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Forests
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Biodiversity, Conservation and Phylogeny of Trees
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Biodiversity, Conservation and Phylogeny of Trees

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

Deadline for manuscript submissions: closed (1 August 2023) | Viewed by 5273

Special Issue Editors

Prof. Dr. Wenbin Yu

E-Mail Website
Guest Editor
Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
Interests: conservation biology; DNA barcoding; molecular evolution; organelle genome; phylogeny; systematics
Dr. Joeri S. Strijk

E-Mail Website
Guest Editor
Associate Professor, Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei
Interests: evolution; genomics; plant biodiversity; phylogenomics; taxonomy

Special Issue Information

Dear Colleagues,

There are around 3.0 trillion trees in forests, which cover more than 30% of the world’s land surface, store an estimated 296 gigatons of carbon, and host the majority of terrestrial biodiversity. A recent study indicates that there are approximately 73,000 tree species in the world. Of them, up to 9000 tree species have not been discovered or described yet. The aim of this Special Issue, entitled “Biodiversity, Conservation and Phylogeny of Trees”, calls together tree specialists and researchers to develop state-of-the-art methodologies and techniques in investigations on biodiversity and conservation of trees. As tree species are long-lived and difficult to identify using vegetative specimens alone by non-specialists, molecular approaches or DNA barcoding could be standardized and reproducible in species identification and new species discovery. Moreover, genetic or genomic data may be useful for biodiversity and conservation assessments. Therefore, research articles and reviews on all aspects of genetics and genomics for tree biodiversity, conservation, phylogeny, species delimitation, as well as regional biodiversity inventory can be included in this Special Issue.

Potential topics include, but are not limited to:

  • Biodiversity inventory
  • Biogeography
  • DNA barcoding and species delimitation
  • Genomics
  • Phylogeny and systematics
  • Phylogeography
  • Population and conservation genetics

Prof. Dr. Wenbin Yu
Dr. Joeri S. Strijk
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

  • biodiversity
  • biogeography
  • conservation biology
  • genomics
  • phylogeny
  • systematics
 

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Published Papers (3 papers)

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Research

13 pages, 2479 KiB  
Article
Analysis of the Conservation Status, Genetic Diversity and Population Structure of Endangered Ostrya rehderiana Resources Using SSR Markers
by Qi Zhou, Guangjiong Wang and Yingang Li
Forests 2023, 14(8), 1519; https://doi.org/10.3390/f14081519 - 26 Jul 2023
Cited by 2 | Viewed by 1384
Abstract
Climate change and anthropogenic habitat destruction have led to the extinction of many species. Ostrya rehderiana (Betulaceae) is a typical rare and endangered species, and only five wild individuals have survived. In the 1980s, the offspring of the five wild trees were planted [...] Read more.
Climate change and anthropogenic habitat destruction have led to the extinction of many species. Ostrya rehderiana (Betulaceae) is a typical rare and endangered species, and only five wild individuals have survived. In the 1980s, the offspring of the five wild trees were planted for ex situ conservation and have grown into stable cultivated populations. To protect O. rehderiana resources, the genetic diversity and genetic structure of this species were analysed using SSR markers. A total of 167 alleles were detected among 116 individuals from the only wild population and five cultivated populations at 12 SSR loci. The genetic diversity level of O. rehderiana was He = 0.88. Genetic differentiations occurred among populations (Fst = 0.17), which was also validated via an analysis of molecular variance (AMOVA). The cultivated populations TM1, TM2 and WC showed considerable genetic differences from the wild population WP based on Bayesian clustering analysis, phylogenetic tree reconstruction and principal coordinate analysis (PCoA). The cultivated populations had more genetic diversity than the wild one. It is speculated that novel alleles may have emerged out of natural processes of evolution and adaptation. The cultivated population QY with the most unique alleles has begun to propagate seedlings naturally, and the small population size and geographical isolation may negatively influence the founding of this population. To weaken the effects of bottlenecks and genetic drift, anthropogenic gene flow among populations is necessary. In addition to the wild population, the cultivated population QY and six individuals from populations QY and WC were also found to be important for the conservation of O. rehderiana. The results of this study may guide the development of conservation policies for endangered O. rehderiana. Full article
(This article belongs to the Special Issue Biodiversity, Conservation and Phylogeny of Trees)
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17 pages, 9005 KiB  
Article
Complete Chloroplast Genome Sequences of Two Ehretia Trees (Ehretia cymosa and Ehretia obtusifolia): Genome Structures and Phylogenetic Analysis
by Mohammad S. Alawfi, Dhafer A. Alzahrani and Enas J. Albokhari
Forests 2023, 14(7), 1486; https://doi.org/10.3390/f14071486 - 20 Jul 2023
Cited by 3 | Viewed by 1468
Abstract
Ehretiaceae is a family in the order Boraginales. It contains more than 150 species. The Ehretiaceae classification has remained elusive and changed over time from subfamily to family, or vice versa. In this paper, we sequenced, characterized, and analyzed the complete chloroplast (cp) [...] Read more.
Ehretiaceae is a family in the order Boraginales. It contains more than 150 species. The Ehretiaceae classification has remained elusive and changed over time from subfamily to family, or vice versa. In this paper, we sequenced, characterized, and analyzed the complete chloroplast (cp) genomes of Ehretia cymosa and Ehretia obtusifolia, and their cp genomes were compared to those of related species. The length of the chloroplast genomes of E. cymosa was 156,328 bp, whereas that of E. obtusifolia was 155,961 bp. Each genome contained 114 genes, including 80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Repeat analysis revealed that complement, forward, palindromic, and reverse repeats were present in the chloroplast genomes of both species. Simple sequence repeat analysis showed that the chloroplast genomes of E. cymosa and E. obtusifolia comprise 141 and 139 microsatellites, respectively. Phylogenetic analysis based on Bayesian and maximum likelihood analyses divided the order Boraginales into two well-supported clades. The first clade includes a single family (Boraginaceae), and the second clade includes three families (Ehretiaceae, Cordiaceae, and Heliotropiaceae). This study provides valuable genomic resources and insights into the evolutionary relationships within Boraginales. Full article
(This article belongs to the Special Issue Biodiversity, Conservation and Phylogeny of Trees)
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22 pages, 4287 KiB  
Article
Synonymous Codon Usage Bias in the Chloroplast Genomes of 13 Oil-Tea Camellia Samples from South China
by Jing Chen, Wuqiang Ma, Xinwen Hu and Kaibing Zhou
Forests 2023, 14(4), 794; https://doi.org/10.3390/f14040794 - 13 Apr 2023
Cited by 3 | Viewed by 2089
Abstract
Synonymous codon usage (SCU) bias in oil-tea camellia cpDNAs was determined by examining 13 South Chinese oil-tea camellia samples and performing bioinformatics analysis using GenBank sequence information, revealing conserved bias among the samples. GC content at the third position (GC3) was the lowest, [...] Read more.
Synonymous codon usage (SCU) bias in oil-tea camellia cpDNAs was determined by examining 13 South Chinese oil-tea camellia samples and performing bioinformatics analysis using GenBank sequence information, revealing conserved bias among the samples. GC content at the third position (GC3) was the lowest, with a preference for A or T, suggesting weak SCU bias. The GC contents at the first two codon positions (GC1 and GC2) were extremely significantly correlated with one another but not with the expected number of codons (ENC). GC3 was not correlated with GC1 and GC2 but was extremely significantly correlated with ENC. Of the 30 high-frequency codons, 15, 14, 1 and 0 codons had U, A, G and C at the third position, respectively. The points for most genes were distributed above the neutrality plot diagonal. The points for 20 genes, accounting for 37.74% of all coding sequences (CDSs), were distributed on or near the ENC plot standard curve, and the ENC ratio ranged from −0.05–0.05. However, those of the other genes were under the standard curve, with higher ENC ratios. The points for most genes were distributed in the lower part of the PR2 plot, especially the bottom right corner. Twenty-eight highly expressed codons were screened and 11, 9, 7 and 1 codons had U, A, C and G as the third base, respectively. Twenty optimal codons were screened by comparing high-frequency codons and 11, 8, 0 and 1 codons had U, A, C and G as the third base, respectively. All samples were divided into six clades (r2 = 0.9190, d = 0.5395) according to a relative synonymous codon usage (RSCU)-based phylogenetic tree. Camellia gauchowensis, C. vietnamensis, an undetermined oil-tea camellia species from Hainan province, and C. osmantha belonged to the same clade; the genetic relationships between C. gauchowensis, C. vietnamensis and the undetermined species were the closest. In summary, SCU bias is influenced by selection, while the influence of mutation cannot be ignored. As the SCU bias differed between species, this feature can be used to identify plant species and infer their genetic relationships. For example, C. vietnamensis and C. gauchowensis can be merged into one species, and the undetermined species can be considered C. vietnamensis. The results described here provide a basis for studying cpDNA gene expression and the development of cpDNA genetic engineering. Full article
(This article belongs to the Special Issue Biodiversity, Conservation and Phylogeny of Trees)
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