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Plant Phylogenomics and Genetic Diversity (2nd Edition)

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 November 2024) | Viewed by 11183

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Dr. Wenpan Dong

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Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
Interests: chloroplast genome evolution; DNA barcoding; plant genetic diversity; plant phylogenomics; Oleaceae; medicinal plants; biogeography; molecular evolution
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Dear Colleagues,

Phylogenomics is the intersection of the fields of phylogeny and genomics. Phylogenomics aims at reconstructing the evolutionary histories of organisms, taking into account whole genomes or large fractions of genomes. Compared with traditional phylogenetic studies, phylogenomics has the advantage of manipulating a large amount of information to produce more reliable results. The challenge is to make the best use of genomic data to establish robust and realistic phylogenetic relationships and elucidate evolutionary relationships. The genomic era has arrived, and more than 1000 plant genome sequences have been published, representing 788 different species. Genetic diversity serves as a way for populations to adapt to changing environments. The development of phylogenomics will bring new insights into the study of population genetics in terms of population structure, population history, geographic isolation, gene flow, ecological and genomic interactions, and genotype–phenotype relationships.

This Special Issue welcomes manuscripts that advance the knowledge and understanding of plant phylogeny, evolutionary history, and genetic diversity on a genomic basis. Topics covered by this Special Issue include, but are not limited to, the following:

Establishment and clarification of plant evolutionary relationships.
Gene family evolution.
Species diversity.
Improvements in methods for acquiring genomic data.
Plant speciation.
Ecological and genomic interactions.
Genotype–phenotype relationships.

Dr. Wenpan Dong
Guest Editor

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Keywords

plant phylogenomics
genome
gene evolution
species diversity
speciation
ecogenomics

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Plant Phylogenomics and Genetic Diversity in International Journal of Molecular Sciences (8 articles)

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Research

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20 pages, 6317 KiB

Open AccessArticle

Repeatome Analysis and Satellite DNA Chromosome Patterns in Hedysarum Species

by Olga Yu. Yurkevich, Tatiana E. Samatadze, Svyatoslav A. Zoshchuk, Alexey R. Semenov, Alexander I. Morozov, Inessa Yu. Selyutina, Alexandra V. Amosova and Olga V. Muravenko

Int. J. Mol. Sci. 2024, 25(22), 12340; https://doi.org/10.3390/ijms252212340 - 17 Nov 2024

Viewed by 425

Abstract

The cosmopolitan genus Hedysarum L. (Fabaceae) is divided into sections Hedysarum, Stracheya, and Multicaulia. This genus includes many valuable medicinal, melliferous, and forage species. The species taxonomy and genome relationships within the sections are still unclear. We examined intra- and interspecific diversity in the section (sect.) Hedysarum based on repeatome analyses using NGS data, bioinformatic technologies, and chromosome FISH mapping of 35S rDNA, 5S rDNA, and the identified satellite DNA families (satDNAs). A comparison of repeatomes of H. alpinum, H. theinum, and H. flavescens revealed differences in their composition. However, similarity in sequences of most satDNAs indicated a close relationship between genomes within sect. Hedysarum. New effective satDNA chromosomal markers were detected, which is important for karyotype analyses within Hedysarum. Intra- and interspecific variability in the chromosomal distribution patterns of the studied markers were revealed, and species karyograms were constructed. These results provided new insight into the karyotype structures and genomic diversity within sect. Hedysarum, clarified the systematic position of H. sachalinense and H. arcticum, and confirmed the distant genomic relationships between species from sections Hedysarum and Multicaulia. Our findings are important for further comparative genome studies within the genus Hedysarum. Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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13 pages, 26304 KiB

Open AccessArticle

Assessing Genetic Diversity in Endangered Plant Orchidantha chinensis: Chloroplast Genome Assembly and Simple Sequence Repeat Marker-Based Evaluation

by Yiwei Zhou, Jianjun Tan, Lishan Huang, Yuanjun Ye and Yechun Xu

Int. J. Mol. Sci. 2024, 25(20), 11137; https://doi.org/10.3390/ijms252011137 - 17 Oct 2024

Viewed by 514

Abstract

Orchidantha chinensis T. L. Wu, an endemic species in China, is listed as a key protected wild plant in Guangdong Province. However, the lack of reports on the chloroplast genome and simple sequence repeat (SSR) markers has hindered the assessment of its genetic diversity and conservation strategies. The limited number of molecular markers to assess the genetic diversity of this species, and thus develop proper conservation strategies, highlighted the urgent need to develop new ones. This study developed new SSR markers and investigated genetic variation using 96 samples of O. chinensis from seven populations. Through high-throughput sequencing, a complete chloroplast genome of 134,407 bp was assembled. A maximum-likelihood phylogenetic tree, based on the chloroplast genome, showed that O. chinensis is closely related to Ravenala madagascariensis. The study identified 52 chloroplast SSRs (cpSSRs) and 5094 expressed sequence tag SSRs (EST-SSRs) loci from the chloroplast genome and leaf transcriptome, respectively. Twenty-one polymorphic SSRs (seven cpSSRs and fourteen EST-SSRs) were selected to evaluate the genetic variation in 96 accessions across seven populations. Among these markers, one cpSSR and 11 EST-SSRs had high polymorphism information content (>0.5). Cluster, principal coordinate, and genetic structure analyses indicated that groups G1 and G6 were distinct from the other five groups. However, an analysis of molecular variance showed greater variation within groups than among groups. The genetic distance among the populations was significantly positively correlated with geographical distance. These findings provide new markers for studying the genetic variability of O. chinensis and offer a theoretical foundation for its conservation strategies. Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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17 pages, 4672 KiB

Open AccessArticle

Chloroplast Genome Variation and Phylogenetic Relationships of Autochthonous Varieties of Vitis vinifera from the Don Valley

by F. S. Sharko, K. O. Petrova, M. V. Patrushev, D. Y. Fedosov and S. V. Toshchakov

Int. J. Mol. Sci. 2024, 25(18), 9928; https://doi.org/10.3390/ijms25189928 - 14 Sep 2024

Viewed by 994

Abstract

The autochthonous grape varieties of the Don Valley, situated in southern Russia, constitute a distinctive element of regional cultural heritage. These varieties have been adapted over centuries to the region’s specific local climatic and soil conditions. For the most part, these varieties are not imported from other countries. They are closely related to varieties found in Crimea and the North Caucasus. In this study, we obtained the first complete, unfragmented sequences of the chloroplast genomes of eight autochthonous varieties from the Don Valley and one from Crimea. We also performed a comparative analysis of their genomic features. The size of Vitis vinifera chloroplast genome sequences varied from 160,925 to 160,991 bp, depending on the cultivar, with a uniform GC ratio of 37.38%. Each genome consists of four subregions: a single copy region (LSC) ranging from 89,158 to 89,336 bp, a small single copy region (SSC) ranging from 19,070 to 19,073 bp, and a pair of inverted repeat regions (IRa and IRb) in the range of 26,292 to 26,353 bp. The chloroplast genomes of the studied V. vinifera varieties contained 130 genes, including 85 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The sequence divergence analysis has enabled the identification of four highly variable regions, which may be utilized as potential markers for phylogenetic analysis. The analysis revealed the presence of 58 to 61 SSRs and multiple long repeated sequences in the chloroplast genomes of these varieties. The phylogenetic analyses of the sequences obtained and complete chloroplast genomes available from public databases indicated that the majority of autochthonous V. vinifera varieties do not have a direct origin from any European variety. Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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15 pages, 3538 KiB

Open AccessArticle

Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation of Gastrochilus (Aeridinae, Orchidaceae), with a Focus on the Systematic Position of Haraella retrocalla

by Peng Zhou, Wan-Shun Lei, Ying-Kang Shi, Yi-Zhen Liu, Yan Luo, Ji-Hong Li and Xiao-Guo Xiang

Int. J. Mol. Sci. 2024, 25(15), 8500; https://doi.org/10.3390/ijms25158500 - 4 Aug 2024

Viewed by 835

Abstract

Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this genus have not been fully resolved, and the plastome evolution has not been investigated either. In this study, five plastomes of Gastrochilus were newly reported, and sixteen plastomes of Gastrochilus were used to conduct comparative and phylogenetic analyses. Our results showed that the Gastrochilus plastomes ranged from 146,183 to 148,666 bp, with a GC content of 36.7–36.9%. There were 120 genes annotated, consisting of 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. Additionally, the repeat sequences and codon usage bias of Gastrochilus plastomes were highly conserved. Twenty hypervariable regions were selected as potential DNA barcodes. The phylogenetic relationships within Gastrochilus were well resolved based on the whole plastome, especially among main clades. Furthermore, both molecular and morphological data strongly supported Haraella retrocalla as a member of Gastrochilus (G. retrocallus). Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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15 pages, 4755 KiB

Open AccessArticle

Chloroplast Genomes Evolution and Phylogenetic Relationships of Caragana species

by Xingyong Cui, Kangjia Liu, Enze Li, Zhixiang Zhang and Wenpan Dong

Int. J. Mol. Sci. 2024, 25(12), 6786; https://doi.org/10.3390/ijms25126786 - 20 Jun 2024

Viewed by 852

Abstract

Caragana sensu lato (s.l.) includes approximately 100 species that are mainly distributed in arid and semi-arid regions. Caragana species are ecologically valuable for their roles in windbreaking and sand fixation. However, the taxonomy and phylogenetic relationships of the genus Caragana are still unclear. In this study, we sequenced and assembled the chloroplast genomes of representative species of Caragana and reconstructed robust phylogenetic relationships at the section level. The Caragana chloroplast genome has lost the inverted repeat region and wascategorized in the inverted repeat loss clade (IRLC). The chloroplast genomes of the eight species ranged from 128,458 bp to 135,401 bp and contained 110 unique genes. All the Caragana chloroplast genomes have a highly conserved structure and gene order. The number of long repeats and simple sequence repeats (SSRs) showed significant variation among the eight species, indicating heterogeneous evolution in Caragana. Selective pressure analysis of the genes revealed that most of the protein-coding genes evolved under purifying selection. The phylogenetic analyses indicated that each section forms a clade, except the section Spinosae, which was divided into two clades. This study elucidated the evolution of the chloroplast genome within the widely distributed genus Caragana. The detailed information obtained from this study can serve as a valuable resource for understanding the molecular dynamics and phylogenetic relationships within Caragana. Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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18 pages, 2621 KiB

Open AccessArticle

Study of Dispersed Repeats in the Cyanidioschyzon merolae Genome

by Valentina Rudenko and Eugene Korotkov

Int. J. Mol. Sci. 2024, 25(8), 4441; https://doi.org/10.3390/ijms25084441 - 18 Apr 2024

Viewed by 1161

Abstract

In this study, we applied the iterative procedure (IP) method to search for families of highly diverged dispersed repeats in the genome of Cyanidioschyzon merolae, which contains over 16 million bases. The algorithm included the construction of position weight matrices (PWMs) for repeat families and the identification of more dispersed repeats based on the PWMs using dynamic programming. The results showed that the C. merolae genome contained 20 repeat families comprising a total of 33,938 dispersed repeats, which is significantly more than has been previously found using other methods. The repeats varied in length from 108 to 600 bp (522.54 bp in average) and occupied more than 72% of the C. merolae genome, whereas previously identified repeats, including tandem repeats, have been shown to constitute only about 28%. The high genomic content of dispersed repeats and their location in the coding regions suggest a significant role in the regulation of the functional activity of the genome. Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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19 pages, 6962 KiB

Open AccessArticle

Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom

by Hanbing Cai, Rong Xu, Ping Tian, Mengjie Zhang, Ling Zhu, Tuo Yin, Hanyao Zhang and Xiaozhen Liu

Int. J. Mol. Sci. 2024, 25(1), 257; https://doi.org/10.3390/ijms25010257 - 23 Dec 2023

Cited by 2 | Viewed by 1603

Abstract

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687–152,759 bp in length. Each genome contains 126–132 genes, including 81–87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61–64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae. Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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15 pages, 4812 KiB

Open AccessArticle

Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots

by Cheng-Yuan Zhou, Wen-Jun Lin, Ruyi Li, Yuhan Wu, Zhong-Jian Liu and Ming-He Li

Int. J. Mol. Sci. 2024, 25(1), 184; https://doi.org/10.3390/ijms25010184 - 22 Dec 2023

Cited by 2 | Viewed by 1320

Abstract

Angraecum, commonly known as Darwin’s orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of Angraecum were firstly reported and the potential variability hotspots were explored. The plastomes possessed the typical quadripartite structure and ranged from 150,743 to 151,818 base pair (bp), with a guanine–cytosine (GC) content of 36.6–36.9%. The plastomes all contained 120 genes, consisting of 74 protein-coding genes (CDS), 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes; all ndh genes were pseudogenized or lost. A total of 30 to 46 long repeats and 55 to 63 SSRs were identified. Relative synonymous codon usage (RSCU) analysis indicated a high degree of conservation in codon usage bias. The Ka/Ks ratios of most genes were lower than 1, indicating that they have undergone purifying selection. Based on the ranking of Pi (nucleotide diversity) values, five regions (trnS^GCU-trnG^GCC, ycf1-trnN^GGU, trnN^GUU-rpl32, psaC-ndhE and trnS^GCU-trnG^GCC) and five protein-coding genes (rpl32, rps16, psbK, rps8, and ycf1) were identified. The consistent and robust phylogenetic relationships of Angraecum were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus Angraecum was strongly supported as a monophyletic group and sister to Aeridinae. Our study provides an ideal system for investigating molecular identification, plastome evolution and DNA barcoding for Angraecum. Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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Review

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15 pages, 4357 KiB

Open AccessReview

Species of the Sections Hedysarum and Multicaulia of the Genus Hedysarum (Fabaceae): Taxonomy, Distribution, Chromosomes, Genomes, and Phylogeny

by Olga Yu. Yurkevich, Tatiana E. Samatadze, Svyatoslav A. Zoshchuk, Alexandra V. Amosova and Olga V. Muravenko

Int. J. Mol. Sci. 2024, 25(15), 8489; https://doi.org/10.3390/ijms25158489 - 3 Aug 2024

Viewed by 827

Abstract

The genus Hedysarum L. (Fabaceae) includes about 200 species of annual and perennial herbs distributed in Asia, Europe, North Africa, and North America. Many species of this genus are valuable medicinal, melliferous, and forage resources. In this review, we consider the taxonomic history of the genus Hedysarum, the chromosomal organization of the species from the sections Hedysarum and Multicaulia, as well as phylogenetic relationships between these sections. According to morphological, genetic, and phylogenetic data, the genus Hedysarum is divided into three main sections: Hedysarum (= syn. Gamotion), Multicaulia, and Stracheya. In species of this genus, two basic chromosome numbers, x = 7 (section Hedysarum) and x = 8 (sections Multicaulia and Stracheya), were determined. The systematic positions of some species within the sections are still uncertain due to their morphological similarities. The patterns of distribution of molecular chromosomal markers (45S rDNA, 5S rDNA, and different satellite DNAs) in karyotypes of various Hedysarum species made it possible to determine their ploidy status and also specify genomic relationships within the sections Hedysarum and Multicaulia. Recent molecular phylogenetic studies clarified significantly the taxonomy and evolutionary development of the genus Hedysarum. Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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14 pages, 921 KiB

Open AccessReview

Research Progress in the Regulation of the ABA Signaling Pathway by E3 Ubiquitin Ligases in Plants

by Hongyun Kou, Xiaopei Zhang, Jinghao Jia, Ming Xin, Jinhui Wang, Lili Mao, Ahmedov Miraziz Baltaevich and Xianliang Song

Int. J. Mol. Sci. 2024, 25(13), 7120; https://doi.org/10.3390/ijms25137120 - 28 Jun 2024

Cited by 1 | Viewed by 1557

Abstract

E3 ubiquitin ligases (UBLs), as enzymes capable of specifically recognizing target proteins in the process of protein ubiquitination, play crucial roles in regulating responses to abiotic stresses such as drought, salt, and temperature. Abscisic acid (ABA), a plant endogenous hormone, is essential to regulating plant growth, development, disease resistance, and defense against abiotic stresses, and acts through a complex ABA signaling pathway. Hormone signaling transduction relies on protein regulation, and E3 ubiquitin ligases play important parts in regulating the ABA pathway. Therefore, this paper reviews the ubiquitin–proteasome-mediated protein degradation pathway, ABA-related signaling pathways, and the regulation of ABA-signaling-pathway-related genes by E3 ubiquitin ligases, aiming to provide references for further exploration of the relevant research on how plant E3 ubiquitin ligases regulate the ABA pathway. Full article

(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity (2nd Edition))

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