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Recent Advancements in Taxonomy and Phylogeny of Plants
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Recent Advancements in Taxonomy and Phylogeny of Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Systematics, Taxonomy, Nomenclature and Classification".

Deadline for manuscript submissions: closed (30 June 2025) | Viewed by 2111

Special Issue Editor

Dr. Eduardo Estrada-Castillón

E-Mail Website
Guest Editor
Faculty of Forestry Sciences, Autonomous University of Nuevo León, San Nicolás de los Garza 67700, Mexico
Interests: plant taxonomy; plant systematics; biodiversity and plant conservation

Special Issue Information

Dear Colleagues,

Plant taxonomy and phylogenetics play a key role in understanding plant diversity and its evolution. In recent years, with the advancement of molecular biology techniques, researchers have been able to explore the genetic relationships and taxonomic status of plants in greater depth. These techniques allow researchers to not only analyze plant genomes, but also reveal the complexity of their phylogenetic trees, promoting a re-examination of the evolutionary history of plants.

Overall, the latest research progress in plant taxonomy and phylogenetics provides important theoretical support and practical guidance for revealing the evolutionary mechanisms of plants, promoting species conservation and ecosystem management.

The present topic on taxonomy and phylogeny of plants aims to create a representative and updated collection of research articles and reviews regarding the taxonomy and phylogeny of plants.

Dr. Eduardo Estrada-Castillón
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant taxonomy
  • plant phylogenetics
  • molecular biology
  • genetics

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

12 pages, 1686 KiB  
Article
Development of Single Nucleotide Polymorphism and Phylogenetic Analysis of Rhododendron Species in Zhejiang Province, China, Using ddRAD-Seq Technology
by Hong Zhu, Dongbin Li, Chunlei Yue and Hepeng Li
Plants 2025, 14(10), 1548; https://doi.org/10.3390/plants14101548 - 21 May 2025
Viewed by 440
Abstract
The genus Rhododendron presents significant challenges for systematic classification due to extensive hybridization and adaptive radiation. Here, we employed double-digest restriction site-associated DNA sequencing (ddRAD-seq) to resolve phylogenetic relationships among nine ecologically significant Rhododendron species (34 accessions) endemic to Zhejiang Province, China, a [...] Read more.
The genus Rhododendron presents significant challenges for systematic classification due to extensive hybridization and adaptive radiation. Here, we employed double-digest restriction site-associated DNA sequencing (ddRAD-seq) to resolve phylogenetic relationships among nine ecologically significant Rhododendron species (34 accessions) endemic to Zhejiang Province, China, a biodiversity hotspot for this genus. Using R. simsii as the reference genome, we generated 39.40 Gb of high-quality sequencing data with a Q30 score of 96.65% and a GC content of 39.63%, achieving an average alignment rate of 92.79%. Through stringent filtering (QD ≥ 2, MQ ≥ 40), we identified 14,048,702 genome-wide single nucleotide polymorphism (SNP), predominantly characterized by the mutation types T:A>C:G and C:G>T:A. The widespread R. simsii and R. simsii var. putuoense exhibited significant genetic diversity, whereas the low-altitude widespread R. molle and the endemic R. simiarum exhibited lower genetic diversity. Moderate genetic differentiation (Fst = 0.097) was observed between R. simsii and R. simsii var. putuoense, while substantial genetic differentiation was detected among the other Rhododendron species. Principal component analysis (PCA), combined with phylogenomic reconstruction, demonstrated that the Rhododendron genus can be stratified into six well-supported genetic clades. Furthermore, this study provides the first genomic validation of the sibling relationship between R. simsii and its variety, R. simsii var. putuoense, and clarifies the systematic position of R. huadingense, suggesting that it should be classified as a new subgenus. This study establishes ddRAD-seq as a cost-effective tool, providing both a theoretical framework for SNP-based phylogenetics and critical insights for conserving China’s azalea biodiversity. Full article
(This article belongs to the Special Issue Recent Advancements in Taxonomy and Phylogeny of Plants)
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60 pages, 3126 KiB  
Article
The Fabaceae in Northeastern Mexico (Subfamily Papilionoideae, Tribes Amorpheae, Brongniartieae, and Dalbergieae)
by Eduardo Estrada Castillón, José Ángel Villarreal Quintanilla, Juan Antonio Encina Domínguez, Arturo Mora Olivo, Jaime Sánchez Salas, Gisela Muro Pérez, Eduardo Alanís Rodríguez, Renata Aidé Valdés Alameda, Nelly Sandoval Mata and Gilberto Ocampo
Plants 2025, 14(5), 789; https://doi.org/10.3390/plants14050789 - 4 Mar 2025
Viewed by 1134
Abstract
A compendium of the legumes of the subfamily Papilionoideae, tribes Amorpheae, Brongniarteae, and Dalbergieae in northeastern Mexico is presented for the first time, including changes in their botanical nomenclature within tribes and genera. Based on recently published studies, the taxonomic limits of several [...] Read more.
A compendium of the legumes of the subfamily Papilionoideae, tribes Amorpheae, Brongniarteae, and Dalbergieae in northeastern Mexico is presented for the first time, including changes in their botanical nomenclature within tribes and genera. Based on recently published studies, the taxonomic limits of several genera and new ones segregated such as Marina and Ctenodon are clarified and included. Based mainly on fieldwork over the past 40 years, as well as reviewing specimens in national and international herbaria, we show the total diversity of legumes of the subfamily Papilionoideae, tribes Amorpheae, Brongniarteae, and Dalbergieae. The three tribes include 16 genera and 75 species. Tribe Amorpheae comprises five genera (Amorpha, Dalea, Eysenhardtia, Marina, and Psorothamnus) and forty-three species; tribe Brongniartieae comprises two genera Brongniartia and Harpalyce) and eight species; and tribe Dalbergieae comprises nine genera (Aeschynomene, Amicia, Arachis, Ctneodon, Dalbergia, Diphysa, Nissolia, Stylosanthes, and Zornia) and twenty-four species. Dalea is by far the genus with the highest number of species and infraspecific categories, as well as in a number of endemisms because 17 (51%) of them are endemic to Mexico, and six of them are endemic to the northeastern part of the country. Of the 13 species of Eysenhardtia present in Mexico, 31% of them reach the northeast region and three of them are exclusive to this region. There are no species of the Brongniartieae and Dalbergieae tribes endemic to northeastern Mexico, but 10 of their species are endemic to Mexico. Full article
(This article belongs to the Special Issue Recent Advancements in Taxonomy and Phylogeny of Plants)
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