Hieu Xuan Cao

Terrestrialization is an important evolutionary process that plants experienced. However, little is known about how land plants acquired aquatic growth behaviors. Here, we integrate multiproxy evidence to elucidate the evolution of the aquatic plant duckweed. Three genera of duckweeds show chronologically gradual degeneration in root structure and stomatal function and a decrease in lignocellulose content, accompanied by the contraction of relevant gene families and/or a decline in their transcription levels. The number of genes in main phytohormone pathways is also gradually decreased. The coordinated action of genes involved in auxin signaling and rhizoid development causes a gradual decrease in adventitious roots. Additionally, the significant expansion of the flavonoid pathway is related to the adaptation of duckweeds to floating growth. This study reconstructs the evolutionary history of duckweeds, tracing its journey from land back to water — a reverse trajectory of early land plants.

Forests worldwide are under increasing pressure from climate change and emerging diseases, threatening their vital ecological and economic roles. Traditional breeding approaches, while valuable, are inherently slow and limited by the long generation times and existing genetic variation of trees. CRISPR technologies offer a transformative solution, enabling precise and efficient genome editing to accelerate the development of climate-resilient and productive forests. This review provides a comprehensive overview of CRISPR applications in forestry, exploring its potential for enhancing disease resistance, improving abiotic stress tolerance, modifying wood properties, and accelerating growth. We discuss the mechanisms and applications of various CRISPR systems, including base editing, prime editing, and multiplexing strategies. Additionally, we highlight recent advances in overcoming key challenges such as reagent delivery and plant regeneration, which are crucial for successful implementation of CRISPR in trees. We also delve into the potential and ethical considerations of using CRISPR gene drive for population-level genetic alterations, as well as the importance of genetic containment strategies for mitigating risks. This review emphasizes the need for continued research, technological advancements, extensive long-term field trials, public engagement, and responsible innovation to fully harness the power of CRISPR for shaping a sustainable future for forests.

Summary: Tree growth performance can be partly explained by genetics, while a large proportion of growth variation is thought to be controlled by environmental factors. However, to what extent DNA methylation, a stable epigenetic modification, contributes to phenotypic plasticity in the growth performance of long‐lived trees remains unclear. In this study, a comparative analysis of targeted DNA genotyping, DNA methylation and mRNAseq profiling for needles of 44‐year‐old Douglas‐fir trees (Pseudotsuga menziesii (Mirb.) Franco) having contrasting growth characteristics was performed. In total, we identified 195 differentially expressed genes (DEGs) and 115 differentially methylated loci (DML) that are associated with genes involved in fitness‐related processes such as growth, stress management, plant development and energy resources. Interestingly, all four intronic DML were identified in mega‐sized (between 100 and 180 kbp in length) and highly expressed genes, suggesting specialized regulation mechanisms of these long intron genes in gymnosperms. DNA repetitive sequences mainly comprising long‐terminal repeats of retroelements are involved in growth‐associated DNA methylation regulation (both hyper‐ and hypomethylation) of 99 DML (86.1% of total DML). Furthermore, nearly 14% of the DML was not tagged by single nucleotide polymorphisms, suggesting a unique contribution of the epigenetic variation in tree growth.

Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach.

Plants respond to drought by major reprogramming of gene expression enabling the plant to survive this threatening environmental condition. One major upstream signal inducing this multifaceted process is the phytohormone abscisic acid (ABA). In this report, we investigate the drought response in barley plants (Hordeum vulgare, cv. Morex) at both epigenome and transcriptome levels. Leaves of barley plants after 10 days of drought treatment, when soil water content was decreased by about 40%, were compared to well-watered controls. Due to the drought treatment, chlorophyll content and photosystem II-efficiency were decreased by about 10% and some known drought-related genes were already induced. Global ChIPseq analyses were used to identify genes where histones 3 associated with promoter or gene body were modified with euchromatic K4 trimethylation or K9 acetylation during drought. Using stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitive than H3K4 trimethylation. Comparison with differentially expressed genes enabled to identify those genes, which are loaded with the euchromatic marks and are induced in response to the drought treatment. The results show that a major part of these genes is involved in ABA-signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which are involved in the central regulatory machinery of ABA signaling, were also identified by this approach.

Terrestialization is supposedly an important evolutionary process plant experience. However, directions of land back to water acquired little attention. Here we integrate multiproxy evidence to elucidate the evolution of duckweed. Three genera of duckweed show chronologically gradient degeneration in roots structure and stomatal function and decrease in lignocellulose content, accompanied by gradual contraction in relevant gene numbers and/or decline in transcription. The gene numbers in the main phytohormonal pathway are also gradually decreased. The co-action of auxin and rhizoid development gene causes a gradual decrease in adventitious roots. The significant expansion of the flavonoid pathway is also related to the adaptation of duckweed to floating growth. This study reconstructs the evolution history of duckweeds from land back to water, reverse to that of early land plants. Summary: With terrestrialization being the popularly acknowledged plant evolutionary process, little is known about the evolution of higher plant from land back to water. Here we integrate multiproxy evidence to elucidate the gradual reverse evolution of duckweed. Three genera of duckweed show chronologically gradient degeneration in the structure of roots, the function of stomata, and decrease in lignocellulose content, accompanied by gradient contraction in relevant gene numbers and/or decline in transcript expression. The gene numbers in the main phytohormonal pathway are also gradually decreased. The co-action of auxin and rhizoid development gene causes a gradual decrease in adventitious roots. The significant expansion of the flavonoid pathway is also highly related to the adaptation of duckweed to floating growth. Our study combined with the fossil evidence reconstruct the evolution history of duckweeds from land back to water, reverse to that of early land plants. This study reconstructed the process of how a land plant returns to water, a reverse evolutionary approach which is different from what we studied in textbook about plant terrestrialization. This finding could be helpful for us to deeply and widely understand the adaptation of plant to the environment, and to expand and deepen the knowledge of evolution theory.

Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.

Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.

Duckweeds are small, free-floating, morphologically highly reduced organisms belonging to the monocot order Alismatales. They display the most rapid growth among flowering plants, vary ~ 14-fold in genome size and comprise five genera. Spirodela is the phylogenetically oldest genus with only two mainly asexually propagating species: S. polyrhiza (2n = 40; 160 Mbp/1C) and S. intermedia (2n = 36; 160 Mbp/1C). This study combined comparative cytogenetics and de novo genome assembly based on PacBio, Illumina and Oxford Nanopore (ON) reads to obtain the first genome reference for S. intermedia and to compare its genomic features with those of the sister species S. polyrhiza. Both species’ genomes revealed little more than 20,000 putative protein-coding genes, very low rDNA copy numbers and a low amount of repetitive sequences, mainly Ty3/gypsy retroelements. The detection of a few new small chromosome rearrangements between both Spirodela species refined the karyotype and the chromosomal sequence assignment for S. intermedia.