The Genomic and Evolutionary Basis of Forest Trees Adaptation to Changing Environments

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (5 March 2022) | Viewed by 2691

Special Issue Editors

Guest Editor
Instituto Nacional de Investigação Agrária e Veterinária, 1649-023 Lisbon, Portugal
Interests: ecology and evolution; conservation biodiversity; biodiversity and conservation; evolution; ecology; conservation biology; genetics; plant ecology; climate change

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Guest Editor
Instituto Nacional de Investigação Agrária e Veterinária, I.P. Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
Interests: gene expression; transcriptome analysis; RNA-sequencing; pine wilt disease; Pinus pinaster; Bursaphelenchus xylophilus; Castanea spp.; molecular breeding; biotic stresses

Special Issue Information

Dear Colleagues,

In this Special Issue, we aim to collect submissions reporting on the discovery, measurement, annotation, functional characterization, and deposition of research on the state of the art in the genomic and evolutionary basis of forest tree adaptation to changing environments, including transcriptomics. Although genomic data on the evolutionary basis of forest tree adaptation to changing environments are increasingly being relied upon, such data still require more visibility.
Forest trees are unique among living beings. Forest trees are long living, large, and motionless and are constantly exposed to climate variations in both time and geographic location. Long-living trees in particular have evolved a wide spectrum of molecular mechanisms to coordinate growth and development under stressful conditions, thus minimizing fitness costs. Forests also directly affect the local climate by interacting with the biogeochemical water cycle.

Seed production in forest trees, a key aspect for evolution and adaptation, varies as a rule from year to year, ranging from heavy to negligible, and population effective size is in general inferior to the population census. During the long life of a forest tree, which can be centuries or even millennia for some species, they must cope with environmental changes without the chance to migrate in search of suitable conditions elsewhere. Short-living plants face adverse environmental changes mainly by producing large amounts of seed, which is an indirect process of migration.

Gene flow by means of pollen and seeds is a critical process in long-living forest species. Natural cloning and hybridization occur in various genera and certainly also play a role in evolution and adaptation. Through hybridization, two species of the same genus produce hybrids that can explore the environment and, at the limit, create new species. However, such hybridization, even among highly compatible species, generally succeeds in keeping both species individualized, which raises the issue of genomic control.

Over the course of evolution, the way forest trees use their genomes (inherited genes) to cope and evolve remains to be fully understood. Understanding how forest trees respond to different stresses is fundamental to developing a successful strategy to preserve biodiversity and ecosystem functionality and strategies for genetic improvement and reforestation. Recent advances in next-generation sequencing and biochemical approaches allow for the understanding of the adaptive responses of woody plants to drought, temperature, co-evolution with biotic stresses with special attention to pests and diseases, and inter-specific competition in a context of global climate change. Genomic and transcriptomic findings on the response of forest trees to alien pathogenic agents are increasingly becoming critical issues.

This Special Issue of Plants will address questions concerning the link between genomics and issues such as the following:

  • Phenotypic plasticity;
  • Epigenetics;
  • Pests and diseases;
  • Genomic regulation of reproductive behavior;
  • Genotype–environment interaction;
  • Population genomics;
  • Gene flow by pollen and seeds;
  • Hybridization and introgression;
  • Provenance characterization;
  • Conservation of genetic resources.

    Original research articles, reviews, mini reviews, and methods dealing with these topics are welcome

Dr. Maria Carolina Varela
Dr. Rita Lourenço Costa
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at 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. Plants is an international peer-reviewed open access semimonthly 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 2700 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.


  • forest trees
  • epigenetics
  • quantitative characteristics
  • gene flow
  • hybridization
  • population genomics
  • transcriptomics
  • adaptation
  • biotic and abiotic stresses
  • global climate change

Published Papers (1 paper)

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17 pages, 7107 KiB  
Genome-Wide Analysis of the Homeobox Gene Family and Identification of Drought-Responsive Members in Populus trichocarpa
by Jing Hou, Yan Sun, Lei Wang, Yuanzhong Jiang, Ningning Chen and Shaofei Tong
Plants 2021, 10(11), 2284; - 25 Oct 2021
Cited by 6 | Viewed by 2050
Homeobox (HB) genes play critical roles in the regulation of plant morphogenesis, growth and development. Here, we identified a total of 156 PtrHB genes from the Populus trichocarpa genome. According to the topologies and taxonomy of the phylogenetic tree constructed by Arabidopsis thaliana [...] Read more.
Homeobox (HB) genes play critical roles in the regulation of plant morphogenesis, growth and development. Here, we identified a total of 156 PtrHB genes from the Populus trichocarpa genome. According to the topologies and taxonomy of the phylogenetic tree constructed by Arabidopsis thaliana HB members, all PtrHB proteins were divided into six subgroups, namely HD-ZIP, ZF-HD, HB-PHD, TALE, WOX and HB-OTHERS. Multiple alignments of conserved homeodomains (HDs) revealed the conserved loci of each subgroup, while gene structure analysis showed similar exon–intron gene structures, and motif analysis indicated the similarity of motif number and pattern in the same subgroup. Promoter analysis indicated that the promoters of PtrHB genes contain a series of cis-acting regulatory elements involved in responding to various abiotic stresses, indicating that PtrHBs had potential functions in these processes. Collinearity analysis revealed that there are 96 pairs of 127 PtrHB genes mainly distributing on Chromosomes 1, 2, and 5. We analyzed the spatio-temporal expression patterns of PtrHB genes, and the virus-induced gene silencing (VIGS) of PtrHB3 gene resulted in the compromised tolerance of poplar seedlings to mannitol treatment. The bioinformatics on PtrHB family and preliminary exploration of drought-responsive genes can provide support for further study of the family in woody plants, especially in drought-related biological processes. It also provides a direction for developing new varieties of poplar with drought resistance. Overall, our results provided significant information for further functional analysis of PtrHB genes in poplar and demonstrated that PtrHB3 is a dominant gene regulating tolerance to water stress treatment in poplar seedlings. Full article
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