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Plant Molecular Phylogenetics and Evolutionary Genomics IV
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Plant Molecular Phylogenetics and Evolutionary Genomics IV

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 5822

Editor

Prof. Dr. Alex Troitsky

E-Mail Website
Guest Editor
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia
Interests: plant molecular phylogeny and systematics; genome evolution; biodiversity; phytoplanktonic metagenome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The primary aim of molecular phylogenetics and phylogenomics regarding its part in the genomics era is to infer the evolutionary relationships of living organisms by comparing the structures of their information macromolecules and whole genomes. However, this does not limit the role of molecular phylogenetic approaches in biological research. Molecular phylogenetics and phylogenomics now serve as blueprints for studies of genome organization and investigations in almost all biological disciplines. The evolutionary paradigm is a framework for studying the structural and functional basis of living beings. It is applied in a wide range of studies on taxonomy, biodiversity and its conservation, biogeography, population genetics, molecular ecology, and agrobiology.

This Special Issue of Plants is open to research articles on all aspects of plant molecular evolution, including molecular phylogenetics and systematics, phylogenomics, comparative genomics, phylotranscriptomics, gene families’ structure and evolution, cell organelles genomics, DNA barcoding and metabarcoding, molecular ecology and biodiversity, correspondence between molecular and morphological evolution, as well as the bioinformatics and laboratory methods of the aforementioned studies.

Prof. Dr. Alex Troitsky
Guest Editor

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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.

Publisher’s Notice

The Special Issue, together with its publications, has been assigned to Section Plant Genetics, Genomics and Biotechnology on 16 December 2025. The publications remain available in the regular issues in which they were originally published. The Editorial Office confirms that these articles adhered to MDPI's standard editorial process (https://www.mdpi.com/editorial_process).

Keywords

  • molecular phylogeny
  • phylogenomics
  • phylotranscriptomics
  • chloroplast genome
  • mitochomdrial genome
  • evolutionary genomics
  • metagenomics
  • DNA barcoding
  • bioinformatics

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Published Papers (6 papers)

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Research

28 pages, 6954 KB  
Article
Species of the Genus ×Agrotrigia (Hordeeae, Poaceae)—A Case of a Different Pattern of Parental rDNA Elimination
by Alexander A. Gnutikov, Nikolai N. Nosov, Inna E. Evnukova, Victoria S. Shneyer, Aleksey V. Troitsky and Alexander V. Rodionov
Plants 2026, 15(16), 2432; https://doi.org/10.3390/plants15162432 - 10 Aug 2026
Viewed by 167
Abstract
All taxa of plants have undergone several rounds of whole-genome duplication (WGD), accompanying interspecific and intergeneric crosses; subsequently, some part of one or both parent genomes in hybrid plants can be eliminated. The objective of this study was to evaluate the relationships of [...] Read more.
All taxa of plants have undergone several rounds of whole-genome duplication (WGD), accompanying interspecific and intergeneric crosses; subsequently, some part of one or both parent genomes in hybrid plants can be eliminated. The objective of this study was to evaluate the relationships of the intergeneric hybrid ×Agrotrigia (Poaceae) species with the taxa of parental genera Agropyron and Elytrigia and to determine the distribution as well as conservation or loss of parental genomes in the genomes of hybrid species. Molecular phylogenetic analysis of nuclear (ITS, ETS) and several chloroplast DNA markers confirmed that the most likely parents of this hybrid were really species of Agropyron and Elytrigia. The compositions of ribotypes (sequences of the 18S–ITS1–5.8S rDNA region) assessed by next-generation sequencing (NGS) showed that the genomes of hybrid species of ×Agrotrigia hajastanica and of the sample of ×A. androssovii from Turkmenistan carry ribotypes of both Agropyron and Elytrigia. However, the samples of ×A. kotovii and ×A. androssovii from Pskov Oblast bear ribotypes of the Elytrigia type only, whereas the genome of one sample of the ×Agrotrigia genus collected in Stavropol Krai consists exclusively of two clusters of Agropyron-type ribotypes (P genome) and may represent a new species. Therefore, these two (or three) species may be subject to the elimination of portions of the genome of one of the parents, though the extent of elimination may be different. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics IV)
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26 pages, 7026 KB  
Article
Evolution of Tat Retrotransposons Reveals Mosaic Phylogenetic Patterns Among Land Plants
by Antonina Prokopeva, Kirill Plotnikov and Mikhail Biryukov
Plants 2026, 15(15), 2388; https://doi.org/10.3390/plants15152388 - 4 Aug 2026
Viewed by 365
Abstract
Transposable elements (TEs) are rarely used as phylogenetic markers because of their high copy number, frequent recombination, and potential for horizontal transfer. However, their long-term coexistence with host genomes suggests that some TE lineages may preserve information about the evolutionary history of their [...] Read more.
Transposable elements (TEs) are rarely used as phylogenetic markers because of their high copy number, frequent recombination, and potential for horizontal transfer. However, their long-term coexistence with host genomes suggests that some TE lineages may preserve information about the evolutionary history of their genomic environment. Here, we investigate whether Tat LTR retrotransposons of the Ty3/Gypsy superfamily retain a phylogenetic signal informative for deep plant evolution. We reconstructed the phylogeny of Tat reverse transcriptase domains among representative lineages of land plants, including bryophytes, lycophytes, ferns, gymnosperms, and basal angiosperms. The analysis revealed stable clusters characterized by both structural specificity, determined by the position of the additional ribonuclease H domain, and taxonomic specificity. In many cases, the Tat subclusters reproduced established host relationships at the genus and family levels, particularly within conifers, indicating a predominantly vertical mode of inheritance. The distribution of Tat lineages also preserved signals relevant to unresolved questions of plant phylogeny. Among seed plants, different Tat lineages reflected aspects of existing alternative hypotheses, including the association of gnetophytes both with conifers II and angiosperms. Interestingly, the strong separation between two major conifer groups, pines and cypress with yews, was observed. Among non-seed plants, the topology of Tat lineages highlighted the unique position of lycophytes by the preservation of multiple ancient transposon lineages associated with early diversification after aRNH domain acquisition. It also suggested that the origins of mosses and hornworts involved different patterns of lineage elimination from a common ancestor that carried all structures found in lycophytes. We propose a conceptual framework in which TE clusters are interpreted as collections of partially independent evolutionary lineages rather than as a single species tree. Under this view, Tat retrotransposons provide an additional layer of phylogenetic information that complements conventional molecular markers and reflects the mosaic nature of plant genome evolution. The present work, therefore, represents the first implementation of this approach rather than its final methodological form. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics IV)
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15 pages, 1569 KB  
Article
Genomic Footprints of Multiple Host Lineages in the Mitochondrial and Nuclear Genomes of the Holoparasite Prosopanche americana
by Laura E. Garcia, Maria Emilia Roulet, Lucía A. Garay and M. Virginia Sanchez-Puerta
Plants 2026, 15(7), 1121; https://doi.org/10.3390/plants15071121 - 7 Apr 2026
Cited by 1 | Viewed by 1062
Abstract
Horizontal Gene Transfer (HGT) is a hallmark of the evolution of parasitic plants, facilitated by the haustorial connection. While mitochondrial HGT is widespread, the extent of nuclear HGT and the long-term retention of foreign genetic material in holoparasitic lineages remain poorly understood. This [...] Read more.
Horizontal Gene Transfer (HGT) is a hallmark of the evolution of parasitic plants, facilitated by the haustorial connection. While mitochondrial HGT is widespread, the extent of nuclear HGT and the long-term retention of foreign genetic material in holoparasitic lineages remain poorly understood. This study explores the genomic architecture of Prosopanche americana (Hydnoraceae), a non-photosynthetic holoparasite currently specialized on Fabaceae. Through a comparative phylogenomic approach integrating draft mitochondrial genomes (mtDNA) and nuclear transcriptomes of P. americana, we identified a multi-layered landscape of foreign DNA. The mtDNA of P. americana contains 18 foreign regions (>500 bp) primarily derived from Solanales, Malvales, and Fabales. Notably, 13 of these regions are shared with P. panguanensis, indicating they were acquired in their common ancestor before speciation and ecological shift. In the nuclear genome, we identified 303 horizontally acquired transcripts (99 orthogroups) with high confidence. Functional analysis revealed an enrichment of foreign genes involved in metabolic pathways and plastid functions (e.g., photosystems and thylakoids) exclusively derived from the ancestral host order Solanales. Our results demonstrate that the genome of P. americana acts as a “molecular fossil,” preserving evidence of past ecological interactions with diverse host lineages. The disparity in HGT footprints between the current host (Fabaceae) and ancestral hosts suggests a period of high genomic plasticity followed by host specialization, providing new insights into the timing and dynamics of horizontal gene flow in holoparasitic Piperales. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics IV)
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23 pages, 2452 KB  
Article
Resolving Species Limits and Evolutionary Distinctiveness of the Libyan Endemic Arbutus pavarii (Ericaceae) Using Multilocus DNA Barcoding and Phylogenetic Analyses
by Ahmed M. H. Gawhari, Alastair Culham, Faten Y. Ellmouni, Ahmed A. Alghamdi, Stephen L. Jury and Ahmed EL-Banhawy
Plants 2026, 15(4), 653; https://doi.org/10.3390/plants15040653 - 20 Feb 2026
Viewed by 1297
Abstract
The taxonomic status of Arbutus pavarii Pamp., a rare and geographically restricted species endemic to northeastern Libya, has long been debated, with some treatments considering it a synonym of A. unedo. To resolve this uncertainty, we applied an integrative molecular framework that [...] Read more.
The taxonomic status of Arbutus pavarii Pamp., a rare and geographically restricted species endemic to northeastern Libya, has long been debated, with some treatments considering it a synonym of A. unedo. To resolve this uncertainty, we applied an integrative molecular framework that combined multilocus DNA barcoding, phylogenetic inference, and multivariate statistical analyses. Five barcode loci—nrITS, matK, rbcL, trnH–psbA, and rps16—were analyzed using barcode-gap diagnostics, TaxonDNA identification tests, and single-locus and concatenated phylogenetic analyses. Barcode-gap analyses based on Kimura 2-parameter distances revealed clear and reproducible separation between intra- and interspecific variation for A. pavarii, particularly for nrITS and the concatenated multilocus dataset, whereas conserved plastid loci showed limited discriminatory power when used individually. Phylogenetic reconstructions consistently recovered A. pavarii as a strongly supported monophyletic lineage, distinct from A. unedo and other Mediterranean congeners, with congruent topologies across the nuclear, plastid, and combined datasets. Multivariate analyses, including principal component analysis and heatmap clustering, further corroborate the genetic cohesion and distinctiveness of A. pavarii samples. Collectively, these results provide robust molecular evidence supporting the recognition of Arbutus pavarii as a distinct evolutionary lineage, rather than an intraspecific variant of A. unedo. This study established a reproducible multilocus framework for species delimitation in Arbutus and highlighted the importance of integrating nuclear and plastid markers to resolve complex taxonomic relationships. The clarified taxonomic status of A. pavarii has important implications for biodiversity assessment and conservation planning in the Mediterranean region, particularly in the Cyrenaican floristic province. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics IV)
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22 pages, 3068 KB  
Article
Genomic Composition of the Artificial Hybrid ×Trititrigia cziczinii (Hordeeae, Poaceae) and Related Taxa According to Molecular Phylogenetic Data
by Alexander A. Gnutikov, Nikolai N. Nosov, Evgeny V. Zuev, Natalia S. Lysenko, Victoria S. Shneyer, Aleksey V. Troitsky and Alexander V. Rodionov
Plants 2026, 15(1), 70; https://doi.org/10.3390/plants15010070 - 25 Dec 2025
Cited by 1 | Viewed by 1271
Abstract
×Trititrigia cziczinii Tzvelev is a promising crop developed through distant hybridization between Elytrigia intermedia (Host) Nevski (=Thinopyrum intermedium (Host) Barkworth & D.R. Dewey) and Triticum aestivum L., followed by backcrossing with wheat. This study elucidates the genomic composition of this hybrid [...] Read more.
×Trititrigia cziczinii Tzvelev is a promising crop developed through distant hybridization between Elytrigia intermedia (Host) Nevski (=Thinopyrum intermedium (Host) Barkworth & D.R. Dewey) and Triticum aestivum L., followed by backcrossing with wheat. This study elucidates the genomic composition of this hybrid and its parental taxa using molecular phylogenetic analysis of nuclear (ITS, ETS) and chloroplast (trnK–rps16, ndhF) DNA markers, complemented by Next-Generation Sequencing (NGS) of the 18S–ITS1–5.8S rDNA region. Results from Sanger sequencing revealed that the primary nuclear ribosomal DNA (rDNA) of the hybrid originates from Triticum aestivum; a finding strongly supported by both Bayesian inference and Maximum Likelihood analyses. Chloroplast DNA data unequivocally indicate maternal inheritance from T. aestivum. In contrast, ETS sequence analysis showed phylogenetic affinity to Elytrigia intermedia, suggesting complex genomic reorganization or chimeric sequence formation in the hybrid. NGS data corroborate the dominance of T. aestivum-like ribotypes in the hybrid’s rDNA pool, with only a minor fraction identical to the main ribotype of E. intermedia. Genetic structure analysis further revealed geographic heterogeneity in the genomic composition of E. intermedia populations. The predominance of the wheat genome in ×T. cziczinii is likely a consequence of stabilizing backcrosses and illustrates a case of rDNA elimination from one parental genome during hybridization. This research underscores the complex genomic dynamics in artificial hybrids and the utility of multi-marker phylogenetic approaches for clarifying their origins. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics IV)
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32 pages, 3795 KB  
Article
Evaluating Species Delimitation Methods in Chloroidium (Trebouxiophyceae, Chlorophyta): Efficacy of DNA Barcodes and Description of Chloroidium pseudoellipsoideum sp. nov. from Arctic Soils
by Elena Krivina, Maria Sinetova, Alexander Starikov, Aleksey Portnov and Anna Temraleeva
Plants 2025, 14(24), 3739; https://doi.org/10.3390/plants14243739 - 8 Dec 2025
Viewed by 873
Abstract
Despite extensive research into green microalgae belonging to the genus Chloroidium, their species diversity and biotechnological potential remain poorly characterized. The strain VKM Al-418, the subject of this study, was isolated from the soil of Duvannyi Yar (Russian Federation). The independent species [...] Read more.
Despite extensive research into green microalgae belonging to the genus Chloroidium, their species diversity and biotechnological potential remain poorly characterized. The strain VKM Al-418, the subject of this study, was isolated from the soil of Duvannyi Yar (Russian Federation). The independent species status of this strain is supported by distinct morphological characteristics, robust phylogenetic placement based on the 18S-ITS1-5.8S-ITS2 fragment, and unique features in the secondary structures of both ITS1 and ITS2, including one compensatory base change (CBC) in the highly conserved helix III of ITS2. Additionally, the species delimitation was also confirmed using five independent algorithmic approaches analyzing four different DNA barcodes. The concatenated ITS1-5.8S-ITS2 fragment is more reliable for species discrimination than the individual ITS1 or ITS2 barcodes. Of the species delimitation methods evaluated, ASAP (Assemble Species by Automatic Partitioning) and GMYC (Generalized Mixed Yule Coalescent) performed best in distinguishing Chloroidium species across multiple barcode regions in our analysis. The fatty acid profile of strain VKM Al-418 was analyzed at 9 °C, 22 °C, and 27 °C and exhibited high plasticity in response to temperature, indicative of an adaptive strategy to its harsh environment. Using this integrative taxonomic approach, we describe Chloroidium pseudoellipsoideum sp. nov., a new species with a distinct phylogenetic positioning and promising biotechnological properties. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics IV)
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