Identification of Multigene Biomarker for Shrimp White Feces Syndrome by Full-Length Transcriptome Sequencing

Frontiers in Genetics
Shenzheng ZengZhijian Huang

Abstract

The pacific white shrimp, Litopenaeus vannamei, with the largest shrimp industry production in the world, is currently threatened by a severe disease, white feces syndrome (WFS), which cause devastating losses globally, while its causal agents remain largely unknown. Herein, compared to the Control shrimp by metagenomic analysis, we firstly investigated that the altered functions of intestinal microbial community in WFS shrimp were the enrichment of bacterial chemotaxis and flagellar assembly pathways, hinting at a potential role of pathogenic bacteria for growth and development, which might be related to WFS occurrence. Single-molecule real-time (SMRT) sequencing was to further identify the gene structure and gene regulation for more clues in WFS aetiology. Totally 50,049 high quality transcripts were obtained, capturing 39,995 previously mapped and 10,054 newly detected transcripts, which were annotated to 30,554 genes. A total of 158 differentially expressed genes (DEGs) were characterized in WFS shrimp. These DEGs were strongly associated with various immune related genes that regulated the expression of multiple antimicrobial peptides (e.g., antilipopolysaccharide factors, penaeidins, and crustin), which were further exper...Continue Reading

References

Nov 24, 1999·European Journal of Biochemistry·D DestoumieuxE Bachère
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Sep 1, 2009·Annual Review of Genomics and Human Genetics·Olena MorozovaMarco A Marra
Mar 10, 2010·BMC Bioinformatics·Doug HyattLoren J Hauser
Sep 8, 2010·Fish & Shellfish Immunology·Anita OrdasAnnemarie H Meijer
Sep 21, 2010·Molecular Immunology·Oliver W StockhammerHerman P Spaink
Oct 2, 2012·Current Opinion in Biotechnology·Kai-Oliver MutzFrank Stahl
Dec 4, 2012·Microbiology and Molecular Biology Reviews : MMBR·Roman Stocker, Justin R Seymour
Oct 11, 2013·Nature Biotechnology·Donald SharonMichael Snyder
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Aug 29, 2014·Bioinformatics·Leena Salmela, Eric Rivals
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Nov 11, 2014·Nature·Mark J P ChaissonEvan E Eichler
Mar 3, 2017·Journal of Fish Diseases·C-F LowB Syarul Nataqain
Mar 3, 2018·Applied Microbiology and Biotechnology·Jinbo XiongChangrong Ou
Mar 9, 2018·Applied Microbiology and Biotechnology·Dongwei HouJianguo He
Apr 22, 2018·Developmental and Comparative Immunology·Shengwen NiuXiaopeng Xu
Jul 1, 2018·Nature Communications·Martin Steinegger, Johannes Söding
Jul 10, 2018·Applied Microbiology and Biotechnology·Jinbo Xiong

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-Seq
PCA
PCR
Illumina sequencing

Software Mentioned

vegan
BBMap
LoRDEC
randomForest
BLASTN
Trimmomatic
MEGAHIT
HTSeq
SMRTlink
Prodigal

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

Applied Microbiology and Biotechnology
Dongwei HouJian-Guo He
PloS One
Tamara HersheyWashington University Wolfram Study Group
The British Journal of Occupational Therapy
Emily BumpusErin R Foster
Orphanet Journal of Rare Diseases
Allison N BischoffWashington University Wolfram Syndrome Research Group
© 2021 Meta ULC. All rights reserved