98%
921
2 minutes
20
Premise Of The Study: Few genetic markers provide phylogenetic information in closely related species of (Isoëtaceae). We describe the development of primers for several putative low-copy nuclear markers to resolve the phylogeny of , particularly in the southeastern United States.
Methods And Results: We identified regions of interest in transcriptomes based on low-copy genes in other plants. Primers were designed for these regions and tested with 16 taxa of and one species of . Parts of the , , and gene regions show phylogenetic signal within the North American and Mediterranean clades of .
Conclusions: Transcriptome data prove useful for identification and primer design of low-copy genes. Three new markers show potential for inferring phylogenies in regional clades of , and possibly across the entire genus.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947607 | PMC |
http://dx.doi.org/10.1002/aps3.1142 | DOI Listing |
BMC Plant Biol
August 2025
Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, The University of Gdańsk, Wita Stwosza 59, 80-308, Gdansk, Poland.
Background: The taxonomy of Paphiopedilum-a diverse group of slipper orchids-has long posed challenges due to high morphological variability and conflicting phylogenetic signals. Despite intensive research, a clear and stable infrageneric classification remains unresolved.
Results: We present an integrative phylogenetic framework based on multiple nuclear low-copy genes (XDH, PHYC, LFY, RAD51, ACO, DEF4), ITS and plastid (matK) sequences, supported by morphological and biogeographical data.
Syst Biol
August 2025
Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
The Tree of Life is central to evolutionary biology, yet resolving deep, recalcitrant phylogenetic relationships remains challenging due to complex processes such as incomplete lineage sorting (ILS), hybridization, and polyploidization. Although previous phylogenetic studies have advanced our understanding of Leguminosae (Fabaceae), a species-rich and ecologically diverse family, many deep relationships at the tribal and higher levels remain unresolved. Incorporating newly generated genome skimming data for 231 species with previously issued plastid genomic, mitochondrial genomic and transcriptomic data, we reconstructed a phylogeny of the family using whole plastomes, 39 mitochondrial genes, and 1559 low-copy nuclear genes, achieving dense taxonomic sampling across almost all recognized tribes and major unplaced lineages.
View Article and Find Full Text PDFMol Phylogenet Evol
November 2025
State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Colle
Reticulate evolution, driven by incomplete lineage sorting (ILS) and gene flow, is increasingly recognized as a fundamental process shaping lineage diversification, posing both challenges and opportunities for taxonomic treatment. During field investigations in Xizang, China, we discovered a morphologically distinct new species exhibiting certain similarities with the genera Microtoena yet clearly differing in corolla morphology. We sampled all 12 currently recognized genera within the tribe Pogostemoneae and conducted phylogenomic analyses integrating data from 539 low-copy orthologous nuclear genes (ONGs) and complete plastome sequences to clarify the systematic position of this new species.
View Article and Find Full Text PDFBMC Plant Biol
July 2025
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, People's Republic of China.
Phylogenomic data enriched with informative loci have significantly improved phylogenetic resolution and facilitated the elucidation of evolutionary mechanisms underlying phylogenetic discordance. Species of the East Asian lineage (EAL) within the Allium subgenus Anguinum are widespread in the Himalaya-Hengduan Mountains (HHMs), which exhibit long-standing taxonomic ambiguity and phylogenetic discordance, calling for investigation. In this study, we collected 102 samples, including 45 transcriptomes and 57 plastid genomes, covering multiple populations of all currently recognized taxa within the EAL and relatives.
View Article and Find Full Text PDFBMC Plant Biol
July 2025
Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China.
Unlabelled: The order Myrtales, one of the most species-rich lineage within the Superrosidae clade, with the majority of its species distributed across five families: Myrtaceae, Melastomataceae, Lythraceae, Onagraceae, and Combretaceae. Despite the ecological and economic importance of the Myrtales, its phylogenetic relationships remain unresolved, with previous studies yielding inconsistent results based on gene fragments and plastid genomes. Genomic data, particularly single-copy/low-copy nuclear genes, provide valuable insights for resolving these phylogenetic relationships.
View Article and Find Full Text PDF