Cargando…

Genomic Repeat Abundances Contain Phylogenetic Signal

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generat...

Descripción completa

Detalles Bibliográficos
Autores principales:	Dodsworth, Steven, Chase, Mark W., Kelly, Laura J., Leitch, Ilia J., Macas, Jiří, Novák, Petr, Piednoël, Mathieu, Weiss-Schneeweiss, Hanna, Leitch, Andrew R.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2015
Materias:	Regular Articles
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265144/ https://www.ncbi.nlm.nih.gov/pubmed/25261464 http://dx.doi.org/10.1093/sysbio/syu080

Ejemplares similares

Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)
por: Dodsworth, Steven, et al.
Publicado: (2016)

The ecology of palm genomes: repeat‐associated genome size expansion is constrained by aridity
por: Schley, Rowan J., et al.
Publicado: (2022)

Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae)
por: Mccann, Jamie, et al.
Publicado: (2018)

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae
por: Macas, Jiří, et al.
Publicado: (2015)

The Role of Chromatin Modifications in the Evolution of Giant Plant Genomes
por: Leitch, Andrew R., et al.
Publicado: (2023)

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size
por: Kelly, Laura J., et al.
Publicado: (2015)

Genome Size Diversity and Its Impact on the Evolution of Land Plants
por: Pellicer, Jaume, et al.
Publicado: (2018)

Independent, Rapid and Targeted Loss of Highly Repetitive DNA in Natural and Synthetic Allopolyploids of Nicotiana tabacum
por: Renny-Byfield, Simon, et al.
Publicado: (2012)

Repetitive DNA Restructuring Across Multiple Nicotiana Allopolyploidisation Events Shows a Lack of Strong Cytoplasmic Bias in Influencing Repeat Turnover
por: Dodsworth, Steven, et al.
Publicado: (2020)

Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae)
por: Emadzade, Khatere, et al.
Publicado: (2014)

Differential Genome Size and Repetitive DNA Evolution in Diploid Species of Melampodium sect. Melampodium (Asteraceae)
por: McCann, Jamie, et al.
Publicado: (2020)

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification
por: Neumann, Pavel, et al.
Publicado: (2019)

Mega‐sized pericentromeric blocks of simple telomeric repeats and their variants reveal patterns of chromosome evolution in ancient Cycadales genomes
por: Vozárová, Radka, et al.
Publicado: (2022)

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae
por: Novák, Petr, et al.
Publicado: (2014)

Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats
por: Vondrak, Tihana, et al.
Publicado: (2019)

Multiple Origins and Nested Cycles of Hybridization Result in High Tetraploid Diversity in the Monocot Prospero
por: Jang, Tae-Soo, et al.
Publicado: (2018)

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering
por: Johnson, Matthew G, et al.
Publicado: (2019)

Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations
por: Kobert, K., et al.
Publicado: (2017)

Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
por: Lee, Yung-I, et al.
Publicado: (2018)

Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway
por: Ma, Lu, et al.
Publicado: (2015)

The Dark Matter of Large Cereal Genomes: Long Tandem Repeats
por: Kapustová, Veronika, et al.
Publicado: (2019)

Chromosomal diversification and karyotype evolution of diploids in the cytologically diverse genus Prospero (Hyacinthaceae)
por: Jang, Tae-Soo, et al.
Publicado: (2013)

Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome
por: Torres, Giovana A., et al.
Publicado: (2011)

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
por: Novák, Petr, et al.
Publicado: (2010)

Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids
por: Matyášek, Roman, et al.
Publicado: (2012)

Giant Fern Genomes Show Complex Evolution Patterns: A Comparative Analysis in Two Species of Tmesipteris (Psilotaceae)
por: Fernández, Pol, et al.
Publicado: (2023)

Phylogenetic distribution, biogeography and the effects of land management upon bacterial non-specific Acid phosphatase Gene diversity and abundance
por: Neal, Andrew L., et al.
Publicado: (2017)

Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb
por: Wang, Wencai, et al.
Publicado: (2015)

Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms
por: Wang, Wencai, et al.
Publicado: (2019)

The genome sequence of the tree of heaven, Ailanthus altissima (Mill.) Swingle, 1916
por: Schley, Rowan J., et al.
Publicado: (2023)

Molecular and karyological data confirm that the enigmatic genus Platypholis from Bonin-Islands (SE Japan) is phylogenetically nested within Orobanche (Orobanchaceae)
por: Li, Xi, et al.
Publicado: (2016)

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life
por: Baker, William J, et al.
Publicado: (2021)

Genome Insights into Autopolyploid Evolution: A Case Study in Senecio doronicum (Asteraceae) from the Southern Alps
por: Fernández, Pol, et al.
Publicado: (2022)

Survey of extrachromosomal circular DNA derived from plant satellite repeats
por: Navrátilová, Alice, et al.
Publicado: (2008)

Genome size and ploidy influence angiosperm species' biomass under nitrogen and phosphorus limitation
por: Guignard, Maïté S., et al.
Publicado: (2016)

Salix transect of Europe: variation in ploidy and genome size in willow-associated common nettle, Urtica dioica L. sens. lat., from Greece to arctic Norway
por: Cronk, Quentin, et al.
Publicado: (2016)

First Whole-Genome Sequence and Flow Cytometry Genome Size Data for the Lichen-Forming Fungus Ramalina farinacea (Ascomycota)
por: Llewellyn, Theo, et al.
Publicado: (2023)

DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms
por: Piednoël, Mathieu, et al.
Publicado: (2009)

Genome size expansion and the relationship between nuclear DNA content and spore size in the Asplenium monanthes fern complex (Aspleniaceae)
por: Dyer, Robert J, et al.
Publicado: (2013)

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)
por: McCann, Jamie, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_div5o9epubre8lvfql3s6413p0