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Applying Molecular Tools to Genetic Diversity and Divergence in Trees

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

Deadline for manuscript submissions: closed (20 January 2023) | Viewed by 3750

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Special Issue Editor

Prof. Dr. Peng Zhao

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Guest Editor

Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
Interests: genomics; gene expression; evolutionary botany; gene family; molecular markers; DNA methylation; phylogenomic; sub-genomes; genome-wide association studies (GWASs); genetic diversity; domestication
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Special Issue Information

Dear Colleagues,

Genomes, chloroplast genomes, and gene families are becoming increasingly serious concerns in forest tree species, and have influenced many studies in several fields of forest sciences, including genetic diversity, phylogenetics, evolution, gene expression, population genetics and molecular breeding. Nowadays, sequencing technologies are developing quickly, aiding the colossal efforts of academic researchers, and being used for general applications in genomes, chloroplast genomes, and gene family data. Therefore, using data from these genomes to study forest tree species constitutes an urgently needed and promising research approach. This Special Issue plans to provide an overview of the most recent advances in the field of genomes, chloroplast genomes, and gene families of tree species and their applications in diverse areas. This Special Issue aims to publish selected contributions on advances in the synthesis, characterization, and applications of these data in tree species.

Potential topics include, but are not limited to:

Genome variation;
Gene family evolution;
Comparative chloroplast genomes and evolution;
Genetic diversity and population structure;
Gene expression and evolutionary adaption.

Prof. Dr. Peng Zhao
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. 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

genomes
genetic diversity
population structure
gene family evolution
chloroplast
genetic variation
transcriptome

Published Papers (2 papers)

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Research

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14 pages, 5265 KiB

Open AccessArticle

Codon Usage Profiling of Chloroplast Genome in Juglandaceae

by Yajun Zeng, Lianwen Shen, Shengqun Chen, Shuang Qu and Na Hou

Forests 2023, 14(2), 378; https://doi.org/10.3390/f14020378 - 13 Feb 2023

Cited by 4 | Viewed by 1510

Abstract

Juglandaceae (walnut) is made up of several economically and ecologically valuable tree species. Chloroplasts, vitally important for plant growth, are also a rich source of genetic and evolutionary information. Both mutational pressure and natural selection are drivers of codon usage pattern variation among genes. Here, we studied the codon usage of Juglandaceae chloroplast genomes in order to further our understanding of the biology and evolution of this plant family. The codon usage patterns associated with the chloroplast genomes of 26 Juglandaceae samples were analyzed. Short CDS sequences (<100 amino acids) and sequencing containing internal stop codons were removed from comparative analyses. The contents of uracil (U) (31.5%–32.0%) and adenine (A) (30.0%–31.2%) of all 26 samples were higher than those of cytosine (C) (17.2%–17.7%) and guanine (G) 19.9%–20.7%. According to the neutrality and correspondence analyses, chloroplast codons tended to exhibit conserved GC content and were primarily altered by natural selection. The parity rule 2 plot analysis revealed that AU were more common than GC at the third-codon position. According to the effective number of codon (ENC) plot analysis, codon preference was driven by natural selection and protein translation, among other factors. This study represents the first examination of the codon usage characteristics of Juglandaceae plants, as revealed through the study of codon bias in 26 Juglandaceae samples. Full article

(This article belongs to the Special Issue Applying Molecular Tools to Genetic Diversity and Divergence in Trees)

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Review

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24 pages, 1189 KiB

Open AccessReview

Molecular Traits for Adaptation to Drought and Salt Stress in Birch, Oak and Poplar Species

by Tatyana S. Tikhomirova, Konstantin V. Krutovsky and Konstantin A. Shestibratov

Forests 2023, 14(1), 7; https://doi.org/10.3390/f14010007 - 21 Dec 2022

Cited by 4 | Viewed by 1681

Abstract

Betula spp., Quercus spp., and Populus spp. are the most promising deciduous woody plants in forestry. However, these species were found to be sensitive to climate change that can badly affect their plantations. Thus, a deep understanding of genetic mechanisms of adaptation to adverse environmental conditions plays an important role in preventing the reduction of deciduous forest area. This mini review describes the stress responses of Betula spp., Quercus spp., and Populus spp. to drought and salt stresses. The overall stress response of the reviewed tree species includes ROS scavenging, ABA- and JA-mediated signaling pathways, and antioxidant and chaperone activities. Short-term drought promotes accumulation of proline, indicating the osmotic stress response. In turn, long-term drought stress activates the DNA repair and chromatin remodeling systems aimed at adapting and gene protecting. Furthermore, alternative pathways of carbohydrate production are used under nutrient deficiencies. It should be noted that stomatal movement control and cell wall remodeling are always observed during drought. In turn, the main response to salt stress includes the maintenance of ion homeostasis and the accumulation of osmoprotectant, as well as cell wall remodeling due to the biosynthesis of cellulotic and non-cellulotic cell wall compounds. It should be noted that the described species demonstrate similar molecular traits for adaptation to drought and salt stress, which may be due to their common habitats. Full article

(This article belongs to the Special Issue Applying Molecular Tools to Genetic Diversity and Divergence in Trees)

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