Designing a transcriptome next‐generation sequencing project for a nonmodel plant species1

SR Strickler, A Bombarely… - American journal of …, 2012 - Wiley Online Library
The application of next‐generation sequencing (NGS) to transcriptomics, commonly called
RNA‐seq, allows the nearly complete characterization of transcriptomic events occurring in …

Catalyzing plant science research with RNA-seq

LBB Martin, Z Fei, JJ Giovannoni… - Frontiers in plant …, 2013 - frontiersin.org
Next generation DNA sequencing technologies are driving increasingly rapid, affordable
and high resolution analyses of plant transcriptomes through sequencing of their associated …

Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution

A Karlgren, N Gyllenstrand, T Källman… - Plant …, 2011 - academic.oup.com
The phosphatidyl ethanolamine-binding protein (PEBP) gene family is present in all
eukaryote kingdoms, with three subfamilies identified in angiosperms (FLOWERING LOCUS …

The evolutionary history of ferns inferred from 25 low‐copy nuclear genes

CJ Rothfels, FW Li, EM Sigel, L Huiet… - American Journal of …, 2015 - Wiley Online Library
• Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary
timescale is critical for broad investigations of the evolution of land plants, and for providing …

Transcriptome Analysis and SSR/SNP Markers Information of the Blunt Snout Bream (Megalobrama amblycephala)

Z Gao, W Luo, H Liu, C Zeng, X Liu, S Yi, W Wang - 2012 - journals.plos.org
Background Blunt snout bream (Megalobrama amblycephala) is an herbivorous freshwater
fish species native to China and has been recognized as a main aquaculture species in the …

Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic

XY Du, JM Lu, LB Zhang, J Wen, LY Kuo… - …, 2021 - Wiley Online Library
Comprising about 82% of the extant fern species diversity, Polypodiales are generally
believed to have diversified in the Late Cretaceous. We estimated the divergence times of …

Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty

Z Yang, EK Wafula, LA Honaas, H Zhang… - Molecular biology …, 2015 - academic.oup.com
The origin of novel traits is recognized as an important process underlying many major
evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel …

Strategies for transcriptome analysis in nonmodel plants

JA Ward, L Ponnala, CA Weber - American journal of botany, 2012 - Wiley Online Library
Even with recent reductions in sequencing costs, most plants lack the genomic resources
required for successful short‐read transcriptome analyses as performed routinely in model …

Reprint of: using nuclear gene data for plant phylogenetics: progress and prospects

EA Zimmer, J Wen - Molecular Phylogenetics and Evolution, 2013 - Elsevier
The paper reviews the current state of low and single copy nuclear markers that have been
applied successfully in plant phylogenetics to date, and discusses case studies highlighting …

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome

LA Honaas, EK Wafula, NJ Wickett, JP Der, Y Zhang… - PloS one, 2016 - journals.plos.org
Whereas de novo assemblies of RNA-Seq data are being published for a growing number of
species across the tree of life, there are currently no broadly accepted methods for …