Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome

Great Abundance of Satellite DNA in Proceratophrys (Anura, Odontophrynidae) Revealed by Genome Sequencing

(2020) Marcelo J. da Silva et al.   CYTOGENETIC AND GENOME RESEARCH

Comparative cytogenetic maps of Passiflora alata and P. watsoniana (Passifloraceae) using BAC-FISH

(2020) Yhanndra Dias et al.   PLANT SYSTEMATICS AND EVOLUTION

Differential Genome Size and Repetitive DNA Evolution in Diploid Species of Melampodium sect. Melampodium (Asteraceae)

(2020) Jamie McCann et al.   Frontiers in Plant Science

High dynamism for neo-sex chromosomes: satellite DNAs reveal complex evolution in a grasshopper

(2020) Ana B. S. M. Ferretti et al.   HEREDITY

Satellitome Analysis in the Ladybird Beetle Hippodamia variegata (Coleoptera, Coccinellidae)

(2020) Pablo Mora et al.   Genes

Impact of parasitic lifestyle and different types of centromere organization on chromosome and genome evolution in the plant genus Cuscuta

(2020) Pavel Neumann et al.   NEW PHYTOLOGIST

Chromosome‐level reference genome assembly provides insights into aroma biosynthesis in passion fruit ( Passiflora edulis )

(2020) Dongna Ma et al.   Molecular Ecology Resources

The role of chromosome changes in the diversification of Passiflora L. (Passifloraceae)

(2019) Mariela A. Sader et al.   SYSTEMATICS AND BIODIVERSITY

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

(2019) Pavel Neumann et al.   Mobile DNA

Correction to: low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA

(2019) Vanessa Carvalho Cayres Pamponét et al.   BMC GENOMICS

Identification of passion fruit (Passiflora edulis) chromosomes using BAC-FISH

(2019) M. A. Sader et al.   CHROMOSOME RESEARCH

Satellitome landscape analysis of Megaleporinus macrocephalus (Teleostei, Anostomidae) reveals intense accumulation of satellite sequences on the heteromorphic sex chromosome

(2019) Ricardo Utsunomia et al.   Scientific Reports

Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis

(2019) Zirlane Portugal da Costa et al.   MOLECULAR BIOLOGY REPORTS

Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi

(2019) Tiago Ribeiro et al.   CHROMOSOME RESEARCH

Evolutionary convergence or homology? Comparative cytogenomics of Caesalpinia group species (Leguminosae) reveals diversification in the pericentromeric heterochromatic composition

(2019) Brena Van-Lume et al.   PLANTA

Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing

(2018) Laura Ávila Robledillo et al.   Scientific Reports

Tandem Repeats and Repeatomes: Delving Deeper into the ‘Dark Matter’ of Genomes

(2018) Anthony J. Hannan   EBioMedicine

OUP accepted manuscript

(2018)   ANNALS OF BOTANY

Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat

(2018) Ilya Kirov et al.   Comparative Cytogenetics

TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

(2017) Petr Novák et al.   NUCLEIC ACIDS RESEARCH

Satellite DNA: An Evolving Topic

(2017) Manuel Garrido-Ramos   Genes

Comparative repeatome analysis on Triatoma infestans Andean and Non-Andean lineages, main vector of Chagas disease

(2017) Sebastián Pita et al.   PLoS One

Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening

(2016) Ophélie Jouffroy et al.   BMC GENOMICS

Impact and insights from ancient repetitive elements in plant genomes

(2016) Florian Maumus et al.   CURRENT OPINION IN PLANT BIOLOGY

NOVOPlasty:de novoassembly of organelle genomes from whole genome data

(2016) Nicolas Dierckxsens et al.   NUCLEIC ACIDS RESEARCH

Evolutionary dynamics of satellite DNA repeats from Phaseolus beans

(2016) Tiago Ribeiro et al.   PROTOPLASMA

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

High-throughput analysis of the satellitome illuminates satellite DNA evolution

(2016) Francisco J. Ruiz-Ruano et al.   Scientific Reports

Repetitive DNA in eukaryotic genomes

(2015) Maria Assunta Biscotti et al.   CHROMOSOME RESEARCH

Completing the human genome: the progress and challenge of satellite DNA assembly

(2015) Karen H. Miga   CHROMOSOME RESEARCH

Satellite DNA in Plants: More than Just Rubbish

(2015) Manuel A. Garrido-Ramos   CYTOGENETIC AND GENOME RESEARCH

The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology

(2015) Martijn F.L. Derks et al.   Genome Biology and Evolution

An Exploration into Fern Genome Space

(2015) Paul G. Wolf et al.   Genome Biology and Evolution

De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

(2015) Clément Goubert et al.   Genome Biology and Evolution

TheSolanum commersoniiGenome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

(2015) Riccardo Aversano et al.   PLANT CELL

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

(2015) Jiří Macas et al.   PLoS One

Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms

(2014) Andreas Fleischmann et al.   ANNALS OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons

(2014) Guilherme M. Q. Cruz et al.   PLoS One

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

The holocentric speciesLuzula elegansshows interplay between centromere and large-scale genome organization

(2012) Stefan Heckmann et al.   PLANT JOURNAL

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Organisation of the plant genome in chromosomes

(2011) J. S. Pat Heslop-Harrison et al.   PLANT JOURNAL

Does Variation in Genome Sizes Reflect Adaptive or Neutral Processes? New Clues from Passiflora

(2011) Karla S. C. Yotoko et al.   PLoS One

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

(2011) Jiří Macas et al.   PLoS One

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Plant centromeric retrotransposons: a structural and cytogenetic perspective

(2011) Pavel Neumann et al.   Mobile DNA

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

The largest eukaryotic genome of them all?

(2010) JAUME PELLICER et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Cytogenetic map of common bean (Phaseolus vulgaris L.)

(2010) Artur Fonsêca et al.   CHROMOSOME RESEARCH

Role of Fluorescence in situ Hybridization in Sequencing the Tomato Genome

(2009) S.M. Stack et al.   CYTOGENETIC AND GENOME RESEARCH

Transposable Elements and Factors Influencing their Success in Eukaryotes

(2009) E. J. Pritham   JOURNAL OF HEREDITY

Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants

(2009) J. S. Hawkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE