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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 (30 November 2023) | Viewed by 14343

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Special Issue Editors

Dr. Wenpan Dong

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Guest Editor

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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Dr. Shiliang Zhou

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Guest Editor

State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
Interests: DNA barcoding; phylogeography; genomics; population genetics; speciation; conservation genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

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 large amount of information to produce more reliable results. The challenge is to make the best use of genomic data to establish robust, realistic phylogenetic relationships and to 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, genotype-phenotype relationships.

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

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
Dr. Shiliang Zhou
Guest Editors

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 phylogenomics
genome
gene evolution
species diversity
speciation
ecogenomics

Related Special Issue

Plant Phylogenomics and Genetic Diversity 2.0 in International Journal of Molecular Sciences (3 articles)

Published Papers (8 papers)

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Research

14 pages, 6168 KiB

Open AccessArticle

Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae)

by Xinyu Liu, Yuran Bai, Yachao Wang, Yifeng Chen, Wenpan Dong and Zhixiang Zhang

Int. J. Mol. Sci. 2023, 24(22), 16130; https://doi.org/10.3390/ijms242216130 - 9 Nov 2023

Cited by 2 | Viewed by 1254

Abstract

Hypericum perforatum (St. John’s Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of H. perforatum and compared the genome variation among five Hypericum species to discover dynamic changes and elucidate the mechanisms that lead to genome rearrangements in the Hypericum chloroplast genomes. The H. perforatum chloroplast genome is 139,725 bp, exhibiting a circular quadripartite structure with two copies of inverted repeats (IRs) separating a large single-copy region and a small single-copy region. The H. perforatum chloroplast genome encodes 106 unique genes, including 73 protein-coding genes, 29 tRNAs, and 4 rRNAs. Hypericum chloroplast genomes exhibit genome rearrangement and significant variations among species. The genome size variation among the five Hypericum species was remarkably associated with the expansion or contraction of IR regions and gene losses. Three genes—trnK-UUU, infA, and rps16—were lost, and three genes—rps7, rpl23, and rpl32—were pseudogenized in Hypericum. All the Hypericum chloroplast genomes lost the two introns in clpP, the intron in rps12, and the second intron in ycf3. Hypericum chloroplast genomes contain many long repeat sequences, suggesting a role in facilitating rearrangements. Most genes, according to molecular evolution assessments, are under purifying selection. Full article

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

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18 pages, 4083 KiB

Open AccessArticle

Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes

by Xin Shen, Wenjin Zong, Yingang Li, Xinhong Liu, Fei Zhuge, Qi Zhou, Shiliang Zhou and Dongyue Jiang

Int. J. Mol. Sci. 2023, 24(21), 15612; https://doi.org/10.3390/ijms242115612 - 26 Oct 2023

Cited by 2 | Viewed by 1342

Abstract

Cherries (Prunus Subgenus Cerasus) have economic value and ecological significance, yet their phylogeny, geographic origin, timing, and dispersal patterns remain challenging to understand. To fill this gap, we conducted a comprehensive analysis of the complete chloroplast genomes of 54 subg. Cerasus individuals, along with 36 additional genomes from the NCBI database, resulting in a total of 90 genomes for comparative analysis. The chloroplast genomes of subg. Cerasus exhibited varying sizes and consisted of 129 genes, including protein-coding, transfer RNA, and ribosomIal RNA genes. Genomic variation was investigated through InDels and SNPs, showcasing distribution patterns and impact levels. A comparative analysis of chloroplast genome boundaries highlighted variations in inverted repeat (IR) regions among Cerasus and other Prunus species. Phylogeny based on whole-chloroplast genome sequences supported the division of Prunus into three subgenera, I subg. Padus, II subg. Prunus and III subg. Cerasus. The subg. Cerasus was subdivided into seven lineages (IIIa to IIIg), which matched roughly to taxonomic sections. The subg. Padus first diverged 51.42 Mya, followed by the separation of subg. Cerasus from subg. Prunus 39.27 Mya. The subg. Cerasus started diversification at 15.01 Mya, coinciding with geological and climatic changes, including the uplift of the Qinghai–Tibet Plateau and global cooling. The Himalayans were the refuge of cherries, from which a few species reached Europe through westward migration and another species reached North America through northeastward migration. The mainstage of cherry evolution was on the Qing–Tibet Plateau and later East China and Japan as well. These findings strengthen our understanding of the evolution of cherry and provide valuable insights into the conservation and sustainable utilization of cherry’s genetic resources. Full article

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

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16 pages, 1496 KiB

Open AccessArticle

Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants

by Zhi-Qiong Mo, Jie Wang, Michael Möller, Jun-Bo Yang and Lian-Ming Gao

Int. J. Mol. Sci. 2023, 24(17), 13216; https://doi.org/10.3390/ijms241713216 - 25 Aug 2023

Viewed by 1224

Abstract

Accurate species identification is key to conservation and phylogenetic inference. Living plant collections from botanical gardens/arboretum are important resources for the purpose of scientific research, but the proportion of cultivated plant misidentification are un-tested using DNA barcodes. Here, we assembled the next-generation barcode (complete plastid genome and complete nrDNA cistron) and mitochondrial genes from genome skimming data of Torreya species with multiple accessions for each species to test the species discrimination and the misidentification proportion of cultivated plants used in Torreya studies. A total of 38 accessions were included for analyses, representing all nine recognized species of genus Torreya. The plastid phylogeny showed that all 21 wild samples formed species-specific clades, except T. jiulongshanensis. Disregarding this putative hybrid, seven recognized species sampled here were successfully discriminated by the plastid genome. Only the T. nucifera accessions grouped into two grades. The species identification rate of the nrDNA cistron was 62.5%. The Skmer analysis based on nuclear reads from genome skims showed promise for species identification with seven species discriminated. The proportion of misidentified cultivated plants from arboreta/botanical gardens was relatively high with four accessions (23.5%) representing three species. Interspecific relationships within Torreya were fully resolved with maximum support by plastomes, where Torreya jackii was on the earliest diverging branch, though sister to T. grandis in the nrDNA cistron tree, suggesting that this is likely a hybrid species between T. grandis and an extinct Torreya ancestor lineage. The findings here provide quantitative insights into the usage of cultivated samples for phylogenetic study. Full article

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

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17 pages, 2994 KiB

Open AccessArticle

Genome-Wide Comparison and Functional Characterization of HMGR Gene Family Associated with Shikonin Biosynthesis in Lithospermum erythrorhizon

by Xuan Wang, Changyi Wang, Minkai Yang, Wencai Jie, Aliya Fazal, Jiangyan Fu, Tongming Yin, Jinfeng Cai, Bao Liu, Guihua Lu, Hongyan Lin, Hongwei Han, Zhongling Wen, Jinliang Qi and Yonghua Yang

Int. J. Mol. Sci. 2023, 24(15), 12532; https://doi.org/10.3390/ijms241512532 - 7 Aug 2023

Cited by 2 | Viewed by 2642

Abstract

3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), as the rate-limiting enzyme in the mevalonate pathway, is essential for the biosynthesis of shikonin in Lithospermum erythrorhizon. However, in the absence of sufficient data, the principles of a genome-wide in-depth evolutionary exploration of HMGR family members in plants, as well as key members related to shikonin biosynthesis, remain unidentified. In this study, 124 HMGRs were identified and characterized from 36 representative plants, including L. erythrorhizon. Vascular plants were found to have more HMGR family genes than nonvascular plants. The phylogenetic tree revealed that during lineage and species diversification, the HMGRs evolved independently and intronless LerHMGRs emerged from multi-intron HMGR in land plants. Among them, Pinus tabuliformis and L. erythrorhizon had the most HMGR gene duplications, with 11 LerHMGRs most likely expanded through WGD/segmental and tandem duplications. In seedling roots and M9 cultured cells/hairy roots, where shikonin biosynthesis occurs, LerHMGR1 and LerHMGR2 were expressed significantly more than other genes. The enzymatic activities of LerHMGR1 and LerHMGR2 further supported their roles in catalyzing the conversion of HMG-CoA to mevalonate. Our findings provide insight into the molecular evolutionary properties and function of the HMGR family in plants and a basis for the genetic improvement of efficiently produced secondary metabolites in L. erythrorhizon. Full article

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

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14 pages, 2990 KiB

Open AccessArticle

Haplotype Analysis of GmSGF14 Gene Family Reveals Its Roles in Photoperiodic Flowering and Regional Adaptation of Soybean

by Liwei Jiang, Peiguo Wang, Hongchang Jia, Tingting Wu, Shan Yuan, Bingjun Jiang, Shi Sun, Yuxian Zhang, Liwei Wang and Tianfu Han

Int. J. Mol. Sci. 2023, 24(11), 9436; https://doi.org/10.3390/ijms24119436 - 29 May 2023

Cited by 1 | Viewed by 1096

Abstract

Flowering time and photoperiod sensitivity are fundamental traits that determine soybean adaptation to a given region or a wide range of geographic environments. The General Regulatory Factors (GRFs), also known as 14-3-3 family, are involved in protein–protein interactions in a phosphorylation-dependent manner, thus regulating ubiquitous biological processes, such as photoperiodic flowering, plant immunity and stress response. In this study, 20 soybean GmSGF14 genes were identified and divided into two categories according to phylogenetic relationships and structural characteristics. Real-time quantitative PCR analysis revealed that GmSGF14g, GmSGF14i, GmSGF14j, GmSGF14k, GmSGF14m and GmSGF14s were highly expressed in all tissues compared to other GmSGF14 genes. In addition, we found that the transcript levels of GmSGF14 family genes in leaves varied significantly under different photoperiodic conditions, indicating that their expression responds to photoperiod. To explore the role of GmSGF14 in the regulation of soybean flowering, the geographical distribution of major haplotypes and their association with flowering time in six environments among 207 soybean germplasms were studied. Haplotype analysis confirmed that the GmSGF14m^H4 harboring a frameshift mutation in the 14-3-3 domain was associated with later flowering. Geographical distribution analysis demonstrated that the haplotypes related to early flowering were frequently found in high-latitude regions, while the haplotypes associated with late flowering were mostly distributed in low-latitude regions of China. Taken together, our results reveal that the GmSGF14 family genes play essential roles in photoperiodic flowering and geographical adaptation of soybean, providing theoretical support for further exploring the function of specific genes in this family and varietal improvement for wide adaptability. Full article

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

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17 pages, 3041 KiB

Open AccessArticle

Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies

by Roman Zhidkin, Peter Zhurbenko, Olesya Bogomaz, Elizaveta Gorodilova, Ivan Katsapov, Dmitry Antropov and Tatiana Matveeva

Int. J. Mol. Sci. 2023, 24(8), 6932; https://doi.org/10.3390/ijms24086932 - 8 Apr 2023

Cited by 2 | Viewed by 1657

Abstract

A variety of plant species found in nature contain agrobacterial T-DNAs in their genomes which they transmit in a series of sexual generations. Such T-DNAs are called cellular T-DNAs (cT-DNAs). cT-DNAs have been discovered in dozens of plant genera, and are suggested to be used in phylogenetic studies, since they are well-defined and unrelated to other plant sequences. Their integration into a particular chromosomal site indicates a founder event and a clear start of a new clade. cT-DNA inserts do not disseminate in the genome after insertion. They can be large and old enough to generate a range of variants, thereby allowing the construction of detailed trees. Unusual cT-DNAs (containing the rolB/C-like gene) were found in our previous study in the genome data of two Vaccinium L. species. Here, we present a deeper study of these sequences in Vaccinium L. Molecular-genetic and bioinformatics methods were applied for sequencing, assembly, and analysis of the rolB/C-like gene. The rolB/C-like gene was discovered in 26 new Vaccinium species and Agapetes serpens (Wight) Sleumer. Most samples were found to contain full-size genes. It allowed us to develop approaches for the phasing of cT-DNA alleles and reconstruct a Vaccinium phylogenetic relationship. Intra- and interspecific polymorphism found in cT-DNA makes it possible to use it for phylogenetic and phylogeographic studies of the Vaccinium genus. Full article

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

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15 pages, 3103 KiB

Open AccessArticle

Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

by Chang Guo, Kangjia Liu, Enze Li, Yifeng Chen, Jiayao He, Wenying Li, Wenpan Dong and Zhili Suo

Int. J. Mol. Sci. 2023, 24(4), 3606; https://doi.org/10.3390/ijms24043606 - 10 Feb 2023

Cited by 7 | Viewed by 1832

Abstract

Lagerstroemia indica L. is a well-known ornamental plant with large pyramidal racemes, long flower duration, and diverse colors and cultivars. It has been cultivated for nearly 1600 years and is essential for investigating the germplasm and assessing genetic variation to support international cultivar identification and breeding programs. In this study, 20 common Lagerstroemia indica cultivars from different varietal groups and flower morphologies, as well as multiple wild relative species, were analyzed to investigate the maternal donor of Lagerstroemia indica cultivars and to discover the genetic variation and relationships among cultivars based on plastome and nuclear ribosomal DNA (nrDNA) sequences. A total of 47 single nucleotide polymorphisms (SNPs) and 24 insertion/deletions (indels) were identified in the 20 L. indica cultivars’ plastome and 25 SNPs were identified in the nrDNA. Phylogenetic analysis based on the plastome sequences showed that all the cultivars formed a clade with the species of L. indica, indicating that L. indica was the maternal donor of the cultivars. Population structure and PCA analyses supported two clades of cultivars, which exhibited significant genetic differences according to the plastome dataset. The results of the nrDNA supported that all 20 cultivars were divided into three clades and most of the cultivars had at least two genetic backgrounds and higher gene flow. Our results suggest that the plastome and nrDNA sequences can be used as molecular markers for assessing the genetic variation and relationships of L. indica cultivars. Full article

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

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19 pages, 13629 KiB

Open AccessArticle

Phylogeny and Historical Biogeography of the East Asian Clematis Group, Sect. Tubulosae, Inferred from Phylogenomic Data

by Rudan Lyu, Jiamin Xiao, Mingyang Li, Yike Luo, Jian He, Jin Cheng and Lei Xie

Int. J. Mol. Sci. 2023, 24(3), 3056; https://doi.org/10.3390/ijms24033056 - 3 Feb 2023

Cited by 1 | Viewed by 2307

Abstract

The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae. Full article

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

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