Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium

G3 : Genes - Genomes - Genetics
Alexander Q WixomAllan B Caplan

Abstract

Solanum sisymbriifolium, also known as "Litchi Tomato" or "Sticky Nightshade," is an undomesticated and poorly researched plant related to potato and tomato. Unlike the latter species, S. sisymbriifolium induces eggs of the cyst nematode, Globodera pallida, to hatch and migrate into its roots, but then arrests further nematode maturation. In order to provide researchers with a partial blueprint of its genetic make-up so that the mechanism of this response might be identified, we used single molecule real time (SMRT) sequencing to compile a high quality de novo transcriptome of 41,189 unigenes drawn from individually sequenced bud, root, stem, and leaf RNA populations. Functional annotation and BUSCO analysis showed that this transcriptome was surprisingly complete, even though it represented genes expressed at a single time point. By sequencing the 4 organ libraries separately, we found we could get a reliable snapshot of transcript distributions in each organ. A divergent site analysis of the merged transcriptome indicated that this species might have undergone a recent genome duplication and re-diploidization. Further analysis indicated that the plant then retained a disproportionate number of genes associated with photosynth...Continue Reading

References

Jan 27, 1999·Bioinformatics·S R Eddy
Sep 4, 2003·Genome Research·Li LiDavid S Roos
Nov 17, 2006·Nature·Jonathan D G Jones, Jeffery L Dangl
Sep 15, 2007·Nature Protocols·Jaroslav DolezelJan Suda
Nov 28, 2007·Nucleic Acids Research·Robert D FinnAlex Bateman
Nov 22, 2008·Science·John EidStephen Turner
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Nov 19, 2009·Nucleic Acids Research·Robert D FinnAlex Bateman
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Apr 24, 2012·Nature Biotechnology·Nicholas J LomanMark J Pallen
Jan 1, 2011·Frontiers in Plant Science·Stephen A GoffDan Stanzione
May 16, 2013·BMC Genomics·Ya Yang, Stephen A Smith
Jun 27, 2013·Genome Biology·Ksenia V KrasilevaJorge Dubcovsky
Jul 11, 2013·Evidence-based Complementary and Alternative Medicine : ECAM·Valdir Cechinel FilhoAngela Malheiros
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov
Sep 12, 2015·IEEE Transactions on Visualization and Computer Graphics·Alexander LexHanspeter Pfister
Jan 23, 2016·Frontiers in Genetics·Joanna MoretonRichard D Emes
May 18, 2017·Journal of Nematology·N Carol CasavantLouise-Marie Dandurand

❮ Previous
Next ❯

Citations

Oct 6, 2020·The Plant Genome·Alexander Q WixomAllan B Caplan

❮ Previous
Next ❯

Datasets Mentioned

BETA
DQ38616.2
GGFC00000000

Methods Mentioned

BETA
transgenic
RNA-seq
PCR
flow cytometry
454 sequencing

Software Mentioned

HIT
SMRT Analysis
Python scripts
Freebayes
Trimmomatic
Transcriptome
DNA Strider
BLAST CUTOFF
house
EST

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.