De novo construction of an expanded transcriptome assembly for the western tarnished plant bug, Lygus hesperus

GigaScience
Erica E TassoneJ Joe Hull

Abstract

The plant bug Lygus hesperus Knight is a polyphagous pest of many economically important crops. Despite its pest status, little is known about the molecular mechanisms responsible for much of the biology of this species. Earlier Lygus transcriptome assemblies were limited by low read depth, or because they focused on specific conditions. To generate a more comprehensive transcriptome, we supplemented previous datasets with new reads corresponding to specific tissues (heads, antennae, and male reproductive tissues). This transcriptome augments current Lygus molecular resources and provides the foundational knowledge critical for future comparative studies. An expanded, Trinity-based de novo transcriptome assembly for L. hesperus was generated using previously published whole body Illumina data, supplemented with 293 million bp of new raw sequencing data corresponding to five tissue-specific cDNA libraries and 11 Illumina sequencing runs. The updated transcriptome consists of 22,022 transcripts (average length of 2075 nt), 62 % of which contain complete open reading frames. Significant coverage of the BUSCO (benchmarking universal single-copy orthologs) dataset and robust metrics indicate that the transcriptome is a quality assem...Continue Reading

References

Dec 3, 2011·Nucleic Acids Research·Karine MegyUNKNOWN VectorBase Consortium
Dec 18, 2013·Journal of Insect Physiology·Colin S Brent, J Joe Hull
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
May 25, 2015·Insect Biochemistry and Molecular Biology·Jose Manuel Latorre-EstivalisMarcelo Gustavo Lorenzo
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov

❮ Previous
Next ❯

Citations

Mar 23, 2017·GigaScience·Erica E TassoneS J Castle
Feb 15, 2017·BMC Biology·Tomáš PánekMarek Eliáš
Dec 28, 2018·Archives of Insect Biochemistry and Physiology·Colin S Brent, J Joe Hull
Nov 14, 2018·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Jantina ToxopeusBrent J Sinclair
Mar 3, 2020·Journal of Insect Physiology·J Joe HullColin S Brent
May 12, 2021·Journal of Insect Science·Omaththage P PereraGordon L Snodgrass

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRX483877
SRX484042
PRJNA284294

Software Mentioned

FastQC
tBLASTx
Transvestigator
Trimmomatic
Trinity
RSEM
BLASTp
BUSCO
InterProScan5
Transdecoder

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.