Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress

DNA Methylation and Alternative Splicing Safeguard Genome and Transcriptome After a Retrotransposition Burst in Arabidopsis thaliana

Transposable elements (TEs) are major drivers of plant genome plasticity, but the immediate molecular consequences of new TE insertions remain poorly understood. In this study, we generated a wild-type Arabidopsis thaliana population with novel insertions of ONSEN retrotransposon to investigate early epigenomic and transcriptomic changes using whole-genome and cDNA nanopore sequencing. We found that novel ONSEN insertions were distributed non-randomly, with a strong preference for genic regions, particularly in chromatin enriched for H2A.Z, H3K27me3, and H3K4me2. Most full-length ONSEN insertions within genes were rapidly recognized and spliced out as new introns (intronization), thereby mitigating potential deleterious effects on transcript isoforms. In some cases, ONSEN insertions provided alternative transcription start or termination sites, generating novel transcript isoforms. Genome-wide methylation analysis revealed that new ONSEN copies were efficiently and precisely targeted by DNA methylation. Independently on the location of the original ONSEN element, the euchromatic and heterochromatic insertions display distinct methylation signatures, reflecting the action of different epigenetic pathways. In conclusion, our results demonstrate that DNA methylation and alternative splicing are effective control mechanisms safeguarding the plant genome and transcriptome integrity after retrotransposition burst.

Heat stress response and transposon control in plant shoot stem cells

Plants have an impressive repertoire to react to stress conditions that limit regular growth. Elevated temperatures beyond the optimal range cause rapid and specific transcriptional responses, resulting in developmental alterations and plasticity. Heat stress also causes chromatin decondensation and activation of some transposable elements (TEs), endangering genomic integrity. This is especially risky for stem cells in the shoot apical meristem (SAM) that potentially contribute to the next generation. We examined how the heat stress response in SAM stem cells of Arabidopsis (Arabidopsis thaliana) is different from that in other tissues and whether the elements of epigenetic TE control active in the meristem are involved in specific heat protection of stem cells. Using fluorescence-activated nuclear sorting to isolate and characterize SAM stem cells after exposure to conditions that activate a heat-responsive TE, we found that SAM stem cells maintain their developmental program and suppress the heat-response pathways dominating in surrounding somatic cells. Furthermore, mutants defective in DNA methylation recovered less efficiently from heat stress and persistently activated heat response factors and heat-responsive TEs. Heat stress also induced epimutations at the level of DNA methylation, especially in the CHG sequence context. Regions with modified DNA methylation patterns remained altered for at least 3 wk beyond the stress. These findings urge for disentangling cell type-specific responses under different stress types, especially for stem cells as bridges to the next generation.

Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton

BACKGROUND

Cold stress significantly challenges cotton growth and productivity, yet the genetic and molecular mechanisms underlying cold tolerance remain poorly understood.

RESULTS

We employed RNA-seq and iterative weighted gene co-expression network analysis (WGCNA) to investigate gene and transposable element (TE) expression changes at six cold stress time points (0 h, 2 h, 4 h, 6 h, 12 h, 24 h). Thousands of differentially expressed genes (DEGs) were identified, exhibiting time-specific patterns that highlight a phase-dependent transcriptional response. While the A and D subgenomes contributed comparably to DEG numbers, numerous homeologous gene pairs showed differential expression, indicating regulatory divergence. Iterative WGCNA uncovered 125 gene co-expression modules, with some enriched in specific chromosomes or chromosomal regions, suggesting localized regulatory hotspots for cold stress response. Notably, transcription factors, including MYB73, ERF017, MYB30, and OBP1, emerged as central regulators within these modules. Analysis of 11 plant hormone-related genes revealed dynamic expression, with ethylene (ETH) and cytokinins (CK) playing significant roles in stress-responsive pathways. Furthermore, we documented over 15,000 expressed TEs, with differentially expressed TEs forming five distinct clusters. TE families, such as LTR/Copia, demonstrated significant enrichment in these expression clusters, suggesting their potential role as modulators of gene expression under cold stress.

CONCLUSIONS

These findings provide valuable insights into the complex regulatory networks underlying cold stress response in cotton, highlighting key molecular components involved in cold stress regulation. This study provides potential genetic targets for breeding strategies aimed at enhancing cold tolerance in cotton.

Repeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication

BACKGROUND AND AIMS

Ornamental hortensias are bred from a reservoir of over 200 species in the genus Hydrangea s.l. (Hydrangeaceae), and are valued in gardens, households and landscapes across the globe. The phenotypic diversity of hortensia cultivars, hybrids and wild relatives is mirrored by their genomic variation, with differences in genome size, base chromosome numbers and ploidy level. We aim to understand the genomic and chromosomal basis of hortensia genome variation. Therefore, we analysed six hortensias with different origins and chromosomal setups for repeatome divergence, the genome fraction with the highest sequence turnover. This holds information from the hortensias' evolutionary paths and can guide breeding initiatives.

METHODS

We compiled a hortensia genotype panel representing members of the sections Macrophyllae, Hydrangea, Asperae and Heteromallae and reconstructed a plastome-based phylogenetic hypothesis as the evolutionary basis for all our analyses. We comprehensively characterized the repeatomes by whole-genome sequencing and comparative repeat clustering. Major tandem repeats were localized by multicolour FISH.

KEY RESULTS

The Hydrangea species show differing repeat profiles reflecting their separation into the two major Hydrangea clades: diploid Hydrangea species from Japan show a conserved repeat profile, distinguishing them from Japanese polyploids as well as Chinese and American hortensias. These results are in line with plastome-based phylogenies. The presence of specific repeats indicates that H. paniculata was not polyploidized directly from the common ancestor of Japanese Hydrangea species, but evolved from a distinct progenitor. Major satellite DNAs were detected over all H. macrophylla chromosomes.

CONCLUSIONS

Repeat composition among the Hydrangea species varies in congruence with their origins and phylogeny. Identified species-specific satDNAs may be used as cytogenetic markers to identify Hydrangea species and cultivars, and to infer parental species of old Hydrangea varieties. This repeatome and cytogenetics information helps to expand the genetic toolbox for tracing hortensia evolution and guiding future hortensia breeding.

DNAJ protein gene expansion mechanism in Panicoideae and PgDNAJ functional identification in pearl millet

KEY MESSAGE

Analyze the evolutionary pattern of DNAJ protein genes in the Panicoideae, including pearl millet, to identify and characterize the biological function of PgDNAJ genes in pearl millet. Global warming has become a major factor threatening food security and human development. It is urgent to analyze the heat-tolerant mechanism of plants and cultivate crops that are adapted to high temperature conditions. The Panicoideae are the second largest subfamily of the Poaceae, widely distributed in warm temperate and tropical regions. Many of these species have been reported to have strong adaptability to high temperature stress, such as pearl millet, foxtail millet and sorghum. The evolutionary differences in DNAJ protein genes among 12 Panicoideae species and 10 other species were identified and analyzed. Among them, 79% of Panicoideae DNAJ protein genes were associated with retrotransposon insertion. Analysis of the DNAJ protein pan-gene family in six pearl millet accessions revealed that the non-core genes contained significantly more TEs than the core genes. By identifying and analyzing the distribution and types of TEs near the DNAJ protein genes, it was found that the insertion of Copia and Gypsy retrotransposons provided the source of expansion for the DNAJ protein genes in the Panicoideae. Based on the analysis of the evolutionary pattern of DNAJ protein genes in Panicoideae, the PgDNAJ was obtained from pearl millet through identification. PgDNAJ reduces the accumulation of reactive oxygen species caused by high temperature by activating ascorbate peroxidase (APX), thereby improving the heat resistance of plants. In summary, these data provide new ideas for mining potential heat-tolerant genes in Panicoideae, and help to improve the heat tolerance of other crops.

Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh

Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed genome wide association studies (GWASs) on seven rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width, and leaf angle) based on a population of 183 rice landraces of Bangladesh. Our GWASs reveal various chromosomal regions and candidate genes that are associated with different traits in Bangladeshi rice varieties. Noteworthy was the recurrent implication of chromosome 10 in all three grain-shape-related traits (grain length, grain width, and grain weight), indicating its pivotal role in shaping rice grain morphology. Our study also underscores the involvement of transposon gene families across these three traits. For leaf related traits, chromosome 10 was found to harbor regions that are significantly associated with leaf length and leaf width. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. This is the first known GWAS study on various yield-related traits in the varieties of Oryza sativa available in Bangladesh-the fourth largest rice-producing country. We believe this study will accelerate rice genetics research and breeding stable high-yielding rice in Bangladesh.

High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes of Tetraodontiformes

This study aimed to investigate the evolutionary profile (including diversity, activity, and abundance) of retrotransposons (RTNs) with long terminal repeats (LTRs) in ten species of Tetraodontiformes. These species, Arothron firmamentum, Lagocephalus sceleratus, Pao palembangensis, Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, Takifugu rubripes, Tetraodon nigroviridis, Mola mola, and Thamnaconus septentrionalis, are known for having the smallest genomes among vertebrates. Data mining revealed a high diversity and wide distribution of LTR retrotransposons (LTR-RTNs) in these compact vertebrate genomes, with varying abundances among species. A total of 819 full-length LTR-RTN sequences were identified across these genomes, categorized into nine families belonging to four different superfamilies: ERV (Orthoretrovirinae and Epsilon retrovirus), Copia, BEL-PAO, and Gypsy (Gmr, Mag, V-clade, CsRN1, and Barthez). The Gypsy superfamily exhibited the highest diversity. LTR family distribution varied among species, with Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, and Takifugu rubripes having the highest richness of LTR families and sequences. Additionally, evidence of recent invasions was observed in specific tetraodontiform genomes, suggesting potential transposition activity. This study provides insights into the evolution of LTR retrotransposons in Tetraodontiformes, enhancing our understanding of their impact on the structure and evolution of host genomes.

Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-retrotransposons; they are the most abundant type of transposons in plant genomes. They have many important functions involving gene regulation and the rise of new genes and pseudo genes in response to severe stress. Additionally, LTR-retrotransposons have several applications in biotechnology. Due to the abundance and the importance of LTR-retrotransposons, multiple computational tools have been developed for their detection. However, none of these tools take advantages of the availability of related genomes; they process one chromosome at a time. Further, recently nested LTR-retrotransposons (multiple elements of the same family are inserted into each other) cannot be annotated accurately - or cannot be annotated at all - by the currently available tools. Motivated to overcome these two limitations, we built Look4LTRs, which can annotate LTR-retrotransposons in multiple related genomes simultaneously and discover recently nested elements. The methodology of Look4LTRs depends on techniques imported from the signal-processing field, graph algorithms, and machine learning with a minimal use of alignment algorithms. Four plant genomes were used in developing Look4LTRs and eight plant genomes for evaluating it in contrast to three related tools. Look4LTRs is the fastest while maintaining better or comparable F1 scores (the harmonic average of recall and precision) to those obtained by the other tools. Our results demonstrate the added benefit of annotating LTR-retrotransposons in multiple related genomes simultaneously and the ability to discover recently nested elements. Expert human manual examination of six elements - not included in the ground truth - revealed that three elements belong to known families and two elements are likely from new families. With respect to examining recently nested LTR-retrotransposons, three out of five were confirmed to be valid elements. Look4LTRs - with its speed, accuracy, and novel features - represents a true advancement in the annotation of LTR-retrotransposons, opening the door to many studies focused on understanding their functions in plants.

The power of retrotransposons in high-throughput genotyping and sequencing

The use of molecular markers has become an essential part of molecular genetics through their application in numerous fields, which includes identification of genes associated with targeted traits, operation of backcrossing programs, modern plant breeding, genetic characterization, and marker-assisted selection. Transposable elements are a core component of all eukaryotic genomes, making them suitable as molecular markers. Most of the large plant genomes consist primarily of transposable elements; variations in their abundance contribute to most of the variation in genome size. Retrotransposons are widely present throughout plant genomes, and replicative transposition enables them to insert into the genome without removing the original elements. Various applications of molecular markers have been developed that exploit the fact that these genetic elements are present everywhere and their ability to stably integrate into dispersed chromosomal localities that are polymorphic within a species. The ongoing development of molecular marker technologies is directly related to the deployment of high-throughput genotype sequencing platforms, and this research is of considerable significance. In this review, the practical application to molecular markers, which is a use of technology of interspersed repeats in the plant genome were examined using genomic sources from the past to the present. Prospects and possibilities are also presented.

Genome Size Variation across a Cypriot Fabeae Tribe Germplasm Collection

DNA content is an important trait linked to the evolutionary routes of taxa and often connected to speciation. In the present study, we studied C-values variation across the Cypriot Fabeae gene pool. Several hundred plants (Vicia spp., Lens spp., Pisum spp.) were sampled across Cyprus. Accurate estimates were established by flow cytometry and propidium iodine staining for 155 discrete populations/accessions. A ten-fold variation was detected across lineages with 1C DNA content varying from 1.584 pg for V. cretica (ARI02420) to 13.983 pg for V. faba (ARI00187). In general, flow cytometry was precise for the characterization of species, even though there were instances of genome overlapping across taxa. Most analyses in the current work refer to species that have not been characterized before by flow cytometry (or any other DNA content estimation method). Still, a correlation to C-values previously reported in Kew Plant DNA C-values database was attempted. A high degree of correlation except for V. dalmatica was established. The evaluation of genome size trait in relation with the Fabeae phylogeny, revealed that Pisum and Lens genera were rather homogenous, but an astonishing fluctuation was shown for Vicia spp. Moreover, it was established that genome up- or down-scaling was not directly linked to speciation drivers. The genomic size measurements presented here could deliver extra quality control for the identification and characterization of taxa in germplasm collections, particularly in cases where species share morphological characters.

TEMM: A Curated Data Resource for Transposon Element-Based Molecular Markers in Plants

Transposon elements (TEs) are mobile genetic elements that can insert themselves into new locations and modify the plant genome. In recent years, they have been used as molecular markers in plant breeding programs. TE-based molecular markers (TE-markers) are divided into two categories depending on the transcription mechanism of the TEs. The first category is retrotransposon-based molecular markers, which include RBIP, IRAP, REMAP, and iPBS. The second group is DNA-based-TE-markers, which include MITE, TE-junction, and CACTA TE-markers. These markers are a good tool for studying genetic diversity and can provide information on plants' phylogenetic and evolutionary history. They can help improve breeding programs to increase agronomic traits and develop new varieties. Overall, TE-markers play an important role in plant genetics and plant breeding and contribute to a better understanding of plant biology. Here, we present TEMM, a curated data resource for TE-markers in plants. Relevant research articles were screened to collect primer sequences and related information. Only articles containing primer sequences are added to the present data resource. TEMM contains 784 primers with their associated PCR reaction programs and their applications in various crops. These include 203 IPBS, 191 RBIP, 140 IRAP, 78 TE-junction, 76 IRAPS, 47 RBIP-IRAP, 16 IRAP-REMAP, 12 REMAP, 12 REMA-IRAP, 6 REMA, and 3 ISBP primers. The data resource is freely available at https://bioinformatics.um6p.ma/TEMM .