Plant Phylogeny and Genome Evolution

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 30 July 2024 | Viewed by 3468

Special Issue Editor

College of Life Science, Northwest University, Xi'an, China
Interests: plant phylogeny; genome evolution; molecular evolution of cytoplasmic genomes; species divergence

Special Issue Information

Dear Colleagues,

Green plants, representing an important photosynthetic autotrophic taxon, provide oxygen, food, and other raw materials necessary for human life. Chloroplasts, vital organelles found in green plants, play key roles in photosynthesis and carbohydrate metabolism. Cytoplasmic genomes (including chloroplast and mitochondrial genomes) are ring-shaped DNA molecule structures in land plants with features, such as uniparental inheritance and being recombination-free, which make them unique model systems in the studies of phylogeny, genome evolution, origin and divergence of species, etc.

This Special Issue focuses on the molecular evolution of various plant genomes, including, but not limited to, that of chloroplasts and mitochondrial genomes. We aim to address structural variations (including tRNA structural variations of chloropalst genomes), copy number variations, mutations, selection, intracellular gene transfer, and molecular evolution of plant genomes. The phylogenetic relationships, origin and divergence, and genome evolution of plants are also of interest.

If you are interested in contributing to this Special Issue, please contact us at your earliest convenience. We looking forward to hearing from you.

Prof. Dr. Zhonghu Li
Guest Editor

Manuscript Submission Information

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Keywords

  • cytoplasmic genomes
  • molecular evolution
  • phylogeny
  • species divergence
  • structural variation
  • intracellular gene transfer
  • genomics

Published Papers (2 papers)

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Research

16 pages, 3382 KiB  
Article
DNA Barcoding and Species Classification of Morchella
by Wei Sa, Jinxia Qiao, Qiyuan Gao, Zhonghu Li and Qianhan Shang
Genes 2022, 13(10), 1806; https://doi.org/10.3390/genes13101806 - 06 Oct 2022
Cited by 4 | Viewed by 1614
Abstract
True morels (Morchella) are a well-known edible fungi, with economically and medicinally important values. However, molecular identification and species taxonomy of the genus Morchella have long been controversial, due to numerous intermediate morphologies among species. In this study, we determined the [...] Read more.
True morels (Morchella) are a well-known edible fungi, with economically and medicinally important values. However, molecular identification and species taxonomy of the genus Morchella have long been controversial, due to numerous intermediate morphologies among species. In this study, we determined the identification efficiency of DNA barcoding and species classification of 260 individuals from 45 Morchella species, on the basis of multiple nuclear DNA markers. DNA barcoding analysis showed that the individual DNA fragment has a lower resolution of species identification than that of combined multiple DNA markers. ITS showed the highest level of species discrimination among the individual genetic markers. Interestingly, the combined DNA markers significantly increased the resolution of species identification. A combination of four DNA genes (EF1-α, RPB1, RPB2 and ITS) showed a higher species delimitation than that any combination of two or three markers. Phylogenetic analysis suggested that the species in genus Morchella could have been divided into two large genetic clades, the Elata Clade and Esculenta Clade lineages. The two lineages divided approximately 133.11 Mya [95% HPD interval: 82.77–197.95] in the early Cretaceous period. However, some phylogenetic species of Morchella showed inconsistent evolutionary relationships with the traditional morphological classifications, which may have resulted from incomplete lineage sorting and/or introgressive hybridization among species. These findings demonstrate that the interspecific gene introgression may have affected the species identification of true morels, and that the combined DNA markers significantly improve the resolution of species discrimination. Full article
(This article belongs to the Special Issue Plant Phylogeny and Genome Evolution)
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20 pages, 8564 KiB  
Article
Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes of Scrophularia incisa Complex (Scrophulariaceae)
by Ruihong Wang, Jing Gao, Jieying Feng, Zhaoping Yang, Zhechen Qi, Pan Li and Chengxin Fu
Genes 2022, 13(10), 1691; https://doi.org/10.3390/genes13101691 - 21 Sep 2022
Cited by 6 | Viewed by 1422
Abstract
The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the [...] Read more.
The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai–Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia. Full article
(This article belongs to the Special Issue Plant Phylogeny and Genome Evolution)
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