[PDF][PDF] Utility of transcriptome sequencing for phylogenetic inference and character evolution

J Wen, AN Egan, RB Dikow… - … -generation sequencing in …, 2015 - repository.si.edu
Transcriptome sequencing or RNA-Seq is one of the most efficient and cost-effective
methods currently available for gene discovery in non-model organisms. Recent studies …

Making next-generation sequencing work for you: approaches and practical considerations for marker development and phylogenetics

GT Godden, IE Jordon-Thaden, S Chamala… - Plant Ecology & …, 2012 - Taylor & Francis
Recent reviews are setting the stage for the use of next-generation sequencing technologies
in phylogenetic applications. However, the processes for developing new markers for …

The potential of genomics in plant systematics

DE Soltis, MA Gitzendanner, G Stull, M Chester… - Taxon, 2013 - Wiley Online Library
Next‐generation sequencing (NGS) has revolutionized molecular systematics as well as
population and conservation genetics. It is now possible to obtain enormous amounts of …

[PDF][PDF] Is phylotranscriptomics as reliable as phylogenomics?

S Cheon, J Zhang, C Park - Molecular biology and evolution, 2020 - academic.oup.com
Phylogenomics, the study of phylogenetic relationships among taxa based on their genome
sequences, has emerged as the preferred phylogenetic method because of the wealth of …

PLAZA: a comparative genomics resource to study gene and genome evolution in plants

S Proost, M Van Bel, L Sterck, K Billiau… - The Plant …, 2009 - academic.oup.com
The number of sequenced genomes of representatives within the green lineage is rapidly
increasing. Consequently, comparative sequence analysis has significantly altered our view …

[HTML][HTML] Tools for building de novo transcriptome assembly

M Geniza, P Jaiswal - Current Plant Biology, 2017 - Elsevier
The availability of RNA-Seq method allows researchers to capture the spatial or temporal
profile of transcriptomes from various types of biological samples. The transcriptome data …

Leafing through the genomes of our major crop plants: strategies for capturing unique information

AH Paterson - Nature Reviews Genetics, 2006 - nature.com
Crop plants not only have economic significance, but also comprise important botanical
models for evolution and development. This is reflected by the recent increase in the …

[HTML][HTML] How to utilize comparative transcriptomics to dissect morphological diversity in plants

S Li, H Nakayama, NR Sinha - Current Opinion in Plant Biology, 2023 - Elsevier
Comparative transcriptomics has emerged as a powerful approach that allows us to unravel
the genetic basis of organ morphogenesis and its diversification processes during evolution …

Genome-guided phylo-transcriptomic methods and the nuclear phylogenetic tree of the Paniceae grasses

JD Washburn, JC Schnable, GC Conant, TP Brutnell… - Scientific reports, 2017 - nature.com
The past few years have witnessed a paradigm shift in molecular systematics from
phylogenetic methods (using one or a few genes) to those that can be described as …

Phylogenomic approaches to deal with particularly challenging plant lineages

M Escudero, G Nieto Feliner, L Pokorny… - Frontiers in Plant …, 2020 - frontiersin.org
Molecular phylogenetics has been revolutionized in the past two decades by the
development of increasingly cheap high-throughput sequencing (HTS) technologies. The …