Computational tools to unmask transposable elements
P Goerner-Potvin, G Bourque - Nature Reviews Genetics, 2018 - nature.com
A substantial proportion of the genome of many species is derived from transposable
elements (TEs). Moreover, through various self-copying mechanisms, TEs continue to …
elements (TEs). Moreover, through various self-copying mechanisms, TEs continue to …
[HTML][HTML] Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
Background Sequencing technology and assembly algorithms have matured to the point
that high-quality de novo assembly is possible for large, repetitive genomes. Current …
that high-quality de novo assembly is possible for large, repetitive genomes. Current …
The impact of transposable elements on the structure, evolution and function of the rice genome
R Akakpo, MC Carpentier, Y Ie Hsing… - New …, 2020 - Wiley Online Library
Transposable elements (TEs) are ubiquitous in plants and are the primary genomic
component of the majority of taxa. Knowledge of their impact on the structure, function and …
component of the majority of taxa. Knowledge of their impact on the structure, function and …
[HTML][HTML] Rice Gene Index: a comprehensive pan-genome database for comparative and functional genomics of Asian rice
Asian rice (Oryza sativa) is the staple food for half the world and is a model crop that has
been extensively studied. It contributes $20% of calories to the human diet (Stein et al …
been extensively studied. It contributes $20% of calories to the human diet (Stein et al …
Structural variants in 3000 rice genomes
Investigation of large structural variants (SVs) is a challenging yet important task in
understanding trait differences in highly repetitive genomes. Combining different …
understanding trait differences in highly repetitive genomes. Combining different …
[HTML][HTML] Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution
The ultimate goal of genome assembly is a high-accuracy gapless genome. Here, we report
a new assembly pipeline that is used to produce a gapless genome for the indica rice …
a new assembly pipeline that is used to produce a gapless genome for the indica rice …
[HTML][HTML] Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice
Background The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many
iconic varieties and is widespread in the Indian subcontinent. Despite its economic and …
iconic varieties and is widespread in the Indian subcontinent. Despite its economic and …
[HTML][HTML] Retrotranspositional landscape of Asian rice revealed by 3000 genomes
MC Carpentier, E Manfroi, FJ Wei, HP Wu… - Nature …, 2019 - nature.com
The recent release of genomic sequences for 3000 rice varieties provides access to the
genetic diversity at species level for this crop. We take advantage of this resource to unravel …
genetic diversity at species level for this crop. We take advantage of this resource to unravel …
[HTML][HTML] Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions
Background The plant immune system is innate and encoded in the germline. Using it
efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens …
efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens …
Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti
Few clades of plants have proven as difficult to classify as cacti. One explanation may be an
unusually high level of convergent and parallel evolution (homoplasy). To evaluate support …
unusually high level of convergent and parallel evolution (homoplasy). To evaluate support …