Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

(2013) Moaine El Baidouri et al.   Genome Biology and Evolution

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

(2012) P. Roxanne Steele et al.   AMERICAN JOURNAL OF BOTANY

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

(2012) Michael R. McKain et al.   AMERICAN JOURNAL OF BOTANY

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae

(2012) Mathieu Piednoël et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ty1-Copia retrotransposons are heterogeneous, extremely high copy number and are major players in the genome organization and evolution of Agave tequilana

(2011) Ishtiaq Khaliq et al.   GENETIC RESOURCES AND CROP EVOLUTION

Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians

(2011) Maud I. Tenaillon et al.   Genome Biology and Evolution

Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs

(2011) S. Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies

(2010) Kateřina Ambrožová et al.   ANNALS OF BOTANY

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

A triptych of the evolution of plant transposable elements

(2010) Maud I. Tenaillon et al.   TRENDS IN PLANT SCIENCE

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

A shotgun approach to discovering and reconstructing consensus retrotransposons ex novo from dense contigs of short sequences derived from Genbank Genome Survey Sequence database records

(2009) Howard M. Laten et al.   GENE

Evolution of Genome Size and Complexity in Pinus

(2009) Alison M. Morse et al.   PLoS One

Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm

(2008) Jeremy D DeBarry et al.   BMC BIOINFORMATICS

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

(2008) Thomas Wicker et al.   BMC GENOMICS

Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium

(2008) Jennifer S. Hawkins et al.   GENOME

Repeated big bangs and the expanding universe: Directionality in plant genome size evolution

(2008) Jennifer S. Hawkins et al.   PLANT SCIENCE