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Plant Molecular Phylogenetics and Evolutionary Genomics III

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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: 31 December 2024 | Viewed by 20602

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Prof. Dr. Alex Troitsky

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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
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Prof. Dr. Jaakko Hyvönen

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1. Finnish Museum of Natural History (Botany), PO Box 7, 00014 Univ. Helsinki, Helsinki, Finland
2. Organismal & Evol. Biology & Viikki Plant Sci. Center, Univ. Helsinki, Helsinki, Finland
Interests: biological sciences; bryophyta; cladistics; mosses; systematics taxonomy

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 serves as a blueprint for investigations in almost all biological disciplines. The evolutionary paradigm is a framework for studying the structural and functional basis of living beings, and 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, barcoding and biogeography, molecular ecology, and evo-devo, as well as the bioinformatic and laboratory methods of the aforementioned studies.

Prof. Dr. Alex Troitsky
Prof. Dr. Jaakko Hyvönen
Guest Editors

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Keywords

molecular phylogeny
evolutionary genomics
molecular evolution
phylogenomics
genomic biodiversity
taxonomy
DNA barcoding
bioinformatics

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Research

24 pages, 3840 KiB

Open AccessArticle

Comparative Plastomics of Plantains (Plantago, Plantaginaceae) as a Tool for the Development of Species-Specific DNA Barcodes

by Furrukh Mehmood, Mingai Li, Alessio Bertolli, Filippo Prosser and Claudio Varotto

Plants 2024, 13(19), 2691; https://doi.org/10.3390/plants13192691 - 25 Sep 2024

Viewed by 604

Abstract

Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications with potentially serious consequences for product safety/quality. To test the possibility of developing species-specific barcoding markers, we de novo assembled plastome sequences of individuals of Plantago argentea, Plantago atrata, P. lanceolata, and Plantago maritima. These genomes were characterized in comparison with both previously sequenced conspecific accessions and other publicly available plastomes, thus providing an assessment of both intraspecific and interspecific genetic variation in Plantago plastomes. Additionally, molecular evolutionary analyses indicated that eleven protein-coding genes involved in different plastid functions in Plantago plastomes underwent positive selection, suggesting they might have contributed to enhancing species’ adaptation during the evolutionary history of Plantago. While the most variable mutational hotspots in Plantago plastomes were not suitable for the development of species-specific molecular markers, species-specific polymorphisms could discriminate P. lanceolata from its closest relatives. Taken together, these results highlight the potential of plastome sequencing for the development of molecular markers to improve the identification of species with relevance in herbal products. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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11 pages, 1131 KiB

Open AccessArticle

A Diverging Species within the Stewartia gemmata (Theaceae) Complex Revealed by RAD-Seq Data

by Hanyang Lin, Wenhao Li and Yunpeng Zhao

Plants 2024, 13(10), 1296; https://doi.org/10.3390/plants13101296 - 8 May 2024

Viewed by 1043

Abstract

Informed species delimitation is crucial in diverse biological fields; however, it can be problematic for species complexes. Showing a peripatric distribution pattern, Stewartia gemmata and S. acutisepala (the S. gemmata complex) provide us with an opportunity to study species boundaries among taxa undergoing nascent speciation. Here, we generated genomic data from representative individuals across the natural distribution ranges of the S. gemmata complex using restriction site-associated DNA sequencing (RAD-seq). Based on the DNA sequence of assembled loci containing 41,436 single-nucleotide polymorphisms (SNPs) and invariant sites, the phylogenetic analysis suggested strong monophyly of both the S. gemmata complex and S. acutisepala, and the latter was nested within the former. Among S. gemmata individuals, the one sampled from Mt. Tianmu (Zhejiang) showed the closest evolutionary affinity with S. acutisepala (which is endemic to southern Zhejiang). Estimated from 2996 high-quality SNPs, the genetic divergence between S. gemmata and S. acutisepala was relatively low (an F_st of 0.073 on a per-site basis). Nevertheless, we observed a proportion of genomic regions showing relatively high genetic differentiation on a windowed basis. Up to 1037 genomic bins showed an F_st value greater than 0.25, accounting for 8.31% of the total. After SNPs subject to linkage disequilibrium were pruned, the principal component analysis (PCA) showed that S. acutisepala diverged from S. gemmata along the first and the second PCs to some extent. By applying phylogenomic analysis, the present study determines that S. acutisepala is a variety of S. gemmata and is diverging from S. gemmata, providing empirical insights into the nascent speciation within a species complex. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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21 pages, 5910 KiB

Open AccessArticle

Genome-Wide Analysis of MYB Gene Family in Chrysanthemum ×morifolium Provides Insights into Flower Color Regulation

by Bohao Wang, Xiaohui Wen, Boxiao Fu, Yuanyuan Wei, Xiang Song, Shuangda Li, Luyao Wang, Yanbin Wu, Yan Hong and Silan Dai

Plants 2024, 13(9), 1221; https://doi.org/10.3390/plants13091221 - 28 Apr 2024

Viewed by 1561

Abstract

MYBs constitute the second largest transcription factor (TF) superfamily in flowering plants with substantial structural and functional diversity, which have been brought into focus because they affect flower colors by regulating anthocyanin biosynthesis. Up to now, the genomic data of several Chrysanthemum species have been released, which provides us with abundant genomic resources for revealing the evolution of the MYB gene family in Chrysanthemum species. In the present study, comparative analyses of the MYB gene family in six representative species, including C. lavandulifolium, C. seticuspe, C. ×morifolium, Helianthus annuus, Lactuca sativa, and Arabidopsis thaliana, were performed. A total of 1104 MYBs, which were classified into four subfamilies and 35 lineages, were identified in the three Chrysanthemum species (C. lavandulifolium, C. seticuspe, and C. ×morifolium). We found that whole-genome duplication and tandem duplication are the main duplication mechanisms that drove the occurrence of duplicates in CmMYBs (particularly in the R2R3-MYB subfamily) during the evolution of the cultivated chrysanthemums. Sequence structure and selective pressure analyses of the MYB gene family revealed that some of R2R3-MYBs were subjected to positive selection, which are mostly located on the distal telomere segments of the chromosomes and contain motifs 7 and 8. In addition, the gene expression analysis of CmMYBs in different organs and at various capitulum developmental stages of C. ×morifolium indicated that CmMYBS2, CmMYB96, and CmMYB109 might be the negative regulators for anthocyanin biosynthesis. Our results provide the phylogenetic context for research on the genetic and functional evolution of the MYB gene family in Chrysanthemum species and deepen our understanding of the regulatory mechanism of MYB TFs on the flower color of C. ×morifolium. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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24 pages, 16963 KiB

Open AccessArticle

Comparative Study of Plastomes in Solanum tuberosum with Different Cytoplasm Types

by Svetlana Goryunova, Anastasia Sivolapova, Oksana Polivanova, Evgeniia Sotnikova, Alexey Meleshin, Natalia Gaitova, Anna Egorova, Anatoly Semenov, Ekaterina Gins, Alina Koroleva, Evgeny Moskalev, Elena Oves, Oleg Kazakov, Aleksey Troitsky and Denis Goryunov

Plants 2023, 12(23), 3995; https://doi.org/10.3390/plants12233995 - 28 Nov 2023

Viewed by 1567

Abstract

The potato is one of the most important food crops in the world. Improving the efficiency of potato breeding is of great importance for solving the global food problem. Today, researchers distinguish between six potato cytoplasm types: A, M, P, T, W, D. In the current study, the complete chloroplast genomes of Solanum tuberosum accessions with five out of the six major cytoplasmic genome types were sequenced (T-, W-, D-, A-, and P-genomes). A comparative analysis of the plastomes in potato accessions with different cytoplasm types was carried out for the first time. The time of origin of the different cytoplasm types was estimated. The presence of two main groups of chloroplast genomes among cultivated potato was confirmed. Based on the phylogenetic analysis of the complete plastome sequences, five main evolutionary branches of chloroplast genomes can be distinguished within the Petota section. Samples with A- and P- cytoplasm formed isolated and distant groups within a large and polymorphic group of samples with M-type cytoplasm, suggesting that A and P genomes arose independently. The findings suggest that the diversity of the T-genome in S. tuberosum Group Tuberosum could be initially low due to a bottle neck already existing at the origin of the Chilean clade. Differences in the rbcL gene sequence may be one of the factors causing differences in economically important traits in species with A and T-type cytoplasm. The data obtained will contribute to the development of methods for molecular marking of cytoplasm types and increase knowledge about the evolution and diversity of potato. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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23 pages, 11317 KiB

Open AccessArticle

Analysis of Carica papaya Informs Lineage-Specific Evolution of the Aquaporin (AQP) Family in Brassicales

by Zhi Zou, Yujiao Zheng and Zhengnan Xie

Plants 2023, 12(22), 3847; https://doi.org/10.3390/plants12223847 - 14 Nov 2023

Cited by 3 | Viewed by 1425

Abstract

Aquaporins (AQPs), a type of intrinsic membrane proteins that transport water and small solutes across biological membranes, play crucial roles in plant growth and development. This study presents a first genome-wide identification and comparative analysis of the AQP gene family in papaya (Carica papaya L.), an economically and nutritionally important fruit tree of tropical and subtropical regions. A total of 29 CpAQP genes were identified, which represent five subfamilies, i.e., nine plasma intrinsic membrane proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), seven NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). Although the family is smaller than the 35 members reported in Arabidopsis, it is highly diverse, and the presence of CpXIP genes as well as orthologs in Moringa oleifera and Bretschneidera sinensis implies that the complete loss of the XIP subfamily in Arabidopsis is lineage-specific, sometime after its split with papaya but before Brassicaceae–Cleomaceae divergence. Reciprocal best hit-based sequence comparison of 530 AQPs and synteny analyses revealed that CpAQP genes belong to 29 out of 61 identified orthogroups, and lineage-specific evolution was frequently observed in Brassicales. Significantly, the well-characterized NIP3 group was completely lost; lineage-specific loss of the NIP8 group in Brassicaceae occurred sometime before the divergence with Cleomaceae, and lineage-specific loss of NIP2 and SIP3 groups in Brassicaceae occurred sometime after the split with Cleomaceae. In contrast to a predominant role of recent whole-genome duplications (WGDs) on the family expansion in B. sinensis, Tarenaya hassleriana, and Brassicaceae plants, no recent AQP repeats were identified in papaya, and ancient WGD repeats are mainly confined to the PIP subfamily. Subfamily even group-specific evolution was uncovered via comparing exon–intron structures, conserved motifs, the aromatic/arginine selectivity filter, and gene expression profiles. Moreover, down-regulation during fruit ripening and expression divergence of duplicated CpAQP genes were frequently observed in papaya. These findings will not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further studies of AQP genes in papaya and species beyond. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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14 pages, 2761 KiB

Open AccessArticle

Genome-Wide Analysis of Lipoxygenase (LOX) Genes in Angiosperms

by Paula Oliveira Camargo, Natália Fermino Calzado, Ilara Gabriela Frasson Budzinski and Douglas Silva Domingues

Plants 2023, 12(2), 398; https://doi.org/10.3390/plants12020398 - 14 Jan 2023

Cited by 8 | Viewed by 2561

Abstract

Lipoxygenases (LOXs) are enzymes that catalyze the addition of an oxygen molecule to unsaturated fatty acids, thus forming hydroperoxides. In plants, these enzymes are encoded by a multigene family found in several organs with varying activity patterns, by which they are classified as LOX9 or LOX13. They are involved in several physiological functions, such as growth, fruit development, and plant defense. Despite several studies on genes of the LOX family in plants, most studies are restricted to a single species or a few closely related species. This study aimed to analyze the diversity, evolution, and expression of LOX genes in angiosperm species. We identified 247 LOX genes among 23 species of angiosperms and basal plants. Phylogenetic analyses identified clades supporting LOX13 and two main clades for LOX9: LOX9_A and LOX9_B. Eudicot species such as Tarenaya hassleriana, Capsella rubella, and Arabidopsis thaliana did not present LOX9_B genes; however, LOX9_B was present in all monocots used in this study. We identified that there were potential new subcellular localization patterns and conserved residues of oxidation for LOX9 and LOX13 yet unexplored. In summary, our study provides a basis for the further functional and evolutionary study of lipoxygenases in angiosperms. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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22 pages, 4355 KiB

Open AccessArticle

Annotation of the Turnera subulata (Passifloraceae) Draft Genome Reveals the S-Locus Evolved after the Divergence of Turneroideae from Passifloroideae in a Stepwise Manner

by Paige M. Henning, Eric H. Roalson, Wali Mir, Andrew G. McCubbin and Joel S. Shore

Plants 2023, 12(2), 286; https://doi.org/10.3390/plants12020286 - 7 Jan 2023

Cited by 3 | Viewed by 2443

Abstract

A majority of Turnera species (Passifloraceae) exhibit distyly, a reproductive system involving both self-incompatibility and reciprocal herkogamy. This system differs from self-incompatibility in Passiflora species. The genetic basis of distyly in Turnera is a supergene, restricted to the S-morph, and containing three S-genes. How supergenes and distyly evolved in Turnera, and the other Angiosperm families exhibiting distyly remain largely unknown. Unraveling the evolutionary origins in Turnera requires the generation of genomic resources and extensive phylogenetic analyses. Here, we present the annotated draft genome of the S-morph of distylous Turnera subulata. Our annotation allowed for phylogenetic analyses of the three S-genes’ families across 56 plant species ranging from non-seed plants to eudicots. In addition to the phylogenetic analysis, we identified the three S-genes’ closest paralogs in two species of Passiflora. Our analyses suggest that the S-locus evolved after the divergence of Passiflora and Turnera. Finally, to provide insights into the neofunctionalization of the S-genes, we compared expression patterns of the S-genes with close paralogs in Arabidopsis and Populus trichocarpa. The annotation of the T. subulata genome will provide a useful resource for future comparative work. Additionally, this work has provided insights into the convergent nature of distyly and the origin of supergenes. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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22 pages, 6198 KiB

Open AccessArticle

Evidence from Phylogenomics and Morphology Provide Insights into the Phylogeny, Plastome Evolution, and Taxonomy of Kitagawia

by Jia-Qing Lei, Chang-Kun Liu, Jing Cai, Megan Price, Song-Dong Zhou and Xing-Jin He

Plants 2022, 11(23), 3275; https://doi.org/10.3390/plants11233275 - 28 Nov 2022

Cited by 9 | Viewed by 2304

Abstract

Kitagawia Pimenov is one of the segregate genera of Peucedanum sensu lato within the Apiaceae. The phylogenetic position and morphological delimitation of Kitagawia have been controversial. In this study, we used plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences to reconstruct the phylogeny of Kitagawia, along with comparative plastome and morphological analyses between Kitagawia and related taxa. The phylogenetic results identified that all examined Kitagawia species were divided into Subclade I and Subclade II within the tribe Selineae, and they were all distant from the representative members of Peucedanum sensu stricto. The plastomes of Kitagawia and related taxa showed visible differences in the LSC/IRa junction (JLA) and several hypervariable regions, which separated Subclade I and Subclade II from other taxa. Fruit anatomical and micromorphological characteristics, as well as general morphological characteristics, distinguished the four Kitagawia species within Subclade I from Subclade II and other related genera. This study supported the separation of Kitagawia from Peucedanum sensu lato, confirmed that Kitagawia belongs to Selineae, and two species (K. praeruptora and K. formosana) within Subclade II should be placed in a new genus. We believe that the “core” Kitagawia should be limited to Subclade I, and this genus can be distinguished by the association of a series of morphological characteristics. Overall, our study provides new insights into the phylogeny, plastome evolution, and taxonomy of Kitagawia. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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10 pages, 13281 KiB

Open AccessCommunication

Phylogenomic Analysis of the Plastid Genome of the Peruvian Purple Maize Zea mays subsp. mays cv. ‘INIA 601’

by Juan D. Montenegro, Irene Julca, Lenin D. Chumbe-Nolasco, Lila M. Rodríguez-Pérez, Ricardo Sevilla Panizo, Alicia Medina-Hoyos, Dina L. Gutiérrez-Reynoso, Juan Carlos Guerrero-Abad, Carlos A. Amasifuen Guerra and Aura L. García-Serquén

Plants 2022, 11(20), 2727; https://doi.org/10.3390/plants11202727 - 15 Oct 2022

Cited by 3 | Viewed by 2966

Abstract

Peru is an important center of diversity for maize; its different cultivars have been adapted to distinct altitudes and water availability and possess an array of kernel colors (red, blue, and purple), which are highly appreciated by local populations. Specifically, Peruvian purple maize is a collection of native landraces selected and maintained by indigenous cultures due to its intense purple color in the seed, bract, and cob. This color is produced by anthocyanin pigments, which have gained interest due to their potential use in the food, agriculture, and pharmaceutical industry. It is generally accepted that the Peruvian purple maize originated from a single ancestral landrace ‘Kculli’, but it is not well understood. To study the origin of the Peruvian purple maize, we assembled the plastid genomes of the new cultivar ‘INIA 601’ with a high concentration of anthocyanins, comparing them with 27 cultivars/landraces of South America, 9 Z. mays subsp. parviglumis, and 5 partial genomes of Z. mays subsp. mexicana. Using these genomes, plus four other maize genomes and two outgroups from the NCBI database, we reconstructed the phylogenetic relationship of Z. mays. Our results suggest a polyphyletic origin of purple maize in South America and agree with a complex scenario of domestication with recurrent gene flow from wild relatives. Additionally, we identify 18 plastid positions that can be used as high-confidence genetic markers for further studies. Altogether, these plastid genomes constitute a valuable resource to study the evolution and domestication of Z. mays in South America. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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17 pages, 3783 KiB

Open AccessFeature PaperArticle

Plastid Genome of Equisetum xylochaetum from the Atacama Desert, Chile and the Relationships of Equisetum Based on Frequently Used Plastid Genes and Network Analysis

by Anchittha Satjarak, Linda E. Graham, Marie T. Trest and Patricia Arancibia-Avila

Plants 2022, 11(7), 1001; https://doi.org/10.3390/plants11071001 - 6 Apr 2022

Viewed by 2537

Abstract

The modern pteridophyte genus Equisetum is the only survivor of Sphenopsida, an ancient clade known from the Devonian. This genus, of nearly worldwide distribution, comprises approximately 15 extant species. However, genomic information is limited. In this study, we assembled the complete chloroplast genome of the giant species Equisetum xylochaetum from a metagenomic sequence and compared the plastid genome structure and protein-coding regions with information available for two other Equisetum species using network analysis. Equisetum chloroplast genomes showed conserved traits of quadripartite structure, gene content, and gene order. Phylogenetic analysis based on plastome protein-coding regions corroborated previous reports that Equisetum is monophyletic, and that E. xylochaetum is more closely related to E. hyemale than to E. arvense. Single-gene phylogenetic estimation and haplotype analysis showed that E. xylochaetum belonged to the subgenus Hippochaete. Single-gene haplotype analysis revealed that E. arvense, E. hyemale, E. myriochaetum, and E. variegatum resolved more than one haplotype per species, suggesting the presence of a high diversity or a high mutation rate of the corresponding nucleotide sequence. Sequences from E. bogotense appeared as a distinct group of haplotypes representing the subgenus Paramochaete that diverged from Hippochaete and Equisetum. In addition, the taxa that were frequently located at the joint region of the map were E. scirpoides and E. pratense, suggesting the presence of some plastome characters among the Equiseum subgenera. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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