Methods used for the study of endophytic fungi: A review on methodologies and challenges, and associated tips

JBA Dos Reis, AS Lorenzi, HMM do Vale - Archives of Microbiology, 2022 - Springer
Endophytic fungi are microorganisms that colonize the interior of plant tissues (eg leaves,
seeds, stem, trunk, roots, fruits, flowers) in intracellular and/or extracellular spaces without …

Intragenomic rDNA variation-the product of concerted evolution, mutation, or something in between?

W Wang, X Zhang, S Garcia, AR Leitch, A Kovařík - Heredity, 2023 - nature.com
The classical model of concerted evolution states that hundreds to thousands of ribosomal
DNA (rDNA) units undergo homogenization, making the multiple copies of the individual …

Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

K Kim, SC Lee, J Lee, Y Yu, K Yang, BS Choi, HJ Koh… - Scientific reports, 2015 - nature.com
Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary
sequences used to understand plant diversity and evolution. We introduce a high …

Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database

S Garcia, A Kovařík, AR Leitch, T Garnatje - The Plant Journal, 2017 - Wiley Online Library
The online resource http://www. plantrdnadatabase. com/stores information on the number,
chromosomal locations and structure of the 5S and 18S‐5.8 S‐26S (35S) ribosomal DNA s …

Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in …

BB Liu, ZY Ma, C Ren, RGJ Hodel… - … of Systematics and …, 2021 - Wiley Online Library
With the decreasing cost and availability of many newly developed bioinformatics pipelines,
next‐generation sequencing (NGS) has revolutionized plant systematics in recent years …

Strategies for molecular authentication of herbal products: from experimental design to data analysis

HY Wu, PC Shaw - Chinese Medicine, 2022 - Springer
Molecular herbal authentication has gained worldwide popularity in the past decade. DNA-
based methods, including DNA barcoding and species-specific amplification, have been …

Multi‐locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

DS Gernandt, X Aguirre Dugua… - American Journal of …, 2018 - Wiley Online Library
Premise of the Study Both incomplete lineage sorting and reticulation have been proposed
as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in …

Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences

H Yang, L Wang, H Chen, M Jiang, W Wu, S Liu… - BMC plant biology, 2021 - Springer
Background Alpinia species are widely used as medicinal herbs. To understand the
taxonomic classification and plastome evolution of the medicinal Alpinia species and …

Allele sorting as a novel approach to resolving the origin of allotetraploids using Hyb-Seq data: a case study of the Balkan mountain endemic Cardamine …

M Šlenker, A Kantor, K Marhold, R Schmickl… - Frontiers in Plant …, 2021 - frontiersin.org
Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species
richness and a large proportion of narrow endemics. Processes that have driven the …

Nightmare or delight: Taxonomic circumscription meets reticulate evolution in the phylogenomic era

ZT Jin, RGJ Hodel, DK Ma, H Wang, GN Liu… - Molecular Phylogenetics …, 2023 - Elsevier
Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution
greatly impedes the accuracy of phylogenetic inference, and consequently can obscure …