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De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp ( Penaeus monodon ) transcriptome

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/9781118657072openalex-snapshot

Biochemical Pathways

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RStudio: A Platform‐Independent IDE for R and Sweave

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Transcriptome Profiles of Penaeus (Marsupenaeus) japonicus Animal and Vegetal Half-Embryos: Identification of Sex Determination, Germ Line, Mesoderm, and Other Developmental Genes

inferredcites →https://doi.org/10.1016/0092-8674(92)90519-iopenalex-snapshot

The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus

inferredcites →https://doi.org/10.1016/j.aquaculture.2012.04.008openalex-snapshot

The importance of selective breeding in aquaculture to meet future demands for animal protein: A review

inferredcites →https://doi.org/10.1016/j.aquaculture.2016.08.003openalex-snapshot

De novo assembly and transcriptome characterization of major growth-related genes in various tissues of Penaeus monodon

inferredcites →https://doi.org/10.1016/j.cbd.2014.07.001openalex-snapshot

RNA-Seq reveals the dynamic and diverse features of digestive enzymes during early development of Pacific white shrimp Litopenaeus vannamei

inferredcites →https://doi.org/10.1016/j.cell.2013.06.009openalex-snapshot

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

inferredcites →https://doi.org/10.1016/j.dci.2013.07.020openalex-snapshot

RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei

inferredcites →https://doi.org/10.1016/j.dci.2016.06.013openalex-snapshot

Differentially expressed transcripts in stomach of Penaeus monodon in response to AHPND infection

inferredcites →https://doi.org/10.1016/j.fsi.2013.09.019openalex-snapshot

Trascriptome analysis of the Paciﬁc white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq

inferredcites →https://doi.org/10.1016/j.fsi.2017.10.028openalex-snapshot

Gill transcriptomes reveal involvement of cytoskeleton remodeling and immune defense in ammonia stress response in the banana shrimp Fenneropenaeus merguiensis

inferredcites →https://doi.org/10.1016/j.fsi.2018.01.045openalex-snapshot

Transcriptome analysis of ‘Huanghai No. 2’ Fenneropenaeus chinensis response to WSSV using RNA-seq

inferredcites →https://doi.org/10.1016/j.gene.2015.12.026openalex-snapshot

De novo assembly and transcriptome analysis of osmoregulation in Litopenaeus vannamei under three cultivated conditions with different salinities

inferredcites →https://doi.org/10.1016/j.margen.2015.04.001openalex-snapshot

Identification of genes involved in reproduction and lipid pathway metabolism in wild and domesticated shrimps

inferredcites →https://doi.org/10.1016/j.margen.2015.04.006openalex-snapshot

De-novo transcriptome analysis of the banana shrimp (Fenneropenaeus merguiensis) and identification of genes associated with reproduction and development

inferredcites →https://doi.org/10.1016/j.margen.2015.07.003openalex-snapshot

Transcriptomic response to low salinity stress in gills of the Pacific white shrimp, Litopenaeus vannamei

inferredcites →https://doi.org/10.1016/j.margen.2017.08.007openalex-snapshot

Transcriptome-based discovery of pathways and genes related to reproduction of the black tiger shrimp (Penaeus monodon)

inferredcites →https://doi.org/10.1016/j.ygcen.2011.11.035openalex-snapshot

The CHH-superfamily of multifunctional peptide hormones controlling crustacean metabolism, osmoregulation, moulting, and reproduction

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Methyl Farnesoate: Crustacean Juvenile Hormone in Search of Functions

inferredcites →https://doi.org/10.1038/nature17161openalex-snapshot

Melanoma addiction to the long non-coding RNA SAMMSON

inferredcites →https://doi.org/10.1038/nature20167openalex-snapshot

Redefining the invertebrate RNA virosphere

inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot

Full-length transcriptome assembly from RNA-Seq data without a reference genome

inferredcites →https://doi.org/10.1038/nbt0502-508openalex-snapshot

Using the transcriptome to annotate the genome

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nrg2484openalex-snapshot

RNA-Seq: a revolutionary tool for transcriptomics

inferredcites →https://doi.org/10.1038/nrm.2016.126openalex-snapshot

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

inferredcites →https://doi.org/10.1038/s41598-017-07290-wopenalex-snapshot

Absence of deformed wing virus and Varroa destructor in Australia provides unique perspectives on honeybee viral landscapes and colony losses

inferredcites →https://doi.org/10.1038/s41598-017-10515-7openalex-snapshot

A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei

inferredcites →https://doi.org/10.1038/srep07081openalex-snapshot

Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

inferredcites →https://doi.org/10.1093/bioinformatics/bti610openalex-snapshot

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

inferredcites →https://doi.org/10.1093/bioinformatics/btt219openalex-snapshot

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

inferredcites →https://doi.org/10.1093/icb/icw029openalex-snapshot

Transcriptional Profiling of Banana ShrimpFenneropenaeus merguiensiswith Differing Levels of Viral Load

inferredcites →https://doi.org/10.1093/nar/gkg095openalex-snapshot

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

inferredcites →https://doi.org/10.1093/nar/gkw1119openalex-snapshot

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

inferredcites →https://doi.org/10.1093/nar/gkw1306openalex-snapshot

FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome

inferredcites →https://doi.org/10.1099/0022-1317-81-6-1473openalex-snapshot

Gill-associated virus of Penaeus monodon prawns: an invertebrate virus with ORF1a and ORF1b genes related to arteri- and coronaviruses

inferredcites →https://doi.org/10.1099/jgv.0.000757openalex-snapshot

ICTV Virus Taxonomy Profile: Iflaviridae

inferredcites →https://doi.org/10.1101/021626openalex-snapshot

TransRate: reference free quality assessment of de-novo transcriptome assemblies

inferredcites →https://doi.org/10.1101/035642openalex-snapshot

Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms

inferredcites →https://doi.org/10.1101/gad.223902openalex-snapshot

Cell surface proteins Nasrat and Polehole stabilize the Torso-like extracellular determinant in Drosophila oogenesis

inferredcites →https://doi.org/10.1101/gr.132159.111openalex-snapshot

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

inferredcites →https://doi.org/10.1101/gr.196469.115openalex-snapshot

TransRate: reference-free quality assessment of de novo transcriptome assemblies

inferredcites →https://doi.org/10.1111/j.1365-2761.2011.01263.xopenalex-snapshot

The effect of Penaeus merguiensis densovirus on Penaeus merguiensis production in Queensland, Australia

inferredcites →https://doi.org/10.1128/jvi.78.2.899-911.2004openalex-snapshot

Genome Structure and Thymic Expression of an Endogenous Retrovirus in Zebrafish

inferredcites →https://doi.org/10.1128/jvi.80.10.4998-5009.2006openalex-snapshot

Molecular and Biological Characterization of Deformed Wing Virus of Honeybees ( Apis mellifera L.)

inferredcites →https://doi.org/10.1146/annurev.ge.29.120195.002103openalex-snapshot

SIGNALING PATHWAYS THAT ESTABLISH THE DORSAL-VENTRAL PATTERN OF THE DROSOPHILA EMBRYO

inferredcites →https://doi.org/10.1158/2159-8290.cd-11-0209openalex-snapshot

The Emergence of lncRNAs in Cancer Biology

inferredcites →https://doi.org/10.1186/1746-6148-9-189openalex-snapshot

Discovery and partial characterization of a non-LTR retrotransposon that may be associated with abdominal segment deformity disease (ASDD) in the whiteleg shrimp Penaeus (Litopenaeus) vannamei

inferredcites →https://doi.org/10.1186/2047-217x-4-1openalex-snapshot

SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations

inferredcites →https://doi.org/10.1186/gb-2014-15-1-r1openalex-snapshot

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

inferredcites →https://doi.org/10.1186/s13059-014-0410-6openalex-snapshot

Corset: enabling differential gene expression analysis for de novoassembled transcriptomes

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-014-0572-2openalex-snapshot

De novo assembly of bacterial transcriptomes from RNA-seq data

inferredcites →https://doi.org/10.1186/s13059-015-0596-2openalex-snapshot

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

inferredcites →https://doi.org/10.1186/s13742-015-0089-yopenalex-snapshot

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

inferredcites →https://doi.org/10.1242/dev.030403openalex-snapshot

The function of non-coding RNAs in genomic imprinting

inferredcites →https://doi.org/10.1242/dev.098343openalex-snapshot

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

inferredcites →https://doi.org/10.1371/journal.pcbi.1004772openalex-snapshot

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

inferredcites →https://doi.org/10.1371/journal.pone.0047442openalex-snapshot

Analysis of Litopenaeus vannamei Transcriptome Using the Next-Generation DNA Sequencing Technique

inferredcites →https://doi.org/10.1371/journal.pone.0057515openalex-snapshot

Transcriptome Analysis of Pacific White Shrimp (Litopenaeus vannamei) Hepatopancreas in Response to Taura Syndrome Virus (TSV) Experimental Infection

inferredcites →https://doi.org/10.1371/journal.pone.0058627openalex-snapshot

Transcriptome Analysis on Chinese Shrimp Fenneropenaeus chinensis during WSSV Acute Infection

inferredcites →https://doi.org/10.1371/journal.pone.0073218openalex-snapshot

Transcriptome Analysis of Litopenaeus vannamei in Response to White Spot Syndrome Virus Infection

inferredcites →https://doi.org/10.1371/journal.pone.0076718openalex-snapshot

Sequencing and De Novo Analysis of the Hemocytes Transcriptome in Litopenaeus vannamei Response to White Spot Syndrome Virus Infection

inferredcites →https://doi.org/10.1371/journal.pone.0085413openalex-snapshot

The Development of a High Density Linkage Map for Black Tiger Shrimp (Penaeus monodon) Based on cSNPs

inferredcites →https://doi.org/10.1371/journal.pone.0087218openalex-snapshot

SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing

inferredcites →https://doi.org/10.1371/journal.pone.0131503openalex-snapshot

Transcriptome and Molecular Pathway Analysis of the Hepatopancreas in the Pacific White Shrimp Litopenaeus vannamei under Chronic Low-Salinity Stress

inferredcites →https://doi.org/10.1371/journal.pone.0164396openalex-snapshot

Transcriptome Analysis of the Hepatopancreas in the Pacific White Shrimp (Litopenaeus vannamei) under Acute Ammonia Stress

inferredcites →https://doi.org/10.3354/dao02894openalex-snapshot

New yellow head virus genotype (YHV7) in giant tiger shrimp Penaeus monodon indigenous to northern Australia

inferredcites →https://doi.org/10.3835/plantgenome2016.03.0027openalex-snapshot

Rascaf: Improving Genome Assembly with RNA Sequencing Data

inferredcites →https://doi.org/10.7554/elife.05378openalex-snapshot

Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3389/fgene.2018.00282openalex-snapshot

The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization

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