ArticleScientific reports2017
Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 18 papers.
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18 citing papers in PubMed, 43 citations in OpenAlex.
- Improving plant breeding through AI-supported data integration.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence.The New phytologist · 2025Article
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- Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics.Zoological research · 2024Article
- Multiple highly expressed phosphoenolpyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses.Annals of botany · 2023Article
- POInTBMC bioinformatics · 2023Article
- Distinct CPlant direct · 2021Article
- Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales).G3 (Bethesda, Md.) · 2021Article
- A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes.Molecular ecology resources · 2021Article
- Using RNA-seq to characterize pollen-stigma interactions for pollination studies.Scientific reports · 2021Article
- Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference.BMC ecology and evolution · 2021Article
- Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet).BMC genomics · 2021Article
- An Overview of the Genetics and Genomics of theFrontiers in plant science · 2021Review
- Modern Approaches for Transcriptome Analyses in Plants.Advances in experimental medicine and biology · 2021Article
- Phylogeny and multiple independent whole-genome duplication events in the Brassicales.American journal of botany · 2020Article
- Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses.Systematic biology · 2020Article
- Article
- IsoSeq transcriptome assembly of CPlant direct · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
9 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 phylogenomics (phylogenetic inference with entire genomes). One approach that has recently emerged is phylo-transcriptomics (transcriptome-based phylogenetic inference). As in any phylogenetics experiment, accurate orthology inference is critical to phylo-transcriptomics. To date, most analyses have inferred orthology based either on pure sequence similarity or using gene-tree approaches. The use of conserved genome synteny in orthology detection has been relatively under-employed in phylogenetics, mainly due to the cost of sequencing genomes. While current trends focus on the quantity of genes included in an analysis, the use of synteny is likely to improve the quality of ortholog inference. In this study, we combine de novo transcriptome data and sequenced genomes from an economically important group of grass species, the tribe Paniceae, to make phylogenomic inferences. This method, which we call "genome-guided phylo-transcriptomics", is compared to other recently published orthology inference pipelines, and benchmarked using a set of sequenced genomes from across the grasses. These comparisons provide a framework for future researchers to evaluate the costs and benefits of adding sequenced genomes to transcriptome data sets.
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