HpeNet: Co-expression Network Database for de novo Transcriptome Assembly of Paeonia lactiflora Pall

Frontiers in Genetics
Minghao ShengXiaodong Zhang

Abstract

The herbaceous peony (Paeonia lactiflora Pall.) is a well-known ornamental flowering and pharmaceutical plant found in China. Its high medicinal value has long been recognized by traditional Chinese medicine (as Radix paeoniae Alba and Radix paeoniae Rubra), and it has become economically valued for its oilseed in recent years; like other Paeonia species, it has been identified as a novel resource for the α-linolenic acid used in seed oil production. However, its genome has not yet been sequenced, and little transcriptome data on Paeonia lactiflora are available. To obtain a comprehensive transcriptome for Paeonia lactiflora, RNAs from 10 tissues of the Paeonia lactiflora Pall. cv Shaoyou17C were used for de novo assembly, and 416,062 unigenes were obtained. Using a homology search, it was found that 236,222 (approximately 57%) unigenes had at least one BLAST hit in one or more public data resources. The construction of co-expression networks is a feasible means for improving unigene annotation. Using in-house transcriptome data, we obtained a co-expression network covering 95.13% of the unigenes. Then we integrated co-expression network analyses and lipid-related pathway genes to study lipid metabolism in Paeonia lactiflora cu...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
May 29, 2007·Nucleic Acids Research·Yuki MoriyaMinoru Kanehisa
Nov 28, 2007·Nucleic Acids Research·Robert D FinnAlex Bateman
May 1, 2008·Nucleic Acids Research·Stefan GötzAna Conesa
Sep 22, 2009·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Takeshi Obayashi, Kengo Kinoshita
Nov 19, 2009·Nucleic Acids Research·Robert D FinnAlex Bateman
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Jun 29, 2011·Proceedings of the National Academy of Sciences of the United States of America·Fabienne BourgisVincent Arondel
Apr 6, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Anh-Tung PhamKristin D Bilyeu
Sep 13, 2012·JAMA : the Journal of the American Medical Association·Evangelos C RizosMoses S Elisaf
Nov 28, 2012·Nucleic Acids Research·Yutaka SatoYoshiaki Nagamura
Mar 19, 2013·The Arabidopsis Book·Yonghua Li-BeissonJohn Ohlrogge
May 2, 2013·Nucleic Acids Research·Xin YiZhen Su
Nov 16, 2013·Trends in Plant Science·Seung Yon Rhee, Marek Mutwil
Feb 14, 2015·Molecular Plant·Qi YouZhen Su
Mar 31, 2015·Nucleic Acids Research·Tak LeeInsuk Lee
Sep 30, 2015·Bioinformatics·Max FranzGary D Bader
Nov 8, 2015·Plant & Cell Physiology·Yuichi AokiTakeshi Obayashi
Feb 29, 2016·Plant Physiology and Biochemistry : PPB·Da-Qiu ZhaoJun Tao
May 18, 2016·Nature Reviews. Genetics·Sara GoodwinW Richard McCombie
Dec 18, 2016·Methods in Molecular Biology·Sebastian Proost, Marek Mutwil
Jan 13, 2017·Briefings in Bioinformatics·Sipko van DamJoão Pedro de Magalhães
May 12, 2017·PloS One·Masayo Inoue, Katsuhisa Horimoto
Jun 18, 2017·Methods in Molecular Biology·Tak Lee, Insuk Lee
Apr 11, 2019·Frontiers in Genetics·Jiajie SheZhen Su

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA656429

Methods Mentioned

BETA
RNA-seq
RNA Assay
Assay

Software Mentioned

diamond
Cytoscape
HpeNet
LAMP Linux Apache
HMMER
ccNET
FastQC
GSEA
RSEM
BLASTX

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Yao xue xue bao = Acta pharmaceutica Sinica
H Y LangX T Liang
Medical Science Monitor : International Medical Journal of Experimental and Clinical Research
Yin ZhangNingxi Yang
© 2021 Meta ULC. All rights reserved