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Forests
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Phylogenetic Relationships and Molecular Evolution of Plants in Forests
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Phylogenetic Relationships and Molecular Evolution of Plants in Forests

A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (30 December 2023) | Viewed by 3036

Special Issue Editors

Dr. Xupo Ding

E-Mail Website
Guest Editor
Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, No. 158, Daxue West Road, Nanning 530006, China
Interests: tree genomics; rare and endangered trees; plant evolution; bioinformatics; special genes
Special Issues, Collections and Topics in MDPI journals
Dr. Chunlai Wu

E-Mail Website
Guest Editor
College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
Interests: tea genomics; bioinformatics; plant evolution
Dr. Minjie Deng

E-Mail Website
Guest Editor
College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
Interests: phytohormone crosstalk; stress response; molecular evolution; regulation of shoot architecture

Special Issue Information

Dear Colleagues,

Forests are typical biodiverse and complex ecosystems on our planet and provide an incredible array of plant species. These plants in forests play critical roles in maintaining the overall health and function of forest ecosystems. Yet the molecular evidence of classification and evolution history of some plants in forests is still inadequate. Recent advances in molecular techniques such as plastid genome and ultra-long sequencing of rDNA have revolutionized our understanding of plant evolution and phylogenetics, allowing for unprecedented resolution in reconstructing the relationships among the lineages of different plants or their germplasm. This Special Issue aims to report the latest progress obtained in phylogenetic relationships and the molecular evolution of plants in forests. All type of articles including original research, reviews and new methods are greatly welcomed. The scope of this research topic includes, but is not limited to, the molecular evolution of tree plants, the phylogenetic relationship, plastid phylogenomics, SNP discovery, structure variation and the innovative evaluation of plant germplasm resources. Plant mitochondrial genome and specific molecular evaluation methods are preferentially considered. Papers exploring the development of molecular markers such as SSR, AFLP, MSAP, are also welcomed, but these markers should be obtained from a range of the population and verified beforehand.

Dr. Xupo Ding
Dr. Chunlai Wu
Dr. Minjie Deng
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. Forests is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • tree plant evolution
  • plastid genomics
  • species relationships
  • ultra-long sequencing of rDNA
  • molecular evaluate method
  • molecular marker
  • mitochondria
  • phylogenetic

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Published Papers (2 papers)

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17 pages, 7777 KiB  
Article
The Complete Plastid Genome Sequences of the Belian (Eusideroxylon zwageri): Comparative Analysis and Phylogenetic Relationships with Other Magnoliids
by Wen Zhu, Yunhong Tan, Xinxin Zhou, Yu Song and Peiyao Xin
Forests 2023, 14(12), 2443; https://doi.org/10.3390/f14122443 - 14 Dec 2023
Cited by 1 | Viewed by 1292
Abstract
The Belian (Eusideroxylon zwageri Teijsm. & Binn.) is a commercially important timber species in Southeast Asia that was listed on the IUCN Red List of threatened species in 1998. Six years ago, we published an article in Genome Biology Ecology entitled “Evolutionary [...] Read more.
The Belian (Eusideroxylon zwageri Teijsm. & Binn.) is a commercially important timber species in Southeast Asia that was listed on the IUCN Red List of threatened species in 1998. Six years ago, we published an article in Genome Biology Ecology entitled “Evolutionary Comparisons of the Chloroplast Genome in Lauraceae and Insights into Loss Events in the Magnoliids” in which one complete plastid genome of Belian was assembled for comparative analyses of the plastomes in Lauraceae. However, a recent study concluded that our sequenced Belian individual can be located in the clade of Myristicaceae instead of that of Lauraceae. Here, we performed reanalyses of an additional two Belian plastomes, along with 42 plastomes from plants spanning 10 families of the Magnoliids. The three Belian plastomes are 39% CG and vary in length from 157,535 to 157,577 bp. A total of 37 tRNA genes, 8 rRNA genes, and 85 protein-coding genes were among the 130 annotated genes. There were 95–101 repeat sequences and 56–61 simple repeat sequences (SSRs). Comparative genomic analysis revealed 170 mutation sites in their plastomes, which include 111 substitutions, 53 indels, and 6 microinversions. Phylogeny was reconstructed using maximum-likelihood and Bayesian approaches for 44 magnoliids species, indicating that the 3 Belian individuals were nested among the species in the Lauraceae family rather than Myristicaceae. Full article
(This article belongs to the Special Issue Phylogenetic Relationships and Molecular Evolution of Plants in Forests)
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12 pages, 4297 KiB  
Article
Complete Chloroplast Genome Structural Characterization and Comparative Analysis of Viburnum japonicum (Adoxaceae)
by Hong Zhu, Juan Liu, Hepeng Li, Chunlei Yue and Meirong Gao
Forests 2023, 14(9), 1819; https://doi.org/10.3390/f14091819 - 6 Sep 2023
Cited by 3 | Viewed by 1410
Abstract
Viburnum japonicum (Thunb.) Sprengel is an endangered species endemic to coastal regions of eastern Asia (China, Japan, and South Korea). However, its systematic position has been controversial. In this study, we present the complete chloroplast (cp) genome of V. japonicum (GenBank OP644292) sequenced [...] Read more.
Viburnum japonicum (Thunb.) Sprengel is an endangered species endemic to coastal regions of eastern Asia (China, Japan, and South Korea). However, its systematic position has been controversial. In this study, we present the complete chloroplast (cp) genome of V. japonicum (GenBank OP644292) sequenced using the Illumina NovaSeq platform. The cp genome has a total length of 158,606 bp and a G+C contents of 38.08%. It consists of a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs) regions measuring 87,060 bp, 18,510 bp, and 26,516 bp, respectively. A total of 131 genes were identified, including 87 protein-coding genes, 36 transfer RNA genes (tRNAs), and 8 ribosomal RNA genes(rRNAs). Additionally, a total of 44 dispersed repeats were detected, including three types: forward, palindromic, and reverse. Among the 38 SSR loci that were discovered, the majority were mononucleotide loci composed of A/T. Furthermore, we found that 15 genes (accD, atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps12, rps16, trnA-UGC, trnI, trnK-UUU, and trnL-UAA) contain one intron, while clpP and ycf3 have two introns. The relative synonymous codon usage (RSCU) analysis detected 31 high-frequency codons, where A/U bases accounted for 93.55% of the total, indicating an asymmetry in chloroplast gene and a presence for A/U bases. Comparative analysis of genome structure and sequences data of V. japonicum chloroplast genomes in comparison with other closely related species demonstrated a high level of conservation in their structure and organization. Furthermore, three mutation hotspots (psbH, rps19, and trnL) were identified, which could be valuable for future phylogenetic and population genetic research. Phylogenetic analysis revealed that the two accessions of V. japonicum are closely related to a group of V. setigerum, V. erosum, and V. fordiae within the Viburnum genus. In conclusion, this study provides important insights for accurately identifying and understanding the phylogeny of Viburnum species through the complete cp genome sequencing of V. japonicum. Full article
(This article belongs to the Special Issue Phylogenetic Relationships and Molecular Evolution of Plants in Forests)
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