Molecular Phylogenetics

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Systematics, Taxonomy, Nomenclature and Classification".

Deadline for manuscript submissions: closed (30 August 2019) | Viewed by 10591

Special Issue Editors


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Guest Editor
Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka 599-8531, Japan
Interests: gene function and evolution; bioinformatics; genome biology; comparative genomics; microbiome; molecular phylogenetics; next-generation sequencing; RNA-seq analysis; correlation network analysis; DNA barcoding

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Guest Editor
Graduate School of Science, Kyoto University, Kyoto 606-8501, Japan
Interests: plant light responses; photoreceptors; evolution of photoreceptors; photoreceptor diversity; evolution of gene functions; molecular structure

Special Issue Information

Dear Colleagues,

Plants originated from algae, came ashore as liverworts and mosses, and then evolved as vascular plants, which includes gymnosperms and angiosperms. To construct the phylogenetic tree of plants along with their speciation, in these decades, molecular-based approaches have been performed, such as the APG system.

For the construction of the phylogenetic tree of plants, particular genes that exist in the most plants are used, e.g., small subunits of ribosomal DNA (16S or 18S rDNA) and internal transcribed spacers (ITS) of ribosomal DNA, cytochrome oxidase 1 (CO1), ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL), and maturase K (matK). Recent reports on the evolution of plant genes has showed that the genes evolved with more or less divergence from the speciation. It is surely expected that the number of such reports will increase because next-generation sequencers have been used in various fields of plant science.

Therefore, this Special Issue will publish articles (original research papers, perspectives, hypotheses, opinions, reviews, modeling approaches, and methods) that focus on molecular phylogenetics in plants and the evolution and diversity of plant genes. Studies of whole plants, model plants, crop plants, trees, aquatic plants, and native species are most welcome.

Dr. Yoshiyuki Ogata
Prof. Dr. Akira Nagatani
Guest Editors

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Keywords

  • phylogenetics
  • phylogenetic tree
  • genome evolution
  • phylogenetic diversity
  • speciation
  • evolution and gene function
  • comparative genomics

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Published Papers (2 papers)

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Research

27 pages, 3326 KiB  
Article
Genetic, Morphological, and Biochemical Diversity of Argan Tree (Argania spinosa L.) (Sapotaceae) in Tunisia
by Marwa Louati, Cuneyt Ucarli, Burcu Arikan, Baraket Ghada, Amel Salhi Hannachi and Neslihan Turgut-Kara
Plants 2019, 8(9), 319; https://doi.org/10.3390/plants8090319 - 1 Sep 2019
Cited by 12 | Viewed by 5043
Abstract
Argan trees are normally endemic to Morocco and Algeria, but hundreds of argan trees exist in Tunisia, some introduced from Morocco and some from unknown origins. The aim of the present study was to evaluate the genetic, morphological, and biochemical diversity of the [...] Read more.
Argan trees are normally endemic to Morocco and Algeria, but hundreds of argan trees exist in Tunisia, some introduced from Morocco and some from unknown origins. The aim of the present study was to evaluate the genetic, morphological, and biochemical diversity of the argan trees in Tunisia. In this study, we used morphometric data collected from vegetative tissue, as well as pomological characteristics related to fruits, stones, and kernels. Genetic variation in 60 trees of Tunisian Argania spinosa L. was estimated using inter-simple sequence repeats (ISSRs). Mutation screening and genotyping by high-resolution melting (HRM) was performed to detect delta-6-desaturase (D6D) variants in the tested individuals, and finally fatty acid analysis of argan leaves with gas chromatography (GC) was performed. The plant materials used in this study originated from four different sites in Tunisia. Analysis of morphological characteristics showed large variability both within and between the studied collections. The analysis of ISSR polymorphisms gave information about the diversity within and between populations. HRM analysis showed that all 60 argan individuals were grouped into 10 different categories. The results of the gas chromatography analysis showed that the presence of omega-3 fatty acids EPA and DHA was noticeable in some argan leaves. Full article
(This article belongs to the Special Issue Molecular Phylogenetics)
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19 pages, 1435 KiB  
Article
Phylogenetic Reconstruction and Divergence Time Estimation of Blumea DC. (Asteraceae: Inuleae) in China Based on nrDNA ITS and cpDNA trnL-F Sequences
by Ying-bo Zhang, Yuan Yuan, Yu-xin Pang, Fu-lai Yu, Chao Yuan, Dan Wang and Xuan Hu
Plants 2019, 8(7), 210; https://doi.org/10.3390/plants8070210 - 8 Jul 2019
Cited by 11 | Viewed by 4970
Abstract
The genus Blumea is one of the most economically important genera of Inuleae (Asteraceae) in China. It is particularly diverse in South China, where 30 species are found, more than half of which are used as herbal medicines or in the chemical industry. [...] Read more.
The genus Blumea is one of the most economically important genera of Inuleae (Asteraceae) in China. It is particularly diverse in South China, where 30 species are found, more than half of which are used as herbal medicines or in the chemical industry. However, little is known regarding the phylogenetic relationships and molecular evolution of this genus in China. We used nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) trnL-F sequences to reconstruct the phylogenetic relationship and estimate the divergence time of Blumea in China. The results indicated that the genus Blumea is monophyletic and it could be divided into two clades that differ with respect to the habitat, morphology, chromosome type, and chemical composition of their members. The divergence time of Blumea was estimated based on the two root times of Asteraceae. The results indicated that the root age of Asteraceae of 76–66 Ma may maintain relatively accurate divergence time estimation for Blumea, and Blumea might had diverged around 49.00–18.43 Ma. This common ancestor had an explosive expansion during the Oligocene and Miocene and two major clades were differentiated during these epochs 29.60 Ma (17.76–45.23 Ma 95% HPD (Highest Posterior Density). Evidence from paleogeography and paleoclimate studies has confirmed that Blumea experienced differentiation and an explosive expansion during the Oligocene and Miocene. Full article
(This article belongs to the Special Issue Molecular Phylogenetics)
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