Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions

Frontiers in Plant Science
Renata de Castro NunesRomain Guyot

Abstract

Centromeric regions of plants are generally composed of large array of satellites from a specific lineage of Gypsy LTR-retrotransposons, called Centromeric Retrotransposons. Repeated sequences interact with a specific H3 histone, playing a crucial function on kinetochore formation. To study the structure and composition of centromeric regions in the genus Coffea, we annotated and classified Centromeric Retrotransposons sequences from the allotetraploid C. arabica genome and its two diploid ancestors: Coffea canephora and C. eugenioides. Ten distinct CRC (Centromeric Retrotransposons in Coffea) families were found. The sequence mapping and FISH experiments of CRC Reverse Transcriptase domains in C. canephora, C. eugenioides, and C. arabica clearly indicate a strong and specific targeting mainly onto proximal chromosome regions, which can be associated also with heterochromatin. PacBio genome sequence analyses of putative centromeric regions on C. arabica and C. canephora chromosomes showed an exceptional density of one family of CRC elements, and the complete absence of satellite arrays, contrasting with usual structure of plant centromeres. Altogether, our data suggest a specific centromere organization in Coffea, contrasting w...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Sep 10, 1998·Nature Genetics·P SanMiguelJ L Bennetzen
Apr 2, 1999·Molecular & General Genetics : MGG·P LashermesA Charrier
Dec 20, 2000·Bioinformatics·K RutherfordB Barrell
Nov 22, 2001·Proceedings of the National Academy of Sciences of the United States of America·C P WitteA Kumar
Feb 14, 2003·Bioinformatics·Eugene M McCarthy, John F McDonald
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
May 5, 2004·Genome Research·Ewan BirneyRichard Durbin
Jul 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jianxin Ma, Jeffrey L Bennetzen
Dec 24, 2004·Molecular Biology and Evolution·Kiyotaka NagakiJiming Jiang
Feb 8, 2006·Molecular Genetics and Genomics : MGG·Weidong BaoZhukuan Cheng
Feb 13, 2007·Current Opinion in Plant Biology·Jeffrey L Bennetzen
Nov 7, 2007·Nature Reviews. Genetics·Thomas WickerAlan H Schulman
Feb 8, 2008·Genome Research·Xiang GaoDaniel F Voytas
Jun 11, 2009·Communicative & Integrative Biology·Olga Novikova
Nov 4, 2009·Biology Direct·Carlos LlorensAndrés Moya
Dec 8, 2009·Science·Patrick S SchnableRichard K Wilson
Dec 17, 2009·The New Phytologist·Christian ParisodMarie-Angèle Grandbastien
Nov 3, 2010·Nucleic Acids Research·Carlos LlorensAndres Moya
Feb 8, 2011·Genome Biology and Evolution·Maud I TenaillonJeffrey Ross-Ibarra
Mar 30, 2011·The Plant Journal : for Cell and Molecular Biology·J S Pat Heslop-Harrison, Trude Schwarzacher
Jul 13, 2011·Proceedings of the National Academy of Sciences of the United States of America·Maryam SaneiAndreas Houben
Dec 21, 2012·The Plant Journal : for Cell and Molecular Biology·Baochun LiXueyong Zhang
Mar 4, 2014·Annual Review of Plant Biology·Jeffrey L Bennetzen, Hao Wang
May 13, 2014·Genome Biology and Evolution·Anupma Sharma, Gernot G Presting
Aug 3, 2014·Biochimica Et Biophysica Acta·Marie-Angèle Grandbastien
Jul 16, 2015·Molecular Biology and Evolution·Walter SanseverinoJosep Maria Casacuberta
Sep 21, 2015·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Fabíola Carvalho SantosAndré Luís Laforga Vanzela
Oct 23, 2015·Proceedings of the National Academy of Sciences of the United States of America·André MarquesAndreas Houben
May 8, 2016·BMC Bioinformatics·Sébastien GuizardYves Bigot
Mar 21, 2017·Molecular Genetics and Genomics : MGG·Mathilde DupeyronRomain Guyot

❮ Previous
Next ❯

Citations

Aug 9, 2019·International Journal of Molecular Sciences·Simon Orozco-AriasRomain Guyot
Nov 3, 2021·Genome Génome / Conseil National De Recherches Canada·Leonardo Adabo CintraAndré Luís Laforga Vanzela

❮ Previous
Next ❯

Datasets Mentioned

BETA
MG242426
MG242429
MG242430
MG242431
G
MG242432
Y
MG242434
X
MG242435

Methods Mentioned

BETA
Hi-C
PCR
electrophoresis
immunoprecipitation

Software Mentioned

Censor
Genewise
BLASTX
FigTree
BLAST
Mauve
DensityMap
ClustalW
STRUC
EMBOSS

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.

© 2022 Meta ULC. All rights reserved