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Forests
Special Issues
Forest-Tree Comparative Genomics and Adaptive Evolution
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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: closed (31 March 2024) | Viewed by 8491

Special Issue Editors

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
Dr. Saeid Kadkhodaei

E-Mail Website
Guest Editor
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 (6 papers)

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Research

17 pages, 9651 KiB  
Article
Complete Plastid Genome Sequences of Three Tropical African Beilschmiediineae Trees (Lauraceae: Crytocaryeae)
by Wen Zhu, Haorong Zhang, Qishao Li, Zhengying Cao, Yu Song and Peiyao Xin
Forests 2024, 15(5), 832; https://doi.org/10.3390/f15050832 - 10 May 2024
Viewed by 426
Abstract
Millions of years of isolation have given Madagascar a unique flora that still reflects some of its relationship with the continents of Africa and India. Here, the complete chloroplast sequence of Beilschmiedia moratii, a tropical tree in Madagascar, was determined. The plastome, [...] Read more.
Millions of years of isolation have given Madagascar a unique flora that still reflects some of its relationship with the continents of Africa and India. Here, the complete chloroplast sequence of Beilschmiedia moratii, a tropical tree in Madagascar, was determined. The plastome, with a length of 158,410 bp, was 143 bp and 187 bp smaller than those of two closely related species, B. pierreana and Potameia microphylla, in sub-Saharan Africa and Madagascar with published sequences, respectively. A total of 124 repeats and 114 simple sequence repeats (SSRs) were detected in the plastome of B. moratii. Six highly variable regions, including ndhF, ndhF-rpl32, trnC-petN, pebE-petL, rpl32-trnL, and ycf1, among the three African species were identified and 1151 mutation events, including 14 SVs, 351 indels, and 786 substitutions, were accurately located. There were 634 mutation events between B. moratii and P. microphylla with a mean nucleotide variability (π) value of 0.00279, while there were 827 mutation events between B. moratii and B. pierreana with a mean π value of 0.00385. The Ka/Ks ratios of 86 protein-coding genes in the three African species were less than 1, and the mean value between B. moratii and P. microphylla was 0.184, while the mean value between B. moratii and B. pierreana was 0.286. In this study, the plastid genomes of the three African Beilschmiediineae species were compared for the first time and revealed that B. moratii and P. microphylla from Madagascar were relatively conserved, with low mutation rates and slower evolutionary rates. Full article
(This article belongs to the Special Issue Forest-Tree Comparative Genomics and Adaptive Evolution)
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16 pages, 6685 KiB  
Article
Transcriptional Profiling Reveals Key Regulatory Roles of the WUSCHEL-Related Homeobox Gene Family in Yellowhorn (Xanthoceras sorbifolia Bunge)
by Wentao Zhang, Xinyao Xie, Linlin Le and Fuliang Cao
Forests 2024, 15(2), 376; https://doi.org/10.3390/f15020376 - 18 Feb 2024
Viewed by 771
Abstract
The WUSCHEL-related homeobox (WOX) gene family plays a crucial role in regulating embryonic development, organ formation, and stress resistance. Yellowhorn (Xanthoceras sorbifolia Bunge), a drought-resistant tree known for its oil production, lacks sufficient information regarding the WOX gene family. To understand the [...] Read more.
The WUSCHEL-related homeobox (WOX) gene family plays a crucial role in regulating embryonic development, organ formation, and stress resistance. Yellowhorn (Xanthoceras sorbifolia Bunge), a drought-resistant tree known for its oil production, lacks sufficient information regarding the WOX gene family. To understand the evolutionary mechanisms and potential functions of this gene family in yellowhorn, we conducted a comprehensive investigation on its expression patterns and evolutionary characteristics. Our analysis revealed the presence of nine XsWOX genes in the yellowhorn genome, which could be categorized into three distinct clades through a phylogenetic analysis. A chromosomal localization analysis indicated that these nine XsWOX genes were situated on six out of the fifteen chromosomes. An intra-species collinear analysis revealed only one pair of tandem duplicated genes within the XsWOX family. The promoter regions of the XsWOX family were found to contain responsive cis-acting elements associated with plant growth and development, stress responses, and hormone signaling. Moreover, an analysis of the gene expression profiles in different developmental stages of callus revealed significant expressions of XsWOX1, XsWOX4, and XsWOX5 in embryogenic callus and somatic embryo formation, suggesting that they have special roles in regulating yellowhorn’s somatic embryogenesis. Furthermore, the expression level of XsWOX5 indicated its potential involvement not only in organ formation but also in responding to low temperature, salt, and saline-alkali stresses. Overall, our findings lay a solid foundation for future in-depth studies on the functionality and evolution of XsWOX genes in yellowhorn. Full article
(This article belongs to the Special Issue Forest-Tree Comparative Genomics and Adaptive Evolution)
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14 pages, 5838 KiB  
Article
Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid Poplar
by Xiawei Ding, Chengjin Wen, Ganggui Yang, Ying Guo and Liangjiao Xue
Forests 2023, 14(11), 2195; https://doi.org/10.3390/f14112195 - 4 Nov 2023
Cited by 1 | Viewed by 979
Abstract
Plant tissue regeneration is a key process for genetic transformation and genome editing. The exploration of regulatory mechanisms in plant regeneration would improve regeneration efficiency. In comparison to some model plants, the genomic heterozygosity is much higher in forest trees, increasing the complexity [...] Read more.
Plant tissue regeneration is a key process for genetic transformation and genome editing. The exploration of regulatory mechanisms in plant regeneration would improve regeneration efficiency. In comparison to some model plants, the genomic heterozygosity is much higher in forest trees, increasing the complexity of transcriptional regulation. Here, we report the allele-specific transcriptional analysis in hybrid poplar 84K (Populus alba × P. tremula var. glandulosa cv. 84K) during the shoot regeneration process. Firstly, 180 regeneration-related genes (REGs) and 2446 REG-homologous genes (REGHs) were identified in hybrid poplar. The expression patterns of REGs exhibited that about half of them were positively correlated between poplar and Arabidopsis at the locus level. The expression levels of REGHs vary among the gene family at different stages during callus and shoot induction. Among the gene clusters with similar expression patterns, the distribution of gene families in poplar and Arabidopsis also exhibits large variations. At the allele level, most of the allele pairs of REGs were positively correlated in expression. The expression patterns of genes in auxin synthesis, transport, and signaling pathways agree with the general patterns. Due to the presence/absence of variations between two subgenomes, two YUC alleles and two IAA alleles are present only in one subgenome, and the expression patterns of the two alleles are greatly different. Our analysis indicates the conservativeness and diversity of transcriptional regulation during shoot regeneration in poplar and Arabidopsis. The complexity in allele expression contributed by heterozygosity suggests the importance of genotyping in the screening of explants for plant regeneration. Full article
(This article belongs to the Special Issue Forest-Tree Comparative Genomics and Adaptive Evolution)
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16 pages, 5563 KiB  
Article
Pan-Transcriptome Analysis of Willow Species from Diverse Geographic Distributions
by Zhenyu Yan, Li Chen, Ying Guo, Xiaogang Dai, Tongming Yin and Liangjiao Xue
Forests 2023, 14(6), 1182; https://doi.org/10.3390/f14061182 - 7 Jun 2023
Viewed by 2013
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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14 pages, 5347 KiB  
Article
Full-Length Transcriptome Sequencing and Identification of Hsf Genes in Cunninghamia lanceolata (Lamb.) Hook
by Yuan Ji, Hua Wu, Xueyan Zheng, Liming Zhu, Zeli Zhu, Ya Chen, Jisen Shi, Renhua Zheng and Jinhui Chen
Forests 2023, 14(4), 684; https://doi.org/10.3390/f14040684 - 27 Mar 2023
Cited by 1 | Viewed by 1897
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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15 pages, 33627 KiB  
Article
OSCA Genes in Liriodendron chinense: Characterization, Evolution and Response to Abiotic Stress
by Yongchao Ke, Mingyue Xu, Delight Hwarari, Baseer Ahmad, Rongxue Li, Yuanlin Guan, Jinhui Chen and Liming Yang
Forests 2022, 13(11), 1835; https://doi.org/10.3390/f13111835 - 3 Nov 2022
Cited by 2 | Viewed by 1583
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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