Special Issue "Forest-Tree Comparative Genomics and Adaptive Evolution"

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

Deadline for manuscript submissions: 31 March 2024 | Viewed by 3899

Special Issue Editors

College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
Interests: plant physiology; biochemistry; molecular biology; stress responses; functional genomics; gene regulation
Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj 31359-33151, Iran
Interests: genome engineering; genomics; genotyping; gene regulation; molecular markers

Special Issue Information

Dear Colleagues,

Forest-tree comparative and evolutionary genomics have gained much attention in recent years. Since these approaches could address fundamental issues of forest biology, including identification of genes or gene families regulating biological processes, unveiling the molecular basis of population adaptive divergence in nature and description of both genetic and phenotypic variations produced through speciation, the industrial and conservational applications are among the ultimate major benefits that could be achieved in this area. To design conservational strategies for forest trees, population genomics could establish potentially useful tools through translating allelic effects on phenotypes and identifying patterns of adaptive variation at the ecosystem level. The most recent advances in molecular biology techniques, mainly next generation sequencing as well as CRISPR technologies, have made evolutionary and comparative genomic approaches much more informative and cost effective comparing traditional approaches for biological studies in forest trees.

This research topic will collect articles dealing with the understanding of genome evolution and convolution of gene regulation for growth, development, reproduction, and responses to abiotic and biotic stresses, epigenomics, interactome analysis, macro- and micro-evolutionary processes and species history, architecture of quantitative traits, applications in industrial sectors, genetic resource conservation and breeding. We invite scientists to contribute their omics research to this topic. Original research papers, perspectives, hypotheses, opinions, reviews, modelling approaches, and methods contributing to forest trees’ comparative and evolutionary genomics, including techniques, applications, trait development, dedicated databases, and computational software, are suitable. This research topic aims to highlight recent progress made in this regard, which includes, but is not limited to:

  • Forest tree genomes;
  • Evolutionary origins and diversification of genes or gene family in trees;
  • Evolution and diversification of trees' traits;
  • Molecular mechanisms involved in biotic and abiotic stress responses, or development;
  • Trees' microbiomes and holobionts (interactions between microorganisms and their host, identification of gene transcripts, proteins, and metabolites expressed by tree-associated microbial communities enabled by meta-“omics” approaches);
  • Molecular interactions (high-throughput experimental techniques and computational predictions);
  • Epigenomics (phenotype variation in a changing environment);
  • Integrating omics into phylogeography and phylogeny;
  • Genotype-phenotype association;
  • Conservation genomics;
  • Mutagenesis and directed evolution.

Prof. Dr. Liming Yang
Dr. Saeid Kadkhodaei
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

  • comparative genomics
  • omics
  • evolutionary genomics
  • microbiome
  • gene family diversification
  • gene function
  • bioinformatics

Published Papers (3 papers)

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Research

Article
Pan-Transcriptome Analysis of Willow Species from Diverse Geographic Distributions
Forests 2023, 14(6), 1182; https://doi.org/10.3390/f14061182 - 07 Jun 2023
Viewed by 1042
Abstract
Willows, in the genus Salix, are widespread on the earth with significant ecological and economic values for humans. Although about 500 Salix species have been estimated, the genomic foundation of their adaptations to environments with diverse stresses has been underexplored. Here, we [...] Read more.
Willows, in the genus Salix, are widespread on the earth with significant ecological and economic values for humans. Although about 500 Salix species have been estimated, the genomic foundation of their adaptations to environments with diverse stresses has been underexplored. Here, we applied a pan-transcriptome approach to investigate the phylogenetic relationships and genetic variations among 16 willow species. A pan-transcriptome of 29,668 gene families was assembled, 69% of which exhibited presence/absence variation across the analyzed species. In comparison to core genes present in all species, shell gene families absent in at least one species were enriched with genes in pathways of signaling transduction and response to stimuli, suggesting their functions in the interaction with diverse environmental factors. A phylogenetic tree of 16 willow species was constructed with high confidence based on 870 single-copy orthologous genes, providing detailed evolutionary relationships of willow sections. The willow species were further assigned into four species clusters using the gene numbers in each family. The diversity of gene family size and gene expression levels among the willow species are closely associated with their geographical distributions. The gene family members involved in DNA repair and cellular response to DNA damage stimuli were expanded in willow species from high-altitude regions in southwestern China, which may contribute to their tolerance to ultraviolet radiation stress. Our study generates a comprehensive pan-transcriptome resource for a large set of Salix species and provides insights into the adaptations of willows to diverse environments, which will be valuable for comparative analysis with other related woody and herbaceous plants. Full article
(This article belongs to the Special Issue Forest-Tree Comparative Genomics and Adaptive Evolution)
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Article
Full-Length Transcriptome Sequencing and Identification of Hsf Genes in Cunninghamia lanceolata (Lamb.) Hook
Forests 2023, 14(4), 684; https://doi.org/10.3390/f14040684 - 27 Mar 2023
Viewed by 1253
Abstract
Cunninghamia lanceolata (Lamb.) Hook. (Chinese fir) is an important timber species that is widely cultivated in southern China. However, the shallow root system and weak drought resistance of Chinese fir are not enough to cope with high temperature and drought. In recent years, [...] Read more.
Cunninghamia lanceolata (Lamb.) Hook. (Chinese fir) is an important timber species that is widely cultivated in southern China. However, the shallow root system and weak drought resistance of Chinese fir are not enough to cope with high temperature and drought. In recent years, molecular biology has been used to modify plants to make them more resilient. Therefore, improving heat and drought resistance of Chinese fir by molecular biology technology is one of the best choices, whereas fewer genetic information resources for C. lanceolata limit more comprehensive molecular studies. In this study, single-molecule full-length transcriptome (SMRT) sequencing technology was used to obtain full-length transcriptome data on Chinese fir. A total of 21,331 transcripts were obtained via co-assembly, and 11,094 gene sets were obtained via further de-redundancy. In addition, gene function annotation and gene structure analysis were performed. We also used these data to identify nine heat shock transcription factors (Hsfs) in Chinese fir, and heat stress transcriptome and real-time quantitative polymerase chain reaction (PCR) analyses revealed expression changes in response to heat stress, indicating that these may play roles in heat resistance. These studies have enriched the genetic information resources of Chinese fir, which may be utilized for further species promotion, improvement, and application. Full article
(This article belongs to the Special Issue Forest-Tree Comparative Genomics and Adaptive Evolution)
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Article
OSCA Genes in Liriodendron chinense: Characterization, Evolution and Response to Abiotic Stress
Forests 2022, 13(11), 1835; https://doi.org/10.3390/f13111835 - 03 Nov 2022
Cited by 2 | Viewed by 1049
Abstract
The hyperosmolality-gated calcium-permeable channels (OSCA) play an imperative role in the plant response to environmental stresses. Moreover, their characteristics in the ornamental woody plant Liriodendron chinense, widely dispersed in the southern region of China, is yet to be elucidated. In the present [...] Read more.
The hyperosmolality-gated calcium-permeable channels (OSCA) play an imperative role in the plant response to environmental stresses. Moreover, their characteristics in the ornamental woody plant Liriodendron chinense, widely dispersed in the southern region of China, is yet to be elucidated. In the present study, 399 OSCA proteins were identified from 31 plant genomes, and comparative phylogenetic analysis revealed that LchiOSCAs gene family is closely related to the Magnolia Cinnamomum kanehirae OSCAs. In L. chinense, 11 LchiOSCA genes were identified and distributed across eight chromosomes. Additionally, phylogenetic analysis of LchiOSCAs exhibited a classification into four subfamilies based on the tree arrangement, similarity in the gene structures, and conserved motif numbers and order. Gene duplication investigations were biased towards the tandem duplication events, accounting for 36% (4/11) of the LchiOSCA gene family. The interspecies collinearity analysis revealed a closer relationship between the L. chinense OSCAs and the P. trichocarpa OSCAs. Analysis in promoter regions of the LchiOSCAs showed the presence of multiple phytohormones and stress responsive elements. Specifically, the ABA-responsive elements had the greatest representation. 3D protein structures of the modeled L. chinense OSCAs exhibited a high homology with the template structures, providing a better understanding of LchiOSCAs’ functionality at the proteome level. The expression pattern analysis of LchiOSCAs based on the transcriptome data and qRT-PCR in L. chinense leaves showed differential responses to drought, cold, and heat stress at varying degrees. Specifically, LchiOSCA2 and LchiOSCA4 were highly expressed under the three abiotic stresses. This research will provide valuable resources and further the understanding of plant OSCA genes in L. chinense for agronomic breeding and bio-engineering purposes. Full article
(This article belongs to the Special Issue Forest-Tree Comparative Genomics and Adaptive Evolution)
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