pubmed
Zhou,
Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus.
2016,
Pubmed
,
Echinobase
Zhu,
Identification and assessment of differentially expressed genes involved in growth regulation in Apostichopus japonicus.
2013,
Pubmed
,
Echinobase
