Plant genome and transcriptome annotations: from misconceptions to simple solutions

ME Bolger, B Arsova, B Usadel - Briefings in bioinformatics, 2018 - academic.oup.com
Next-generation sequencing has triggered an explosion of available genomic and
transcriptomic resources in the plant sciences. Although genome and transcriptome …

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

K Vanneste, G Baele, S Maere… - Genome research, 2014 - genome.cshlp.org
Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations,
have been reported in most evolutionary lineages. Their attributed role remains a major …

AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula

D Sundell, NR Street, M Kumar, EJ Mellerowicz… - The Plant …, 2017 - academic.oup.com
Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose.
There is significant scope for yield and quality improvement in these largely undomesticated …

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

JL Olsen, P Rouzé, B Verhelst, YC Lin, T Bayer… - Nature, 2016 - nature.com
Seagrasses colonized the sea on at least three independent occasions to form the basis of
one of the most productive and widespread coastal ecosystems on the planet. Here we …

[HTML][HTML] Insights into the evolution of multicellularity from the sea lettuce genome

O De Clerck, SM Kao, KA Bogaert, J Blomme… - Current biology, 2018 - cell.com
We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva
mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds …

Characterization of Genetic Diversity in the Nematode Pristionchus pacificus from Population-Scale Resequencing Data

C Rödelsperger, RA Neher, AM Weller, G Eberhardt… - Genetics, 2014 - academic.oup.com
The hermaphroditic nematode Pristionchus pacificus is an established model system for
comparative studies with Caenorhabditis elegans in developmental biology, ecology, and …

Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

Y Yang, MJ Moore, SF Brockington… - Molecular biology …, 2015 - academic.oup.com
Many phylogenomic studies based on transcriptomes have been limited to “single-copy”
genes due to methodological challenges in homology and orthology inferences. Only a …

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

A Del Cortona, CJ Jackson, F Bucchini… - Proceedings of the …, 2020 - pnas.org
The Neoproterozoic Era records the transition from a largely bacterial to a predominantly
eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems …

Articulating “archiannelids”: Phylogenomics and annelid relationships, with emphasis on meiofaunal taxa

SCS Andrade, M Novo, GY Kawauchi… - Molecular Biology …, 2015 - academic.oup.com
Annelid disparity has resulted in morphological-based classifications that disagree with
phylogenies based on Sanger sequencing and phylogenomic analyses. However, the data …

Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates

JD Hackett, JH Wisecaver… - Molecular biology …, 2013 - academic.oup.com
Dinoflagellates produce a variety of toxic secondary metabolites that have a significant
impact on marine ecosystems and fisheries. Saxitoxin (STX), the cause of paralytic shellfish …