Impact of transposable elements on polyploid plant genomes

CM Vicient, JM Casacuberta - Annals of Botany, 2017 - academic.oup.com
Background The growing wealth of knowledge on whole-plant genome sequences is
highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of …

Oleoresin defenses in conifers: chemical diversity, terpene synthases and limitations of oleoresin defense under climate change

JM Celedon, J Bohlmann - New Phytologist, 2019 - Wiley Online Library
Conifers have evolved complex oleoresin terpene defenses against herbivores and
pathogens. In co‐evolved bark beetles, conifer terpenes also serve chemo‐ecological …

Dynamic genome evolution in a model fern

DB Marchant, G Chen, S Cai, F Chen, P Schafran… - Nature Plants, 2022 - nature.com
The large size and complexity of most fern genomes have hampered efforts to elucidate
fundamental aspects of fern biology and land plant evolution through genome-enabled …

Genome annotation and curation using MAKER and MAKER‐P

MS Campbell, C Holt, B Moore… - Current protocols in …, 2014 - Wiley Online Library
This unit describes how to use the genome annotation and curation tools MAKER and
MAKER‐P to annotate protein‐coding and noncoding RNA genes in newly assembled …

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

DB Neale, JL Wegrzyn, KA Stevens, AV Zimin, D Puiu… - Genome biology, 2014 - Springer
Background The size and complexity of conifer genomes has, until now, prevented full
genome sequencing and assembly. The large research community and economic …

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

TA Elliott, TR Gregory - … of the Royal Society B: Biological …, 2015 - royalsocietypublishing.org
Some notable exceptions aside, eukaryotic genomes are distinguished from those of
Bacteria and Archaea in a number of ways, including chromosome structure and number …

Sequencing and assembly of the 22-Gb loblolly pine genome

A Zimin, KA Stevens, MW Crepeau, A Holtz-Morris… - Genetics, 2014 - academic.oup.com
Conifers are the predominant gymnosperm. The size and complexity of their genomes has
presented formidable technical challenges for whole-genome shotgun sequencing and …

Draft genome of the living fossil Ginkgo biloba

R Guan, Y Zhao, HE Zhang, G Fan, X Liu, W Zhou… - …, 2016 - academic.oup.com
Abstract Background Ginkgo biloba L.(Ginkgoaceae) is one of the most distinctive plants. It
possesses a suite of fascinating characteristics including a large genome, outstanding …

The plant genome integrative explorer resource: PlantGenIE. org

D Sundell, C Mannapperuma, S Netotea, N Delhomme… - 2015 - JSTOR
Accessing and exploring large-scale genomics data sets remains a significant challenge to
researchers without specialist bioinformatics training. We present the integrated PlantGenIE …

Next generation sequencing technologies: the doorway to the unexplored genomics of non-model plants

CIN Unamba, A Nag, RK Sharma - Frontiers in plant science, 2015 - frontiersin.org
Non-model plants ie, the species which have one or all of the characters such as long life
cycle, difficulty to grow in the laboratory or poor fecundity, have been schemed out of …