Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.

PLoS Genetics
Regina S BaucomJeffrey L Bennetzen

Abstract

Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelemen...Continue Reading

References

Feb 9, 1978·Nature·W Gilbert
Feb 1, 1990·Theoretical Population Biology·Z B Zeng, C C Cockerham
Jan 1, 1984·Molecular & General Genetics : MGG·J P MottingerM Freeling
Feb 1, 1993·Molecular & General Genetics : MGG·P R Leeton, D R Smyth
May 20, 1994·Cell·T E BureauS R Wessler
Jul 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·Y YoshiokaY Machida
Dec 1, 1995·Current Opinion in Genetics & Development·S R WesslerS E White
Nov 1, 1996·Science·P SanMiguelJ L Bennetzen
Dec 1, 1996·Computer Applications in the Biosciences : CABIOS·N GaltierC Gautier
Sep 10, 1998·Nature Genetics·P SanMiguelJ L Bennetzen
Jun 23, 1999·Proceedings of the National Academy of Sciences of the United States of America·A P TikhonovZ Avramova
Dec 6, 2000·Genome Biology·J L Bennetzen
May 22, 2001·Molecular Genetics and Genomics : MGG·M YamazakiH Hirochika
Jul 12, 2001·Proceedings of the National Academy of Sciences of the United States of America·V V Kapitonov, J Jurka
Jul 24, 2001·Briefings in Bioinformatics·I B RogozinL R Adkison
Dec 26, 2001·Bioinformatics·H H Chou, M H Holmes
Apr 6, 2002·Bioinformatics·Heiko A SchmidtArndt von Haeseler
May 22, 2002·Functional & Integrative Genomics·Phillip J SanMiguelJorge Dubcovsky
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Huihua Fu, Hugo K Dooner
Jul 3, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey L Bennetzen, Wusirika Ramakrishna
Oct 9, 2002·Genome Research·Prescott L Deininger, Mark A Batzer
Feb 14, 2003·Bioinformatics·Eugene M McCarthy, John F McDonald
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jul 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jianxin Ma, Jeffrey L Bennetzen
Jan 22, 2005·The Plant Cell·Stephan BrunnerAntoni Rafalski
May 21, 2005·Annals of Botany·B J M ZonneveldM D Bennett
Oct 13, 2005·Current Opinion in Genetics & Development·Jeffrey L Bennetzen
Dec 14, 2005·International Review of Cytology·Dimitri A Kramerov, Nikita S Vassetzky
Dec 31, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jianxin Ma, Jeffrey L Bennetzen
Feb 1, 1948·Proceedings of the National Academy of Sciences of the United States of America·H Roman
Nov 15, 2006·Proceedings of the National Academy of Sciences of the United States of America·Clémentine Vitte, Jeffrey L Bennetzen
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Jul 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·Renyi LiuJeffrey L Bennetzen

❮ Previous
Next ❯

Citations

Aug 29, 2013·International Journal of Evolutionary Biology·Kazuhiko Ohshima
Dec 21, 2013·Science·UNKNOWN Amborella Genome Project
May 13, 2014·Genome Biology and Evolution·Anupma Sharma, Gernot G Presting
Mar 4, 2014·Annual Review of Plant Biology·Jeffrey L Bennetzen, Hao Wang
Jul 19, 2014·Science·Frédéric ChouletCatherine Feuillet
Nov 26, 2009·PLoS Genetics·Fusheng WeiRod A Wing
Nov 26, 2009·PLoS Genetics·Virginia Walbot
Jan 14, 2010·BMC Biology·Eugene V Koonin
Nov 10, 2010·PLoS Genetics·Mireille Tittel-ElmerIsabelle Vaillant
Dec 28, 2010·Nature Genetics·Vladimir ShulaevKevin M Folta
Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·James C SchnableMichael Freeling
Jan 11, 2012·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Peter J FranksDavid J Beerling
May 23, 2012·International Journal of Plant Genomics·Anton NovikovOlga Novikova
Jun 8, 2012·Molecular Biology and Evolution·Kazuhiko Ohshima
Mar 5, 2013·Mobile DNA·Alexandros Bousios, Nikos Darzentas
Nov 15, 2011·BMC Genomics·Wenxuan LiuDaniel G Peterson
May 2, 2012·BMC Genomics·Alexandros BousiosNikos Darzentas
Aug 21, 2010·Genome Génome / Conseil National De Recherches Canada·Guanjing HuJonathan F Wendel
May 17, 2012·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Debbie M Figueroa, Hank W Bass
Sep 26, 2012·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Ching Man WaiQingyi Yu
Aug 11, 2010·Bioinformatics·N DarzentasA S Tsaftaris
May 15, 2012·Nature Biotechnology·Jeffrey L BennetzenKatrien M Devos
Feb 8, 2011·Genome Biology and Evolution·Maud I TenaillonJeffrey Ross-Ibarra
Jan 26, 2012·Genome Biology and Evolution·James C SchnableEric Lyons
Apr 19, 2013·Genome Biology and Evolution·Natacha SenerchiaChristian Parisod
Dec 29, 2015·Biochimica Et Biophysica Acta·Dongyan ZhaoNing Jiang
Feb 11, 2016·Molecular Genetics and Genomics : MGG·Guilherme ValenteCesar Martins
Dec 18, 2015·The Plant Journal : for Cell and Molecular Biology·Katrin SchwichtenbergThomas Schmidt

❮ Previous
Next ❯

Methods Mentioned

BETA
gypsy
clone-by-clone sequencing

Software Mentioned

LTR
MULEs
BLASTn
Seaview
SE
blast
Resample
PHYLIP
Perl
GeneTrek

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.