The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots

Frontiers in Plant Science
Nanette ChristieCarsten Külheim

Abstract

Eucalyptus grandis is a commercially important hardwood species and is known to be susceptible to a number of pests and pathogens. Determining mechanisms of defense is therefore a research priority. The published genome for E. grandis has aided the identification of one important class of resistance (R) genes that incorporate nucleotide binding sites and leucine-rich repeat domains (NBS-LRR). Using an iterative search process we identified NBS-LRR gene models within the E. grandis genome. We characterized the gene models and identified their genomic arrangement. The gene expression patterns were examined in E. grandis clones, challenged with a fungal pathogen (Chrysoporthe austroafricana) and insect pest (Leptocybe invasa). One thousand two hundred and fifteen putative NBS-LRR coding sequences were located which aligned into two large classes, Toll or interleukin-1 receptor (TIR) and coiled-coil (CC) based on NB-ARC domains. NBS-LRR gene-rich regions were identified with 76% organized in clusters of three or more genes. A further 272 putative incomplete resistance genes were also identified. We determined that E. grandis has a higher ratio of TIR to CC classed genes compared to other woody plant species as well as a smaller per...Continue Reading

References

May 24, 1991·Science·A LupasJ Stock
Jun 30, 2000·Current Opinion in Plant Biology·J EllisT Pryor
Jul 4, 2001·Nature Reviews. Genetics·E B Holub
Dec 18, 2001·Plant Physiology·R Fluhr
May 16, 2002·The Journal of Heredity·R E Voorrips
Oct 12, 2002·Glycoconjugate Journal·H Rüdiger, H J Gabius
Apr 3, 2003·The Plant Cell·Blake C MeyersRichard W Michelmore
May 29, 2004·The Plant Journal : for Cell and Molecular Biology·Eva SinapidouJim Beynon
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
Dec 1, 2005·Bioinformatics·A V McDonnellB Berger
Feb 21, 2006·Plant Physiology·Wladimir I L TamelingFrank L W Takken
May 9, 2006·Genome Biology·Leah McHaleRichard W Michelmore
May 30, 2006·Proceedings of the National Academy of Sciences of the United States of America·Peter N DoddsJeffrey G Ellis
Nov 17, 2006·Nature·Jonathan D G Jones, Jeffery L Dangl
Nov 18, 2006·Nature Immunology·Brody J DeYoung, Roger W Innes
May 30, 1980·Science·P E Kolattukudy
Oct 19, 2007·Current Opinion in Genetics & Development·Aaron R Friedman, Barbara J Baker
Dec 15, 2007·Journal of Experimental Botany·Luis A J MurElena Prats
Feb 6, 2008·Plant Molecular Biology·Annegret KohlerFrancis Martin
Apr 9, 2008·Journal of Experimental Botany·Gerben van OoijenFrank L W Takken
May 10, 2008·PLoS Pathogens·Petra M HoutermanMartijn Rep
Aug 30, 2008·The Plant Cell·Renier A L van der Hoorn, Sophien Kamoun
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Sep 30, 2009·BMC Research Notes·D Ellen K Tarr, Helen M Alexander
Jan 14, 2010·Current Protocols in Molecular Biology·Daniel BlankenbergJames Taylor
Nov 23, 2010·The New Phytologist·Hugo Germain, Armand Séguin
Dec 28, 2010·Nature Genetics·Xavier ArgoutClaire Lanaud
Mar 18, 2011·Genome Biology·Adam RobertsLior Pachter
Jul 5, 2011·Current Opinion in Plant Biology·Maud BernouxPeter N Dodds
Nov 24, 2011·Nucleic Acids Research·David M GoodsteinDaniel S Rokhsar
Jun 5, 2012·Nature·UNKNOWN Tomato Genome Consortium
Jun 14, 2012·Comparative and Functional Genomics·Shenglong Tan, Song Wu
Jun 19, 2012·Current Opinion in Plant Biology·Jacqueline Monaghan, Cyril Zipfel

❮ Previous
Next ❯

Citations

Feb 23, 2017·Annual Review of Plant Biology·David B NealeXiao-Xin Wei
Jun 6, 2018·International Journal of Molecular Sciences·Grazia M BorrelliAnna M Mastrangelo
Aug 8, 2018·BMC Plant Biology·Ana Paula Zotta MotaPatricia Messenberg Guimaraes
Feb 23, 2018·Scientific Reports·Jose V DieLisa J Rowland
Jan 9, 2019·Frontiers in Plant Science·Gerald A TuskanJoshua K Michener
May 26, 2018·The Plant Journal : for Cell and Molecular Biology·Andrew FunkJ Mitchell McGrath
Nov 17, 2020·Frontiers in Plant Science·Andrés J CortésLarry E Bedoya-Canas
Mar 12, 2021·Plant Cell Reports·Ervin D NagyRobert T Gaeta
Sep 28, 2021·Frontiers in Plant Science·Tinggang LiNikhilesh Dhar

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA305347

Methods Mentioned

BETA
RNA-Seq

Software Mentioned

Bowtie
Tophat
gplots
Galaxy
Basic Local Alignment Search Tool ( BLAST )
HMMER
Circos
GenStat
Mapchart
ClustalW

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.