Special Issue "Forest Genomics and Transcriptomics"

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 September 2021).

Special Issue Editor

Prof. Dr. Tadeusz Malewski
E-Mail Website
Guest Editor
Department of Molecular and Biometric Techniques, Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warsaw, Poland
Interests: genomics; transcriptomics; molecular mechanisms of gene expression

Special Issue Information

Dear Colleagues,

Forest genomics and transcriptomics, disciplines that study the genetic composition of trees and the methods required to modify them, began over a quarter of a century ago with the development of the first genetic maps and the establishment of early methods of genetic transformation. Since then, genomics and transcriptomics have impacted all research areas of forestry. Genome analyses of tree populations have uncovered genes involved in traits of economic importance, primarily growth and wood quality, pest and diseases resistance, and adaptation and response to biotic and abiotic stress. Genes that regulate growth and development have been identified, and in many cases their mechanisms of action have been described. Genomics is now making it possible to rapidly improve knowledge and develop tools to accelerate breeding programs. However, in contrast to many annual crops that have benefited from centuries of domestication and extensive genomic and biotechnology research, in forestry, the field is still in its infancy. Bioinformatic analyses derived from RNA-seq of forest trees are particularly challenging because of the massive genome length and the absence of annotated reference genomes. Thus, tremendous opportunities remain unexplored.

The present Special Issue in the journal Forests, entitled "Forest Genomics and Transcriptomisc" encourages the submission of research as well as review papers dealing with new advances in tree genomics and transcriptomics that could be related to new perspectives in tree breeding and management.

Prof. Dr. Tadeusz Malewski
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 papers will be 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 1800 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

  • forest genomics
  • forest transcriptomics
  • regulation of gene expression
  • biotic and abiotic stress
  • mirna
  • epigenomics
  • disease and pest resistance
  • traits of economic importance

Published Papers (7 papers)

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Research

Article
Metabolic and Transcriptional Profiling of Fraxinus chinensis var. rhynchophylla Unravels Possible Constitutive Resistance against Agrilus planipennis
Forests 2021, 12(10), 1373; https://doi.org/10.3390/f12101373 - 09 Oct 2021
Viewed by 191
Abstract
The emerald ash borer (EAB, Agrilus planipennis), an ash-tree wood-boring beetle, has caused widespread mortality of ash. Asian ash, which coevolved with EAB, is considered more resistant than its North American and European congeners. Although some compounds and proteins related to resistance [...] Read more.
The emerald ash borer (EAB, Agrilus planipennis), an ash-tree wood-boring beetle, has caused widespread mortality of ash. Asian ash, which coevolved with EAB, is considered more resistant than its North American and European congeners. Although some compounds and proteins related to resistance to EAB have been identified, the underlying ash resistance mechanism to EAB still needs further study. The Asian ash species, Fraxinus chinensis var. rhynchophylla, is highly resistant to EAB. In this study, metabolic and transcriptional profiling of the phloem of this species was investigated, and differentially expressed metabolites and genes were analyzed by comparing them with those of the susceptible F. pennsylvanica. Four hundred and twenty-eight metabolites were detected in both species, and several coumarins and lignans, which were exclusive to F. chinensis var. rhynchophylla, were identified. Compared with susceptible F. pennsylvanica, genes related to phenylpropanoid biosynthesis, ethylene (ET), and jasmonic acid (JA) biosynthesis and signaling in F. chinensis var. rhynchophylla were found to be up-regulated. It was hypothesized that coumarins, lignans, and ET and JA signaling might contribute to greater resistance to EAB in F. chinensis var. rhynchophylla. This study suggests candidate metabolites and genes for biomarker development in future ash-breeding programs. Full article
(This article belongs to the Special Issue Forest Genomics and Transcriptomics)
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Article
Transcriptomic and Anatomic Profiling Reveal Etiolation Promotes Adventitious Rooting by Exogenous Application of 1-Naphthalene Acetic Acid in Robinia pseudoacacia L.
Forests 2021, 12(6), 789; https://doi.org/10.3390/f12060789 - 15 Jun 2021
Cited by 1 | Viewed by 639
Abstract
The process of etiolation contributes significantly to vegetative propagation and root formation of woody plants. However, the molecular interaction pattern of different factors for etiolated adventitious root development in woody plants remains unclear. In the present study, we explored the changes at different [...] Read more.
The process of etiolation contributes significantly to vegetative propagation and root formation of woody plants. However, the molecular interaction pattern of different factors for etiolated adventitious root development in woody plants remains unclear. In the present study, we explored the changes at different etiolation stages of adventitious root formation in Robinia pseudoacacia. Histological and transcriptomic analyses were performed for the etiolated lower portion of hypocotyls to ascertain the adventitious root responses. We found that the dark-treated hypocotyls formed roots earlier than the control. Exogenous application of NAA (0.3 mg/L) stimulated the expressions of about 310 genes. Among these, 155 were upregulated and 155 were downregulated. Moreover, differentially expressed genes (DEGs) were significantly enriched in multiple pathways, including the biosynthesis of secondary metabolites, metabolic pathway, plant hormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, and carbon metabolism. These pathways could play a significant role during adventitious root formation in etiolated hypocotyls. The findings of this study can provide novel insights and a foundation for further studies to elucidate the connection between etiolation and adventitious root formation in woody plants. Full article
(This article belongs to the Special Issue Forest Genomics and Transcriptomics)
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Article
Comparison and Phylogenetic Analyses of Nine Complete Chloroplast Genomes of Zingibereae
Forests 2021, 12(6), 710; https://doi.org/10.3390/f12060710 - 30 May 2021
Viewed by 812
Abstract
Zingibereae is a large tribe in the family Zingiberaceae, which contains plants with important medicinal, edible, and ornamental values. Although tribes of Zingiberaceae are well circumscribed, the circumscription of many genera within Zingibereae and the relationships among them remain elusive, especially for the [...] Read more.
Zingibereae is a large tribe in the family Zingiberaceae, which contains plants with important medicinal, edible, and ornamental values. Although tribes of Zingiberaceae are well circumscribed, the circumscription of many genera within Zingibereae and the relationships among them remain elusive, especially for the genera of Boesenbergia, Curcuma, Kaempferia and Pyrgophyllum. In this study, we investigated the plastome variation in nine species representing five genera of Zingibereae. All plastomes showed a typical quadripartite structure with lengths ranging from 162,042 bp to 163,539 bp and contained 132–134 genes, consisting of 86–88 coding genes, 38 transfer RNA genes and eight ribosomal RNA genes. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were detected. In addition, we conducted phylogenomic analyses of the Zingibereae and related taxa with plastomes data from additional 32 species from Genbank. Our results confirmed that Stahlianthus is closely related to Curcuma, supporting the idea of merging it into Curcuma. Kaempferia, Boesenbergia and Zingiber were confirmed as close relatives and grouped together as the Kaempferia group. Pyrgophyllum is not allied with the Curcuma clade but instead is embedded within the Hedychium clade. Our results demonstrate the power of plastid phylogenomics in improving the phylogenetic relationships within Zingibereae and provide a new insight into plastome evolution in Zingibereceae. Full article
(This article belongs to the Special Issue Forest Genomics and Transcriptomics)
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Article
Comparative Transcriptome Analysis of Sophora japonica (L.) Roots Reveals Key Pathways and Genes in Response to PEG-Induced Drought Stress under Different Nitrogen Conditions
Forests 2021, 12(5), 650; https://doi.org/10.3390/f12050650 - 20 May 2021
Cited by 1 | Viewed by 745
Abstract
Sophora japonica is a native leguminous tree species in China. The high stress tolerance contributes to its long lifespan of thousands of years. The lack of genomic resources greatly limits genetic studies on the stress responses of S. japonica. In this study, [...] Read more.
Sophora japonica is a native leguminous tree species in China. The high stress tolerance contributes to its long lifespan of thousands of years. The lack of genomic resources greatly limits genetic studies on the stress responses of S. japonica. In this study, RNA-seq was conducted for S. japonica roots grown under short-term 20% polyethylene glycol (PEG) 6000-induced drought stress under normal N and N starvation conditions (1 and 0 mM NH4NO3, respectively). In each of the libraries, we generated more than 25 million clean reads, which were then de novo assembled to 46,852 unigenes with an average length of 1310.49 bp. In the differential expression analyses, more differentially expressed genes (DEGs) were found under drought with N starvation than under single stresses. The number of transcripts identified under N starvation and drought in S. japonica was nearly the same, but more upregulated genes were induced by drought, while more downregulated genes were induced by N starvation. Genes involved in “phenylpropanoid biosynthesis” and “biosynthesis of amino acids” pathways were upregulated according to KEGG enrichment analyses, irrespective of the stress treatments. Additionally, upregulated N metabolism genes were enriched upon drought, and downregulated photosynthesis genes were enriched under N starvation. We found 4,372 and 5,430 drought-responsive DEGs under normal N and N starvation conditions, respectively. N starvation may aggravate drought by downregulating transcripts in the “carbon metabolism”, “ribosome”, “arginine biosynthesis pathway”, “oxidative phosphorylation” and “aminoacyl-tRNA biosynthesis” pathways. We identified 78 genes related to N uptake and assimilation, 38 of which exhibited differential expression under stress. A total of 395 DEGs were categorized as transcription factors, of which AR2/ERF-ERF, WRKY, NAC, MYB, bHLH, C3H and C2C2-Dof families played key roles in drought and N starvation stresses. The transcriptome data obtained, and the genes identified facilitate our understanding of the mechanisms of S. japonica responses to drought and N starvation stresses and provide a molecular foundation for understanding the mechanisms of its long lifespan for breeding resistant varieties for greening. Full article
(This article belongs to the Special Issue Forest Genomics and Transcriptomics)
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Article
Inferring the Phylogeny and Divergence of Chinese Curcuma (Zingiberaceae) in the Hengduan Mountains of the Qinghai–Tibet Plateau by Reduced Representation Sequencing
Forests 2021, 12(5), 520; https://doi.org/10.3390/f12050520 - 23 Apr 2021
Viewed by 428
Abstract
Clarifying the genetic relationship and divergence among Curcuma L. (Zingiberaceae) species around the world is intractable, especially among the species located in China. In this study, Reduced Representation Sequencing (RRS), as one of the next generation sequences, has been applied to infer large [...] Read more.
Clarifying the genetic relationship and divergence among Curcuma L. (Zingiberaceae) species around the world is intractable, especially among the species located in China. In this study, Reduced Representation Sequencing (RRS), as one of the next generation sequences, has been applied to infer large scale genotyping of major Chinese Curcuma species which present little differentiation of morphological characteristics and genetic traits. The 1295 high-quality SNPs (reduced-filtered SNPs) were chosen from 997,988 SNPs of which were detected from the cleaned 437,061 loci by RRS to investigate the phylogeny and divergence among eight major Curcuma species locate in the Hengduan Mountains of the Qinghai–Tibet Plateau (QTP) in China. The results showed that all the population individuals were clustered together within species, and species were obviously separated; the clustering results were recovered in PCA (Principal Component Analysis); the phylogeny was (((((C. Phaeocaulis, C. yunnanensis), C. kwangsiensis), (C. amarissima, C. sichuanensis)), C. longa), (C. wenyujin, C. aromatica)); Curcuma in China originated around ~7.45 Mya (Million years ago) in the Miocene, and interspecific divergence appeared at ca. 4–2 Mya, which might be sped up rapidly along with the third intense uplift of QTP. Full article
(This article belongs to the Special Issue Forest Genomics and Transcriptomics)
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Article
Transcriptome Analysis for Fraxinus mandshurica Rupr. Seedlings from Different Carbon Sequestration Provenances in Response to Nitrogen Deficiency
Forests 2021, 12(2), 257; https://doi.org/10.3390/f12020257 - 23 Feb 2021
Viewed by 560
Abstract
To explore the molecular regulatory mechanism of high-carbon (C) sequestration Fraxinus mandshurica Rupr. (F. mandshurica) provenance and the expression profile of F. mandshurica during nitrogen (N) starvation, the foliage and roots of the annual Wuchang (WC) seedlings with greater C amount [...] Read more.
To explore the molecular regulatory mechanism of high-carbon (C) sequestration Fraxinus mandshurica Rupr. (F. mandshurica) provenance and the expression profile of F. mandshurica during nitrogen (N) starvation, the foliage and roots of the annual Wuchang (WC) seedlings with greater C amount and Hailin (HL) seedlings with smaller C amount, which were grown in N-deficient nutrition and complete N, were used for RNA-seq and physiological determination, respectively. One thousand and fifty-seven differentially expressed genes (DEGs) between WC and HL and 8173 DEGs related to N deficiency were identified, respectively. The root of F. mandshurica responded to N deficiency more strongly than foliar. The target genes that responded to N deficiency in roots were mainly regulatory genes (transcription factors, hormones and protein kinases), and their response patterns were upregulated. The growth and N concentration in both WC and HL were reduced by the N deficiency, which might result from the decrease of the leaf Nitrate reductase (NR) and glutamine synthetase (GS) enzyme activity and ABA content, although the root-to-shoot ratio; lateral root number; lignin content; endogenous hormones content (GA, IAA and ZR); root GS and glutamate synthetase activity and transcriptional level of most of the regulatory genes were increased. The C sequestration capacity in WC was greater than that in HL, which related to the higher GS enzymes activity and transcriptional levels of regulatory genes and metabolic genes (terpenes, carbohydrates, and lipid energy). However, the C sequestration advantage of WC was significantly reduced by the N deficiency, which was due to the smaller response to N deficiency compared to HL. Full article
(This article belongs to the Special Issue Forest Genomics and Transcriptomics)
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Article
Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods
Forests 2021, 12(2), 222; https://doi.org/10.3390/f12020222 - 15 Feb 2021
Cited by 2 | Viewed by 891
Abstract
Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to [...] Read more.
Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak. Full article
(This article belongs to the Special Issue Forest Genomics and Transcriptomics)
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