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

Deadline for manuscript submissions: 30 June 2026 | Viewed by 25291

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Special Issue Editors

Dr. Yin-Long Qiu

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Guest Editor

Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI 48109, USA
Interests: land plant phylogeny and evolution; mitochondrial genome evolution
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Feng Chen

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Guest Editor

Department of Plant Sciences, The University of Tennessee, Knoxville, TN 37996, USA
Interests: biosynthesis; function and evolution of plant secondary metabolites

Special Issue Information

Dear Colleagues,

Land plants are the primary producers of the modern terrestrial biosystem and play a critical role in shaping the Earth’s environment and climate regime. Recent active research on phylogeny, genomes and phenomes of land plants, and their numerous model representatives has brought a new level of understanding of their evolution, function, and interaction with the environment. This Special Issue will publish a collection of review and primary research papers that report on the latest status of this important field. Submissions in phylogenetics, phylogenomics, evolutionary genomics, molecular evolution, evolutionary developmental biology, chemical evolution, evolutionary ecology, biogeography, and paleobotany are welcome.

Prof. Dr. Yinlong Qiu
Prof. Dr. Feng Chen
Guest Editors

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Keywords

land plants
evolution
phylogenetics
evolutionary genomics
biogeography
paleobotany
specialized metabolites
chemical evolution

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Published Papers (9 papers)

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Research

Jump to: Review

17 pages, 579 KB

Open AccessArticle

High Terpene Production in Myrtaceae: Evolutionary Insights from Terpene Pathway Genes

by Xinlu Chen, Jin-Gui Chen, Gerald A. Tuskan and Feng Chen

Plants 2026, 15(9), 1293; https://doi.org/10.3390/plants15091293 - 22 Apr 2026

Viewed by 376

Abstract

Myrtaceae is one of the largest families of flowering plants and is well known for its prolific terpene production. To investigate the genetic basis underlying this high-level terpene output, we conducted comparative genomic analyses of genes of the entire terpene biosynthetic pathways in selected Myrtaceae species and representative species from three other families within the order Myrtales. Our analyses revealed that genes encoding enzymes in the upstream terpene biosynthetic pathways are generally conserved in copy number across Myrtales. Similarly, isoprenyl diphosphate synthases, which are positioned centrally and responsible for producing the direct precursors of major terpene classes, also exhibit conserved gene numbers among these species. In contrast, substantial differences were observed in the number of terpene synthase (TPS) genes, which function downstream and directly catalyze terpene formation. Myrtaceae species possess markedly more TPS genes than species from other Myrtales families. This expansion is primarily attributable to increased gene numbers in the TPS-a, TPS-b, TPS-g, and TPS-e/f subfamilies, with the first three subfamilies largely associated with sesquiterpene and monoterpene biosynthesis. Further analyses indicate that the enlarged TPS-a and TPS-g subfamilies resulted at the origination of Myrtaceae-specific groups, whereas TPS-b exhibited Myrtaceae-specific expansion. In Eucalyptus grandis, tandem duplication makes a larger contribution to the expansion of TPS-a, TPS-b and TPS-g subfamilies than interchromosomal duplication. The majority of these TPS genes exhibit moderate to high levels of expression in leaves, consistent with their role in elevated terpene production in leaves of E. grandis. Collectively, our findings are consistent with the hypothesis that the novel terpene-producing capacity of Myrtaceae is driven primarily by Myrtaceae-specific origination and/or expansion of downstream TPS genes rather than changes in upstream pathway gene copy numbers. Full article

(This article belongs to the Special Issue Evolution of Land Plants)

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18 pages, 9628 KB

Open AccessArticle

Evolution of Plant AIG1-like Proteins: Different Modes of Sequence Divergence and Their Contributions to Functional Diversification

by Jiajing Peng, Liying Xia, Jing Wang and Chunce Guo

Plants 2026, 15(2), 301; https://doi.org/10.3390/plants15020301 - 19 Jan 2026

Viewed by 586

Abstract

AIG1 (avrRpt2-induced gene 1)-like proteins are a class of GTPases that play crucial roles in plants, functioning both in chloroplast protein import and disease resistance. However, their evolutionary history and the mechanisms driving this functional diversification remain poorly understood. Here, we performed a comprehensive genomic and evolutionary analysis of this gene family across the plant kingdom. We identified 90 AIG1-like genes from 11 sequenced plant species, representing major lineages from green algae to angiosperms. Phylogenetic analysis revealed that plant AIG1-like proteins form three monophyletic lineages corresponding to the Toc34, Toc159, and IAN subfamilies, which originated via two ancient duplications predating the divergence of green algae and land plants. These lineages exhibit dramatically divergent evolutionary patterns. The Toc34 subfamily is evolutionarily conserved, maintaining stable copy numbers and gene structure, indicative of strong functional constraints in its core role in plastid import. In contrast, the Toc159 and IAN subfamilies have undergone dynamic expansion via lineage-specific duplication mechanisms, including segmental duplication and prolific tandem duplication, respectively. Notably, we uncovered a novel mechanism for generating head-to-head tandem duplicates in the IAN subfamily, mediated by recombination between inverted repeats. Our analysis of ancestral gene numbers and gene gain/loss dynamics further highlights that functional diversification was driven by both the acquisition of distinct C-terminal targeting domains (M and TM domains) and profound differences in evolutionary rates and duplication modes among subfamilies. This study provides the first full-scale evolutionary framework for plant AIG1-like genes, establishing that functional specialization is rooted in distinct modes of sequence and genomic evolution. Full article

(This article belongs to the Special Issue Evolution of Land Plants)

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13 pages, 4938 KB

Open AccessArticle

Development and Application of SSR Markers for Aquilaria sinensis on the Basis of Whole-Genome Resequencing Data

by Yu Chen, Kunlin Wu, Jieru Xu, Shenghe Zhao, Zhihua Tu, Dandan Rao, Beibei Chen, Nanbo Jiao, Jinhui Chen and Xiaona Dong

Plants 2025, 14(9), 1323; https://doi.org/10.3390/plants14091323 - 27 Apr 2025

Cited by 1 | Viewed by 1266

Abstract

Aquilaria sinensis (Lour.) Spreng. is an economically important tree specie that produces agarwood, a valuable medicinal and aromatic resin, when injured. However, its large-scale cultivation has led to confusion regarding its resources and genetic backgrounds, hindering the conservation and management of A. sinensis accessions. This study systematically developed and validated simple sequence repeat (SSR) molecular markers by using whole-genome resequencing (WGR) data from 60 A. sinensis accessions to elucidate their genetic diversity and population structure. A total of 56,657 SSR sequences (24,430 loci) were identified, which were dominated with dinucleotide repeat motifs (73.59%). After stringent quality control, 46 high-quality SSR loci were obtained, and 93 primer pairs were designed for amplification validation. Ultimately, 20 primer pairs with stable amplification and high polymorphism were selected, of which 11 exhibited high polymorphism (polymorphic information content: 0.554–0.688). These 20 primer pairs identified a total of 121 alleles, with an average of 6 alleles per locus. These primers successfully classified 149 A. sinensis accessions into three subpopulations, achieving a discrimination rate of 95.97%. The analysis of molecular variance revealed that genetic variation within the individuals accounted for 84% of the total variation. This study establishes a rapid and efficient SSR-based method by leveraging resequencing data for large-scale marker discovery in A. sinensis. It further provides a robust technical framework for the conservation and sustainable utilization of this valuable species. Full article

(This article belongs to the Special Issue Evolution of Land Plants)

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20 pages, 5079 KB

Open AccessArticle

Paleovegetation Community and Paleoclimate Succession in Middle Jurassic Coal Seams in Eastern Coalfields in Dzungaria Basin, China

by Xingli Wang, Shuo Feng, Wenfeng Wang, Qin Zhang, Jijun Tian, Changcheng Han and Meng Wang

Plants 2025, 14(5), 695; https://doi.org/10.3390/plants14050695 - 24 Feb 2025

Cited by 1 | Viewed by 1268

Abstract

The Dzungaria Basin is located north of Xinjiang and is one of the largest inland basins in China. The eastern coalfields in the Dzungaria Basin contain a large amount of coal resources, and the thickness of the coal seams is significant. Therefore, the aim of this study was to classify the paleovegetation types and develop paleoclimate succession models of the extra-thick coal seams. We conducted the sampling, separation, and extraction of spores and pollen and carried out microscopic observations in the Wucaiwan mining area of the eastern coalfields in the Dzungaria Basin. The vertical vegetation succession in the thick seam (Aalenian Stage) in the study area was divided into three zones using the CONISS clustering method. The results show that the types of spore and pollen fossils belong to twenty families and forty-five genera, including twenty-three fern, twenty gymnosperm, and two bryophyte genera. The types of paleovegetation in the study area were mainly Lycopodiaceae and Selaginellaceae herb plants, Cyatheaceae, Osmundaceae, and Polypodiaceae shrub plants, and Cycadaceae and Pinaceae coniferous broad-leaved trees. The paleoclimate changed from warm–humid to humid–semi-humid and, finally, to the semi-humid–semi-dry type, all within a tropical–subtropical climate zone. The study area was divided into four paleovegetation communities: the nearshore wetland paleovegetation community, lowland cycad and Filicinae plant community, slope broad-leaved and coniferous plant mixed community, and highland coniferous tree community. This indicates that there was a climate warming event during the Middle Jurassic, which led to a large-scale lake transgression and regression in the basin. This resulted in the transfer of the coal-accumulating center from the west and southwest to the central part of the eastern coalfields in the Dzungaria Basin. Full article

(This article belongs to the Special Issue Evolution of Land Plants)

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29 pages, 2280 KB

Open AccessArticle

Geometric Models of Speciation in Minimally Monophyletic Genera Using High-Resolution Phylogenetics

by Richard H. Zander

Plants 2025, 14(4), 530; https://doi.org/10.3390/plants14040530 - 9 Feb 2025

Viewed by 2221

Abstract

High-resolution phylogenetics using both morphology and molecular data reveal surfactant-like trait buffering of peripatric descendant species that facilitate resilience for supra-specific entities across geologic time. Regular polygons inscribed in circles model balanced areas of survival of various numbers of new species in one genus. This model maximizes the peripatric survival of descendant species, with populations partly in allopatric habitats and in sympatric areas. It extends the theory advanced with Willis’s Age and Area hypothesis. Hollow curves of the areas bounded between a series of inscribed regular polygons and their containing circles show a ranked progression governed by similar power laws of other phenomena, including Zipf’s law and a universal meta-law in physics. This model matches best the physics meta-law (law of laws) but is only one of several somewhat different curves generated by somewhat different processes. A rule of four can explain why most genera in vascular plants exhibit a hollow curve of optimally one to five species per genus. It implies a constraint on variation that enhances survival and provides a physics explanation for the monophyletic skeleton of macrogenera. A high-resolution form of ancestor–descendant analysis is compared to traditional phylogenetic analysis to best modeling of the demonstrable results of evolutionary processes. Arguments are advanced for the preservation of scientific concepts of taxa over cladistic clades. Full article

(This article belongs to the Special Issue Evolution of Land Plants)

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29 pages, 7901 KB

Open AccessEditor’s ChoiceArticle

Origin and Early Evolution of Hydrocharitaceae and the Ancestral Role of Stratiotes

by Silvia Ulrich, Manuel Vieira, Mario Coiro, Johannes M. Bouchal, Christian Geier, Bonnie F. Jacobs, Ellen D. Currano, Olaf K. Lenz, Volker Wilde, Reinhard Zetter and Friðgeir Grímsson

Plants 2024, 13(7), 1008; https://doi.org/10.3390/plants13071008 - 31 Mar 2024

Cited by 8 | Viewed by 6028

Abstract

The combined morphological features of Stratiotes (Hydrocharitaceae) pollen, observed with light and electron microscopy, make it unique among all angiosperm pollen types and easy to identify. Unfortunately, the plant is (and most likely was) insect-pollinated and produces relatively few pollen grains per flower, contributing to its apparent absence in the paleopalynological record. Here, we present fossil Stratiotes pollen from the Eocene of Germany (Europe) and Kenya (Africa), representing the first reliable pre-Pleistocene pollen records of this genus worldwide and the only fossils of this family discovered so far in Africa. The fossil Stratiotes pollen grains are described and compared to pollen from a single modern species, Stratiotes aloides L. The paleophytogeographic significance and paleoecological aspects of these findings are discussed in relation to the Hydrocharitaceae fossil records and molecular phylogeny, as well as the present-day distribution patterns of its modern genera. Full article

(This article belongs to the Special Issue Evolution of Land Plants)

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20 pages, 3898 KB

Open AccessArticle

Phylotranscriptomics Shed Light on Intrageneric Relationships and Historical Biogeography of Ceratozamia (Cycadales)

by Sadaf Habib, Yiqing Gong, Shanshan Dong, Anders Lindstrom, Dennis William Stevenson, Hong Wu and Shouzhou Zhang

Plants 2023, 12(3), 478; https://doi.org/10.3390/plants12030478 - 19 Jan 2023

Cited by 10 | Viewed by 3298

Abstract

Ceratozamia Brongn. is one of the species-rich genera of Cycadales comprising 38 species that are mainly distributed in Mexico, with a few species reported from neighboring regions. Phylogenetic relationships within the genus need detailed investigation based on extensive datasets and reliable systematic approaches. Therefore, we used 30 of the known 38 species to reconstruct the phylogeny based on transcriptome data of 3954 single-copy nuclear genes (SCGs) via coalescent and concatenated approaches and three comparative datasets (nt/nt12/aa). Based on all these methods, Ceratozamia is divided into six phylogenetic subclades within three major clades. There were a few discrepancies regarding phylogenetic position of some species within these subclades. Using these phylogenetic trees, biogeographic history and morphological diversity of the genus are explored. Ceratozamia originated from ancestors in southern Mexico since the mid-Miocene. There is a distinct distribution pattern of species through the Trans-Mexican Volcanic Belt (TMVB), that act as a barrier for the species dispersal at TMVB and its southern and northern part. Limited dispersal events occurred during the late Miocene, and maximum diversification happened during the Pliocene epoch. Our study provides a new insight into phylogenetic relationships, the origin and dispersal routes, and morphological diversity of the genus Ceratozamia. We also explain how past climatic changes affected the diversification of this Mesoamerica-native genus. Full article

(This article belongs to the Special Issue Evolution of Land Plants)

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Review

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18 pages, 2721 KB

Open AccessReview

Function and Evolution of the Plant MES Family of Methylesterases

by Timothy A. Chaffin, Weijiao Wang, Jin-Gui Chen and Feng Chen

Plants 2024, 13(23), 3364; https://doi.org/10.3390/plants13233364 - 29 Nov 2024

Cited by 3 | Viewed by 2272

Abstract

Land plant evolution has been marked by numerous genetic innovations, including novel catalytic reactions. Plants produce various carboxyl methyl esters using carboxylic acids as substrates, both of which are involved in diverse biological processes. The biosynthesis of methyl esters is catalyzed by SABATH methyltransferases, and understanding of this family has broadened in recent years. Meanwhile, the enzymes catalyzing demethylation—known as methylesterases (MESs)—have received less attention. Here, we present a comprehensive review of the plant MES family, focusing on known biochemical and biological functions, and evolution in the plant kingdom. Thirty-two MES genes have been biochemically characterized, with substrates including methyl esters of plant hormones and several other specialized metabolites. One characterized member demonstrates non-esterase activity, indicating functional diversity in this family. MES genes regulate biological processes, including biotic and abiotic defense, as well as germination and root development. While MES genes are absent in green algae, they are ubiquitous among the land plants analyzed. Extant MES genes belong to three groups of deep origin, implying ancient gene duplication and functional divergence. Two of these groups have yet to have any characterized members. Much remains to be uncovered about the enzymatic functions, biological roles, and evolution of the MES family. Full article

(This article belongs to the Special Issue Evolution of Land Plants)

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15 pages, 1782 KB

Open AccessReview

Molecular Phylogenomics Reveals the Deep Evolutionary History of Carnivory across Land Plants

by Steven J. Fleck and Richard W. Jobson

Plants 2023, 12(19), 3356; https://doi.org/10.3390/plants12193356 - 22 Sep 2023

Cited by 8 | Viewed by 6252

Abstract

Plastid molecular phylogenies that broadly sampled angiosperm lineages imply that carnivorous plants evolved at least 11 times independently in 13 families and 6 orders. Within and between these clades, the different prey capture strategies involving flypaper and pitfall structures arose in parallel with the subsequent evolution of snap traps and suction bladders. Attempts to discern the deep ontological history of carnivorous structures using multigene phylogenies have provided a plastid-level picture of sister relationships at the family level. Here, we present a molecular phylogeny of the angiosperms based on nuclear target sequence capture data (Angiosperms-353 probe set), assembled by the Kew Plant Trees of Life initiative, which aims to complete the tree of life for plants. This phylogeny encompasses all carnivorous and protocarnivorous families, although certain genera such as Philcoxia (Plantaginaceae) are excluded. This study offers a novel nuclear gene-based overview of relationships within and between carnivorous families and genera. Consistent with previous broadly sampled studies, we found that most carnivorous families are not affiliated with any single family. Instead, they emerge as sister groups to large clades comprising multiple non-carnivorous families. Additionally, we explore recent genomic studies across various carnivorous clades that examine the evolution of the carnivorous syndrome in relation to whole-genome duplication, subgenome dominance, small-scale gene duplication, and convergent evolution. Furthermore, we discuss insights into genome size evolution through the lens of carnivorous plant genomes. Full article

(This article belongs to the Special Issue Evolution of Land Plants)

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