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Forests
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Genomic Analysis of Growth and Stress Adaptation in Forest Trees
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Genomic Analysis of Growth and Stress Adaptation in Forest 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 (28 February 2025) | Viewed by 2235

Special Issue Editors

Dr. Tao Su

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Guest Editor
College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
Interests: molecular ecophysiology; stress biology; genomic diversity
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Liming Yang

E-Mail Website
Guest Editor
College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
Interests: plant physiology; biochemistry; molecular biology; stress responses; functional genomics; gene regulation
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Fansuo Zeng

E-Mail Website
Guest Editor
State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Northeast Forestry University, Harbin 210037, China
Interests: molecular physiology; metabolomics; variety and trait selection
Dr. Hongbin Wei

E-Mail Website
Guest Editor
School of Life Sciences, Southwest University, Chongqing 400715, China
Interests: molecular biology; transcriptome; phytohormone regulation

Special Issue Information

Dear Colleagues,

In forests, physiological and molecular patterns of stress resilience and adaptation associated with favorable environmental and phytohormone cues are postulated to collectively affect survival and evolution. Tree growth and development, stress adaptation, defense priming, and immunity are mounted with recent innovations in techniques in the genome, genetics, and synergetic muti-omics network underlying fine-tuned regulatory mechanisms. An extensive perception and exploration of cellular and metabolic processes are expected to pave the way toward novel strategies based on the reorientation of tree growth and stress acclimation.

This Special Issue aims to stimulate fundamental research and collect the latest discoveries within genomic and genetic regulatory mechanisms in tree growth, tolerance, and defense immunity to various stress cues. Potential topics include, but are not limited to, the following:

  • Novel findings of genome sequencing (e.g., plastomes and mitogenomes), strategies in genome editing, genetic transformation, and the innovation in forest tree performance;
  • Multi-omics studies to characterize candidate genes/families impacting tree growth, biomass, adapted environment;
  • Development of high-efficiency transformation and genome editing systems for tree species;
  • Applications of synthetic biology to generate valuable bioactive constituents in engineered plants.

All types of submissions, including original research, high-quality reviews, methodologies, perspectives, and opinion articles in this field, are welcome.

Dr. Tao Su
Prof. Dr. Liming Yang
Prof. Dr. Fansuo Zeng
Dr. Hongbin Wei
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

  • genomics
  • functional analyses
  • tree growth
  • stress acclimation
  • multi-omics

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

17 pages, 5413 KiB  
Article
Integrated Multi-Omics Analysis Reveals Photosynthetic Acclimation and Metabolic Reprogramming in Populus ussuriensis kom. Under Cold Stress
by Jingjing Li, Wanxin Li, Zhuolong Li, Lu Yang, Wenhui Zhuang, Jingjing Zhang, Zhaohan Zhang, Zihan Fan, Fude Wang, Shicheng Zhao and Jingli Yang
Forests 2025, 16(4), 660; https://doi.org/10.3390/f16040660 - 10 Apr 2025
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Abstract
Low temperature is a major stress that severely affects tree growth and development. Despite the fact that the molecular mechanisms behind cold tolerance and associated regulatory networks in these trees remain largely unexplored, we conducted a study to examine the overall changes in [...] Read more.
Low temperature is a major stress that severely affects tree growth and development. Despite the fact that the molecular mechanisms behind cold tolerance and associated regulatory networks in these trees remain largely unexplored, we conducted a study to examine the overall changes in metabolites and regulatory pathways of Populus ussuriensis kom. when exposed to cold stress, utilizing a comprehensive multi-omics approach. Transcriptomes exposed to cold stress reveal that most of the candidate genes related to the Calvin–Benson–Bassham cycle and flavonoid synthesis were upregulated. Joint analysis revealed that within 6–48 h of low-temperature treatment, differential genes (such as PAL and CHS) in the flavonoid biosynthesis pathway and metabolites (such as quercetin) were significantly upregulated, indicating a positive correlation under short-term stress. However, prolonged treatment (72 h) may trigger metabolic feedback, leading to a decrease in flavonoid content. In addition, the measurements of gas exchange and metabolite assays of P. ussuriensis showed that photosynthetic acclimation led to a change in the sugar accumulation and starch degradation in response to low temperature, indicating that extensive changes occurred due to the cold and improved tolerance in P. ussuriensis. This study provides a new basis for future studies on the molecular mechanism of cold tolerance at the transcriptional and metabolic levels. Full article
(This article belongs to the Special Issue Genomic Analysis of Growth and Stress Adaptation in Forest Trees)
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12 pages, 2316 KiB  
Article
Polyploid Advantage? Comparing Salt Stress Responses of Di- and Tetraploid Acacia senegal (L.) Willd. Seedlings
by Adja Madjiguene Diallo, Erik Dahl Kjær, Lene Rostgaard Nielsen and Anders Ræbild
Forests 2025, 16(3), 412; https://doi.org/10.3390/f16030412 - 25 Feb 2025
Viewed by 331
Abstract
Polyploidy is often associated with the ability to grow under harsh conditions. The objective of this study was to test whether genome doubling in Acacia senegal confers superiority for growth under saline conditions. For this purpose, we assessed the cytotype distribution across ten [...] Read more.
Polyploidy is often associated with the ability to grow under harsh conditions. The objective of this study was to test whether genome doubling in Acacia senegal confers superiority for growth under saline conditions. For this purpose, we assessed the cytotype distribution across ten natural stands in Senegal, representing different soil salinities. We further compared the growth of diploid and tetraploid A. senegal seedlings in a shared-pot greenhouse experiment, in which seedling pairs (diploids and polyploids) were irrigated with and without added NaCl. We found polyploids in six stands, and the proportion of polyploids in these stands was significantly and positively correlated with their level of soil salinity. Under experimental conditions, we found that the growth rate of diploid and tetraploid seedlings was equally depressed by salt stress, but the mortality rate for tetraploids was lower than that for diploids (34% versus 54%). In addition, the root-top ratio was higher in tetraploids compared to diploids, which may influence fitness under harsh conditions. Overall, this study provides support for polyploid superiority in A. senegal growing in saline soils. The findings of this study may have practical implications for the reforestation of saline soils with polyploid A. senegal, and we recommend further studies to elucidate their potential. Full article
(This article belongs to the Special Issue Genomic Analysis of Growth and Stress Adaptation in Forest Trees)
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17 pages, 4790 KiB  
Article
Integration of Illumina and PacBio HiFi Sequencing Reveals a Three-Linear-Molecule Mitogenome with RNA-Editing Sites and Phylogeny in Arrow Bamboo (Fargesia qinlingensis)
by Hao Wu, Xue Li, Ke Qu, Lele Yang, Tao Su, Lijun Yong, Mei Han and Fuliang Cao
Forests 2024, 15(7), 1267; https://doi.org/10.3390/f15071267 - 20 Jul 2024
Viewed by 1351
Abstract
Arrow bamboo (Fargesia qinlingensis) is endemic to the Qinling Mountains and has remarkable adaptive resilience to changing climates. However, its complete mitogenome remains unknown. Using the Illumina and PacBio HiFi sequencing platforms, we found that the mitogenome assembly of the F. [...] Read more.
Arrow bamboo (Fargesia qinlingensis) is endemic to the Qinling Mountains and has remarkable adaptive resilience to changing climates. However, its complete mitogenome remains unknown. Using the Illumina and PacBio HiFi sequencing platforms, we found that the mitogenome assembly of the F. qinlingensis has a multi-branched skeleton comprising three linear molecules (M1, M2, and M3), with a length of 442,368 bp and a GC content of 44.05%. Thirty-five unique PCGs were identified in the complete mitogenome, including twenty-four core structural genes, eleven noncore structural genes, three rRNAs, and sixteen tRNAs. The GCU for alanine and CAA for glutamine represented the most significant frequency (RSCU = 1.55) in the codon usage preference. A total of 51, 28, and 14 SSRs were determined on M1, M2, and M3, respectively. The mitogenome contained 149 pairs of dispersed repeats with lengths greater than 30 bp, the most abundant of which were 82 forward and 67 palindromic repeats. A long repeat sequence (14,342 bp) was characterized in mediating mitogenome recombination. DNA transfer analyses suggested that 44 MTPTs (30,943 bp, 6.99%) originated from the plastome. Among the 482 potential C-U/T RNA-editing sites predicted in 35 PCGs, ccmFn (38 times) and ccmC (36 times) shoed the highest frequency. Collinearity and phylogenetic trees revealed the close relationship between F. qinlingensis and Bambusa oldhamii. The primary features of the mitogenome of F. qinlingensis will help decipher the functional mitochondrial traits related to growth performance and climate resilience. Moreover, our findings provide insights into the evolution, environmental adaptation, and sustainable use of subalpine bamboo resources in the Qinling Mountains. Full article
(This article belongs to the Special Issue Genomic Analysis of Growth and Stress Adaptation in Forest Trees)
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