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Plant Phylogenomics and Genetic Diversity (2nd Edition)
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Plant Phylogenomics and Genetic Diversity (2nd Edition)

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: 20 November 2024 | Viewed by 4298

Special Issue Editor

Dr. Wenpan Dong

E-Mail Website
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
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 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

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

Published Papers (5 papers)

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Research

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15 pages, 4755 KiB  
Article
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 389
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 [...] Read more.
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  
Article
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 762
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 [...] Read more.
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  
Article
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 1 | Viewed by 1259
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 [...] Read more.
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  
Article
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
Viewed by 899
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 [...] Read more.
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 (trnSGCU-trnGGCC, ycf1-trnNGGU, trnNGUU-rpl32, psaC-ndhE and trnSGCU-trnGGCC) 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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14 pages, 921 KiB  
Review
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
Viewed by 293
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 [...] Read more.
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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