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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) | Viewed by 26442

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Prof. Dr. Tadeusz Malewski

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Museum and Institute of Zoology, Polish Academy of Science, ul. Wilcza 64, 00-679 Warszawa, Poland
Interests: genomics; molecular mechanisms of gene expression; molecular nematology; DNA barcoding; molecular methods of species identification; forensic entomology
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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 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

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

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Published Papers (9 papers)

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Research

17 pages, 4442 KiB

Open AccessArticle

Transcriptome-Wide Identification and Expression Profiling of SPX Domain-Containing Members in Responses to Phosphorus Deprivation of Pinus massoniana

by Conghui Wang, Fuhua Fan, Xianwen Shang, Zijing Zhou and Guijie Ding

Forests 2021, 12(12), 1627; https://doi.org/10.3390/f12121627 - 24 Nov 2021

Cited by 3 | Viewed by 1833

Abstract

The SPX domain-encoding proteins are believed to play important roles in phosphorus (Pi) homeostasis and signal transduction in plants. However, the overall information and responses of SPXs to phosphorus deficiency in pines, remain undefined. In this study, we screened the transcriptome data of Pinus massoniana in response to phosphorus deprivation. Ten SPX domain-containing genes were identified. Based on the conserved domains, the P. massoniana SPX genes were divided into four different subfamilies: SPX, SPX-MFS, SPX-EXS, and SPX-RING. RNA-seq analysis revealed that PmSPX genes were differentially expressed in response to phosphorus deprivation. Furthermore, real-time quantitative PCR (RT-qPCR) showed that PmSPX1 and PmSPX4 showed different expression patterns in different tissues under phosphorus stress. The promoter sequence of 2284 bp upstream of PmSPX1 was obtained by the genome walking method. A cis-element analysis indicated that there were several phosphorus stress response-related elements (e.g., two P1BS elements, a PHO element, and a W-box) in the promoter of PmSPX1. In addition, the previously obtained PmSPX2 promoter sequence contained a W-box, and it was shown that PmWRKY75 could directly bind to the PmSPX2 promoter using yeast one-hybrid analysis in this study. These results presented here revealed the foundational functions of PmSPXs in maintaining plant phosphorus homeostasis. Full article

(This article belongs to the Special Issue Forest Genomics and Transcriptomics)

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14 pages, 3347 KiB

Open AccessArticle

Chloroplast Genome Draft of Dryobalanops aromatica Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study

by Dwi Wahyuni, Fifi Gus Dwiyanti, Rahadian Pratama, Muhammad Majiidu, Henti Hendalastuti Rachmat and Iskandar Zulkarnaen Siregar

Forests 2021, 12(11), 1515; https://doi.org/10.3390/f12111515 - 3 Nov 2021

Cited by 3 | Viewed by 3762

Abstract

Kapur (Dryobalanops aromatica) is an important dipterocarp species currently classified as vulnerable by the IUCN Red List Threatened Species. Science-based conservation and restoration efforts are needed, which can be supported by new genomic data generated from new technologies, including MinION Oxford Nanopore Technology (ONT). ONT allows affordable long-read DNA sequencing, but this technology is still rarely applied to native Indonesian forest trees. Therefore, this study aimed to generate whole genome datasets through ONT and use part of these data to construct the draft of the chloroplast genome and analyze the universal DNA barcode-based genetic relationships for D. aromatica. The method included DNA isolation, library preparation, sequencing, bioinformatics analysis, and phylogenetic tree construction. Results showed that the DNA sequencing of D. aromatica resulted in 1.55 Gb of long-read DNA sequences from which a partial chloroplast genome (148,856 bp) was successfully constructed. The genetic relationship was analyzed using two selected DNA barcodes (rbcL and matK), and its combination showed that species of the genus Dryobalanops had a close relationship as indicated by adjacent branches between species. The phylogenetic tree of matK and the combination of the matK and rbcL genes showed that D. aromatica was closely related to Dryobalanops rappa, whereas the rbcL gene showed group separation between D. aromatica and D. rappa. Therefore, a combination of the matK and rbcL genes is recommended for future use in the phylogenetic or phylogenomic analysis of D. aromatica. Full article

(This article belongs to the Special Issue Forest Genomics and Transcriptomics)

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15 pages, 2698 KiB

Open AccessArticle

Metabolic and Transcriptional Profiling of Fraxinus chinensis var. rhynchophylla Unravels Possible Constitutive Resistance against Agrilus planipennis

by Liangjian Qu, Jifu Li, Ruizhen Wang, Xiaoyi Wang, Tonghai Zhao, Yuequ Chen and Lijuan Wang

Forests 2021, 12(10), 1373; https://doi.org/10.3390/f12101373 - 9 Oct 2021

Cited by 3 | Viewed by 1811

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 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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22 pages, 6999 KiB

Open AccessArticle

Transcriptomic and Anatomic Profiling Reveal Etiolation Promotes Adventitious Rooting by Exogenous Application of 1-Naphthalene Acetic Acid in Robinia pseudoacacia L.

by Muhammad Zeeshan Munir, Saleem Ud Din, Muhammad Imran, Zijie Zhang, Tariq Pervaiz, Chao Han, Zaib Un Nisa, Ali Bakhsh, Muhammad Atif Muneer, Yuhan Sun and Yun Li

Forests 2021, 12(6), 789; https://doi.org/10.3390/f12060789 - 15 Jun 2021

Cited by 7 | Viewed by 2908

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 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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18 pages, 9723 KiB

Open AccessArticle

Comparison and Phylogenetic Analyses of Nine Complete Chloroplast Genomes of Zingibereae

by Heng Liang and Juan Chen

Forests 2021, 12(6), 710; https://doi.org/10.3390/f12060710 - 30 May 2021

Cited by 10 | Viewed by 2805

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 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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18 pages, 6130 KiB

Open AccessArticle

Comparative Transcriptome Analysis of Sophora japonica (L.) Roots Reveals Key Pathways and Genes in Response to PEG-Induced Drought Stress under Different Nitrogen Conditions

by Jing Tian, Yue Pang and Zhong Zhao

Forests 2021, 12(5), 650; https://doi.org/10.3390/f12050650 - 20 May 2021

Cited by 5 | Viewed by 3095

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, 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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14 pages, 2301 KiB

Open AccessArticle

Inferring the Phylogeny and Divergence of Chinese Curcuma (Zingiberaceae) in the Hengduan Mountains of the Qinghai–Tibet Plateau by Reduced Representation Sequencing

by Heng Liang, Jiabin Deng, Gang Gao, Chunbang Ding, Li Zhang, Ke Xu, Hong Wang and Ruiwu Yang

Forests 2021, 12(5), 520; https://doi.org/10.3390/f12050520 - 23 Apr 2021

Cited by 3 | Viewed by 2364

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 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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22 pages, 4430 KiB

Open AccessArticle

Transcriptome Analysis for Fraxinus mandshurica Rupr. Seedlings from Different Carbon Sequestration Provenances in Response to Nitrogen Deficiency

by Xingtang Zhao, Lei Yu, Zhang Liu, Jianfei Liu, Xintong Ji, Xu Zhang, Mengqi Liu, Yushuo Mei, Fansuo Zeng and Yaguang Zhan

Forests 2021, 12(2), 257; https://doi.org/10.3390/f12020257 - 23 Feb 2021

Cited by 5 | Viewed by 2307

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 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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17 pages, 789 KiB

Open AccessArticle

Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

by Bartosz Ulaszewski, Joanna Meger and Jaroslaw Burczyk

Forests 2021, 12(2), 222; https://doi.org/10.3390/f12020222 - 15 Feb 2021

Cited by 14 | Viewed by 4526

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 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

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