Transposable Elements, Epigenetics, and Genome Evolution

Fedoroff, Nina V.

doi:10.1126/science.338.6108.758

Cited by 526 publications

(498 citation statements)

References 206 publications

(212 reference statements)

Supporting

Mentioning

478

Contrasting

Unclassified

Order By: Relevance

“…The underlying mechanism remains unclear, but the low frequency of 24-nucleotide sRNAs, their role in methylation of repeats and their restriction to reproductive tissues may have influenced the process. However, considering the effect of methylation patterns on recombination rates 46 and the fact that 24-nucleotide sRNAs trigger methylation, such low recombination frequencies would more likely result from hypermethylation 47 . A state of 'genome paralysis' could potentially have been triggered once an obesity threshold was reached.…”

Section: Research Articlementioning

confidence: 99%

The Norway spruce genome sequence and conifer genome evolution

Nystedt

Street

Wetterbom

et al. 2013

Nature

1,313

1,464

View full text Add to dashboard Cite

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the .100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (.10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

show abstract

Section: Research Articlementioning

confidence: 99%

The Norway spruce genome sequence and conifer genome evolution

Nystedt

Street

Wetterbom

et al. 2013

Nature

1,313

1,464

View full text Add to dashboard Cite

show abstract

“…As an example the haploid genome of Acipenser brevirostrum Lesuer, 1818 belonging to one of the most basal orders (Acipenseriformes), is 20 times greater than that found in Arothron meleagris (Anonymous, 1798) which belongs to Tetraodontiformes, the most derived teleost order. Molecular analysis suggests that this reduction is the consequence of loss of repetitive sequences and/or other non-coding DNA sequences (Neafsey & Palumbi, 2003), including satellite DNA, ribosomal genes and transposable elements (TEs) (Biémont, 2008;Fedoroff, 2012).…”

Section: Discussionmentioning

confidence: 99%

Chromosome evolution in fishes: a new challenging proposal from Neotropical species

et al. 2014

View full text Add to dashboard Cite

We present a database containing cytogenetic data of Neotropical actinopterygian fishes from Venezuela obtained in a single laboratory for the first time. The results of this study include 103 species belonging to 74 genera assigned to 45 families and 17 out of the 40 teleost orders. In the group of marine fishes, the modal diploid number was 2n=48 represented in 60% of the studied species, while in the freshwater fish group the modal diploid complement was 2n=54, represented in 21.21 % of the studied species. The average number of chromosomes and the mean FN were statistically higher in freshwater fish than in marine fish. The degree of diversification and karyotype variation was also higher in freshwater fish in contrast to a more conserved cytogenetic pattern in marine fish. In contrast to the assumption according to which 48 acrocentric chromosomes was basal chromosome number in fish, data here presented show that there is an obvious trend towards the reduction of the diploid number of chromosomes from values near 2n=60 with high number of biarmed chromosomes in more basal species to 2n=48 acrocentric elements in more derived Actinopterygii.Se presenta una base de datos que contiene los datos citogenéticos de peces Actinopterigios Neotropicales de Venezuela obtenidos por primera vez en un solo laboratorio. Los resultados de este estudio incluyen 103 especies pertenecientes a 74 géneros de 45 familias contenidas en 17 de los 40 órdenes de teleósteos. En el grupo de peces marinos, el número diploide modal fue 2n=48 representado en 60% de las especies estudiadas, mientras que en el grupo de peces de agua dulce el complemento diploide modal fue 2n=54, representado en el 21,21% de las especies estudiadas. El número de cromosomas y FN promedio fueron estadísticamente superiores en peces dulceacuícolas. El grado de diversificación y variación en el cariotipo también fue mayor en peces de agua dulce en contraste con un patrón citogenético más conservado en peces marinos. En contraposición a la suposición según la cual 48 cromosomas acrocentricos era el número cromosómico basal en los peces, los datos aquí presentados muestran que existe una evidente tendencia hacia la reducción del número de cromosomas desde valores cercanos a 2n=60 con alto número de cromosomas birrámeos en las especies más basales a 2n=48 elementos acrocéntricos en los actinopterigios más derivados.

show abstract

“…The major factors that limit de novo genome assembly are heterozygosity and repetitive sequences, such as TEs, which are often collapsed to single copies in draft genomes 1 . In recent years, however, evidence supporting the importance of TEs in genome evolution, genome structure, regulation of gene expression and epigenetics has been mounting [2][3][4][5] . The characterization of sequences and the distribution of TEs within a genome is, therefore, of great importance.…”

mentioning

confidence: 99%

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

et al. 2017

View full text Add to dashboard Cite

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

show abstract

Transposable Elements, Epigenetics, and Genome Evolution

Cited by 526 publications

References 206 publications

The Norway spruce genome sequence and conifer genome evolution

The Norway spruce genome sequence and conifer genome evolution

Chromosome evolution in fishes: a new challenging proposal from Neotropical species

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Contact Info

Product

Resources

About