Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera (Q61798407)

From Wikidata

Jump to navigation Jump to search

article

edit

Language	Label	Description	Also known as
English	Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera	article

Statements

instance of

scholarly article

0 references

title

Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera (English)

0 references

main subject

Pinctada margaritifera

0 references

RNA sequencing

0 references

biotechnology

0 references

biomineralization

1 reference

based on heuristic

inferred from title

author name string

J Le Luyer

series ordinal

1

0 references

P Auffret

series ordinal

2

0 references

V Quillien

series ordinal

3

0 references

N Leclerc

series ordinal

4

0 references

C Reisser

series ordinal

5

0 references

J Vidal-Dupiol

series ordinal

6

0 references

C-L Ky

series ordinal

7

0 references

language of work or name

English

0 references

publication date

6 February 2019

0 references

published in

BMC Genomics

0 references

volume

20

0 references

issue

1

0 references

page(s)

111

0 references

copyright license

Creative Commons Attribution 4.0 International

start time

6 February 2019

1 reference

stated in

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

DESeq2

object named as

DESeq2 R package

1 reference

stated in

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure and expression of an unusually acidic matrix protein of pearl oyster shells

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Role of molecular charge and hydrophilicity in regulating the kinetics of crystal growth

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molluscan shell proteins: primary structure, origin, and evolution

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

In vitro regulation of CaCO(3) crystal polymorphism by the highly acidic molluscan shell protein Aspein

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Sequence Alignment/Map format and SAMtools

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An acidic matrix protein, Pif, is a key macromolecule for nacre formation.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Parallel evolution of nacre building gene sets in molluscs

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Can the quality of pearls from the Japanese pearl oyster (Pinctada fucata) be explained by the gene expression patterns of the major shell matrix proteins in the pearl sac?

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparison of expression patterns of shell matrix protein genes in the mantle tissues between high- and low-quality pearl-producing recipients of the pearl oyster, Pinctada fucata

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcriptome analysis of biomineralisation-related genes within the pearl sac: host and donor oyster contribution.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identification of genes potentially related to biomineralization and immunity by transcriptome analysis of pearl sac in pearl oyster Pinctada martensii

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transposable elements are a significant contributor to tandem repeats in the human genome.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A comparative study of the shell matrix protein aspein in pterioid bivalves

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Characterization of the pearl oyster (Pinctada martensii) mantle transcriptome unravels biomineralization genes

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Gigabase-scale transcriptome analysis on four species of pearl oysters

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The shell-forming proteome of Lottia gigantea reveals both deep conservations and lineage-specific novelties

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Tandem repeats derived from centromeric retrotransposons

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome-wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster, Pinctada maxima.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Differential gene expression identified by RNA-Seq and qPCR in two sizes of pearl oyster (Pinctada fucata).

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Trimmomatic: a flexible trimmer for Illumina sequence data

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Temperature and food influence shell growth and mantle gene expression of shell matrix proteins in the pearl oyster Pinctada margaritifera

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

HTSeq--a Python framework to work with high-throughput sequencing data

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Microarray: a global analysis of biomineralization-related gene expression profiles during larval development in the pearl oyster, Pinctada fucata

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identification of genes associated with shell color in the black-lipped pearl oyster, Pinctada margaritifera

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Yes, it turns: experimental evidence of pearl rotation during its formation

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Interactive Effects of Seawater Acidification and Elevated Temperature on the Transcriptome and Biomineralization in the Pearl Oyster Pinctada fucata

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcriptome and biomineralization responses of the pearl oyster Pinctada fucata to elevated CO2 and temperature

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transposable element influences on gene expression in plants

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Insights from the Shell Proteome: Biomineralization to Adaptation

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Regulatory activities of transposable elements: from conflicts to benefits

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcriptome analysis of the freshwater pearl mussel (Cristaria plicata) mantle unravels genes involved in the formation of shell and pearl

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Characterization of transcriptome and identification of biomineralization genes in winged pearl oyster (Pteria penguin) mantle tissue

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identification of conserved proteins from diverse shell matrix proteome in Crassostrea gigas: characterization of genetic bases regulating shell formation

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Control of nacre biomineralization by Pif80 in pearl oyster.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The receptor genes PfBMPR1B and PfBAMBI are involved in regulating shell biomineralization in the pearl oyster Pinctada fucata

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transposable elements are the primary source of novelty in primate gene regulation.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crossing phenotype heritability and candidate gene expression in grafted black-lipped pearl oyster Pinctada margaritifera, an animal chimera.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Cultured Pearl Surface Quality Profiling by the Shell Matrix Protein Gene Expression in the Biomineralised Pearl Sac Tissue of Pinctada margaritifera.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Optimal age of the donor graft tissue in relation to cultured pearl phenotypes in the mollusc, Pinctada margaritifera.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

GOATOOLS: A Python library for Gene Ontology analyses

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30727965

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/S12864-019-5443-5

0 references

Dimensions Publication ID

1111954472

1 reference

stated in

SciGraph

retrieved

9 September 2019

reference URL

https://scigraph.springernature.com/pub.10.1186/s12864-019-5443-5

PMC publication ID

6366105

0 references

PubMed publication ID

30727965

0 references

 

Sitelinks

Wikipedia(0 entries)

edit

Wikibooks(0 entries)

edit

Wikinews(0 entries)

edit

Wikiquote(0 entries)

edit

Wikisource(0 entries)

edit

Wikiversity(0 entries)

edit

Wikivoyage(0 entries)

edit

Wiktionary(0 entries)

edit

Multilingual sites(0 entries)

edit

Retrieved from "https://www.wikidata.org/w/index.php?title=Q61798407&oldid=2222493590"