Search Results (49)

The blood orange arose from the insertion of a retrotransposon adjacent to the Ruby gene, an MYB-type transcriptional activator of anthocyanin production, as reported previously. However, the intricate process of anthocyanin regulation among different varieties of blood orange remains incompletely understood. In this study, mRNA levels of the transcription factors Ruby and TT8 were found to be upregulated in the juice vesicle tissues of a variety with higher concentrations of anthocyanins in the pulp compared with another variety with a lower anthocyanin content. In contrast, comparative analysis of the two varieties using two-dimensional electrophoresis and mass spectrometry did not identify differentially expressed proteins related to anthocyanin biosynthesis in the juice vesicle tissues. Furthermore, higher anthocyanin contents were observed in various tissues of transgenic Arabidopsis thaliana overexpressing the Ruby gene from blood orange compared with the wildtype plant. Moreover, the long terminal repeat (LTR) region of a retrotransposon inserted upstream of the Ruby locus exhibited the ability to drive reporter expression through histochemical assay in a transgenic seedling. Thus, a PCR-based molecular marker was developed, targeting the upstream sequence of the Ruby locus to identify Citrus hybrids with the unique trait of red-fleshed fruit. Intriguingly, bisulfite sequencing revealed differentially methylated regions within a Gag-Pol polyprotein-encoding sequence of a retrotransposon adjacent to Ruby locus when comparing two varieties with different anthocyanin contents. A higher average level of methylation status was observed in the fruit with a lower anthocyanin content. In conclusion, methylation modifications at specific upstream positions on the Ruby locus may influence anthocyanin production in blood oranges. Full article

Capsicum (pepper) is an economically vital genus in the Solanaceae family, with most species possessing about 3 Gb genomes. However, the recently sequenced Capsicum rhomboideum (~1.7 Gb) represents the first reported case of an extremely compact genome in Capsicum, providing a unique and ideal model for studying genome size evolution. To elucidate the mechanisms driving this variation, we performed comparative genomic analyses between the compact Capsicum rhomboideum and the reference Capsicum annuum cv. CM334 (~2.9 Gb). Although their genome size differences initially suggested whole-genome duplication (WGD) as a potential driver, both species shared two ancient WGD events with identical timing, predating their divergence and thus ruling out WGD as a direct contributor to their size difference. Instead, transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), emerged as the dominant force shaping genome size variation. Genome size strongly correlated with LTR-RT abundance, and multiple LTR-RT burst events aligned with major phases of genome expansion. Notably, the integrity and transcriptional activity of LTR-RTs decline over evolutionary time; older insertions exhibit greater structural degradation and reduced activity, reflecting their dynamic nature. This study systematically delineated the evolutionary trajectory of LTR-RTs—from insertion and proliferation to decay–uncovering their pivotal role in driving Capsicum genome size evolution. Our findings advance the understanding of plant genome dynamics and provide a framework for studying genome size variation across diverse plant lineages. Full article

Auricularia mushrooms, common bulk edible fungi, have considerable culinary and medicinal value. The Qinling region, represented by Zhashui County, is the main production area of Auricularia mushrooms in China. In this study, two wild Auricularia strains, M12 and M13, selected from the Qinling region for their desirable horticultural traits after domestication, were sequenced and characterized. Sequencing assembly results based on Illumina NovaSeq and PacBio Sequel II HiFi showed that the M12 genome was 56.04 Mbp in size, with 2.58% heterozygosity and 14.13% repetitive sequences, and was anchored on 12 chromosomes using HI-C technology. In contrast, the M13 genome was 52.10 Mbp, showed 2.34% heterozygosity, 13.89% repetitive sequences, and was assembled into 12 scaffolds. Collinearity analysis revealed extensive homologous regions between the M12 and M13 genomes. Phylogenetic analysis suggested that the divergence between M12 and M13 occurred approximately 4.575 million years ago (MYAs), while their divergence from Auricularia subglabra TFB-10046 SS5 occurred approximately 33.537 MYAs. Analyses of CYP450, carbohydrate-active enzymes (CAZymes), and gene family expansion/contraction revealed distinct genomic features between the two strains. SSR and LTR insertion time analyses revealed the genome dynamics of the two strains during their evolution. Analysis of secondary metabolite-associated biosynthetic gene clusters (BGCs) provides powerful clues to understand the origin of bioactive compounds in the Auricularia mushroom. This work represents the first genome sequencing of the Auricularia species derived from the Qinling region. These results not only enriched our understanding of the Auricularia genome but also provided an important genomic resource and theoretical basis for the subsequent genetic breeding, functional gene mining, and development of medicinal components of Auricularia species. Full article

Plant genomes possess numerous transposable element (TE) insertions that have occurred during evolution. Most TEs are silenced or diverged; therefore, they lose their ability to encode proteins and are transposed in the genome. Knowledge of active plant TEs and TE-encoded proteins essential for transposition and evasion of plant cell transposon silencing mechanisms remains limited. This study investigated active long terminal repeat (LTR) retrotransposons (RTEs) in sunflowers (Helianthus annuus), revealing heterogeneous and phylogenetically distinct RTEs triggered by epigenetic changes and heat stress. Many of these RTEs belong to three distinct groups within the Tekay clade, showing significant variations in chromosomal insertion distribution. Through protein analysis of these active RTEs, it was found that Athila RTEs and Tekay group 2 elements possess additional open reading frames (aORFs). The aORF-encoded proteins feature a transposase domain, a transmembrane domain, and nuclear localization signals. The aORF proteins of the Tekay subgroup exhibited remarkable conservation among over 500 Tekay members, suggesting their functional importance in RTE mobility. The predicted 3D structure of the sunflower Tekay aORF protein showed significant homology with Tekay proteins in rice, maize, and sorghum. Additionally, the structural features of aORF proteins resemble those of plant DRBM-containing proteins, suggesting their potential role in RNA-silencing modulation. These findings offer insights into the diversity and activity of sunflower RTEs, emphasizing the conservation and structural characteristics of aORF-encoded proteins. Full article

Background: Transposable elements (TEs) and noncoding sequences are major components of the genome, yet their functional contributions to long noncoding RNAs (lncRNAs) are not well understood. Although many lncRNAs originating from TEs (TE-lncRNAs) have been identified across various organisms, their characteristics and regulatory roles, particularly in insects, remain largely unexplored. This study integrated multi-omics data to investigate TE-lncRNAs in D. melanogaster, focusing on the influence of transposons across different omics levels. Results: We identified 16,118 transposons overlapping with lncRNA sequences that constitute 2119 TE-lncRNAs (40.4% of all lncRNAs) using 256 public RNA-seq samples and 15 lncRNA-seq samples of Drosophila S2 cells treated with heavy metals. Of these, 67.2% of TE-lncRNAs contain more than one TE. The LTR/Gypsy family was the most common transposon insertion. Transposons preferred to insert into promoters, transcription starting sites, and intronic regions, especially in chromosome ends. Compared with lncRNAs, TE-lncRNAs showed longer lengths, a lower conservation, and lower levels but a higher specificity of expression. Multi-omics data analysis revealed positive correlations between transposon insertions and chromatin openness at the pre-transcriptional level. Notably, a total of 516 TE-lncRNAs provided transcriptional factor binding sites through transposon insertions. The regulatory network of a key transcription factor was rewired by transposons, potentially recruiting other transcription factors to exert regulatory functions under heavy metal stress. Additionally, 99 TE-lncRNAs were associated with m⁶A methylation modification sites, and 115 TE-lncRNAs potentially provided candidate small open reading frames through transposon insertions. Conclusions: Our data analysis demonstrated that TEs contribute to the regulation of lncRNAs. TEs not only promote the transcriptional regulation of lncRNAs, but also facilitate their post-transcriptional and epigenetic regulation. Full article

The genus Ilex belongs to the sole family and is the single genus within the order Aquifoliales, exhibiting significant phenotypic diversity. However, the genetic differences underlying these phenotypic variations have rarely been studied. In this study, collinearity analyses of three Ilex genomes, Ilex latifolia Thunb., Ilex polyneura (Hand.-Mazz.) S. Y. Hu, and Ilex asprella Champ. ex Benth., indicated a recent fusion event contributing to the reduction of chromosomes in I. asprella. Comparative genome analyses showed slight differences in gene annotation among the three species, implying a minimal disruption of genes following chromosomal fusion in I. asprella. Comprehensive annotation of transposable elements (TEs) revealed that TEs constitute a significant portion of the Ilex genomes, with LTR transposons being predominant. TEs exhibited an inverse relationship with gene density, potentially influencing gene regulation and chromosomal architecture. TE insertions were shown to affect the conformation and binding sites of key genes such as 7-deoxyloganetin glucosyltransferase and transmembrane kinase (TMK) genes, highlighting potential functional impacts. The structural variations caused by TE insertions suggest significant roles in the evolutionary dynamics, leading to either loss or gain of gene function. This study underscores the importance of TEs in shaping the genomic landscape and evolutionary trajectories of Ilex species. Full article

Transposable elements (TEs) significantly contribute to the evolution and diversity of plant genomes. In this study, we explored the roles of TEs in the genomes of Citrus and Citrus-related genera by constructing a pan-genome TE library from 20 published genomes of Citrus and Citrus-related accessions. Our results revealed an increase in TE content and the number of TE types compared to the original annotations, as well as a decrease in the content of unclassified TEs. The average length of TEs per assembly was approximately 194.23 Mb, representing 41.76% (Murraya paniculata) to 64.76% (Citrus gilletiana) of the genomes, with a mean value of 56.95%. A significant positive correlation was found between genome size and both the number of TE types and TE content. Consistent with the difference in mean whole-genome size (39.83 Mb) between Citrus and Citrus-related genera, Citrus genomes contained an average of 34.36 Mb more TE sequences than Citrus-related genomes. Analysis of the estimated insertion time and half-life of long terminal repeat retrotransposons (LTR-RTs) suggested that TE removal was not the primary factor contributing to the differences among genomes. These findings collectively indicate that TEs are the primary determinants of genome size and play a major role in shaping genome structures. Principal coordinate analysis (PCoA) of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers revealed that the fragmented TEs were predominantly derived from ancestral genomes, while intact TEs were crucial in the recent evolutionary diversification of Citrus. Moreover, the presence or absence of intact TEs near the AdhE superfamily was closely associated with the bitterness trait in the Citrus species. Overall, this study enhances TE annotation in Citrus and Citrus-related genomes and provides valuable data for future genetic breeding and agronomic trait research in Citrus. Full article

The genomes and annotated genes of allotetraploid cotton Gossypium hirsutum have been extensively studied in recent years. However, the expression, regulation, and evolution of intergenic genes (ITGs) have not been completely deciphered. In this study, we identified a novel set of actively expressed ITGs in G. hirsutum cotton, through transcriptome profiling based on deep sequencing data, as well as chromatin immunoprecipitation, followed by sequencing (ChIP-seq) of histone modifications and how the ITGs evolved. Totals of 17,567 and 8249 ITGs were identified in G. hirsutum and Gossypium arboreum, respectively. The expression of ITGs in G. hirsutum was significantly higher than that in G. arboreum. Moreover, longer exons were observed in G. hirsutum ITGs. Notably, 42.3% of the ITGs from G. hirsutum were generated by the long terminal repeat (LTR) insertions, while their proportion in genic genes was 19.9%. The H3K27ac and H3K4me3 modification proportions and intensities of ITGs were equivalent to genic genes. The H3K4me1 modifications were lower in ITGs. Additionally, evolution analyses revealed that the ITGs from G. hirsutum were mainly produced around 6.6 and 1.6 million years ago (Mya), later than the pegged time for genic genes, which is 7.0 Mya. The characterization of ITGs helps to elucidate the evolution of cotton genomes and shed more light on their biological functions in the transcriptional regulation of eukaryotic genes, along with the roles of histone modifications in speciation and diversification. Full article

During the last twenty years, minimal white spotting associated with blue eyes was selected by feline breeders to create the Altai, Topaz, and Celestial breeds. Additionally, certain breeders introduced this trait in their lineages of purebred cats. The trait has been called “dominant blue eyes (DBE)” and was confirmed to be autosomal dominant in all lineages. DBE was initially described in outbred cats from Kazakhstan and Russia and in two purebred lineages of British cats from Russia, as well as in Dutch Maine Coon cats, suggesting different founding effects. We have previously identified two variants in the Paired Box 3 (PAX3) gene associated with DBE in Maine Coon and Celestial cats; however, the presence of an underlying variant remains undetermined in other DBE breeding lines. Using a genome-wide association study, we identified a single region on chromosome C1 that was associated with DBE in British cats. Within that region, we identified PAX3 as the strongest candidate gene. Whole-genome sequencing of a DBE cat revealed an RD-114 retrovirus LTR (long terminal repeat) insertion within PAX3 intron 4 (namely NC_018730.3:g.206975776_206975777insN[433]) known to contain regulatory sequences. Using a panel of 117 DBE cats, we showed that this variant was fully associated with DBE in two British lineages, in Altai cats, and in some other DBE lineages. We propose that this NC_018730.3:g.206975776_206975777insN[433] variant represents the DBE^ALT (Altai Dominant Blue Eye) allele in the domestic cat. Finally, we genotyped DBE cats from 14 lineages for the three PAX3 variants and showed that they were not present in four lineages, confirming genetic heterogeneity of the DBE trait in the domestic cat. Full article

A high-quality genome sequence from an Indian isolate of Blumeria graminis f. sp. tritici Wtn1, a persistent threat in wheat farming, was obtained using a hybrid method. The assembly of over 9.24 million DNA-sequence reads resulted in 93 contigs, totaling a 140.61 Mb genome size, potentially encoding 8480 genes. Notably, more than 73.80% of the genome, spanning approximately 102.14 Mb, comprises retro-elements, LTR elements, and P elements, influencing evolution and adaptation significantly. The phylogenomic analysis placed B. graminis f. sp. tritici Wtn1 in a distinct monocot-infecting clade. A total of 583 tRNA anticodon sequences were identified from the whole genome of the native virulent strain B. graminis f. sp. tritici, which comprises distinct genome features with high counts of tRNA anticodons for leucine (70), cysteine (61), alanine (58), and arginine (45), with only two stop codons (Opal and Ochre) present and the absence of the Amber stop codon. Comparative InterProScan analysis unveiled “shared and unique” proteins in B. graminis f. sp. tritici Wtn1. Identified were 7707 protein-encoding genes, annotated to different categories such as 805 effectors, 156 CAZymes, 6102 orthologous proteins, and 3180 distinct protein families (PFAMs). Among the effectors, genes like Avra10, Avrk1, Bcg-7, BEC1005, CSEP0105, CSEP0162, BEC1016, BEC1040, and HopI1 closely linked to pathogenesis and virulence were recognized. Transcriptome analysis highlighted abundant proteins associated with RNA processing and modification, post-translational modification, protein turnover, chaperones, and signal transduction. Examining the Environmental Information Processing Pathways in B. graminis f. sp. tritici Wtn1 revealed 393 genes across 33 signal transduction pathways. The key pathways included yeast MAPK signaling (53 genes), mTOR signaling (38 genes), PI3K-Akt signaling (23 genes), and AMPK signaling (21 genes). Additionally, pathways like FoxO, Phosphatidylinositol, the two-component system, and Ras signaling showed significant gene representation, each with 15–16 genes, key SNPs, and Indels in specific chromosomes highlighting their relevance to environmental responses and pathotype evolution. The SNP and InDel analysis resulted in about 3.56 million variants, including 3.45 million SNPs, 5050 insertions, and 5651 deletions within the whole genome of B. graminis f. sp. tritici Wtn1. These comprehensive genome and transcriptome datasets serve as crucial resources for understanding the pathogenicity, virulence effectors, retro-elements, and evolutionary origins of B. graminis f. sp. tritici Wtn1, aiding in developing robust strategies for the effective management of wheat powdery mildew. Full article

Endogenous retroviruses (ERVs) are one of the superfamilies of long terminal repeat retrotransposons (LTRs) in mice and humans. Approximately 8% of the pig genome is composed of sequences derived from LTRs. While the majority of ERVs in pigs have decayed, a small number of full-length copies can still mobilize within the genome. This study investigated the unexplored retroviral insertion polymorphisms (RIPs) generated by the mobilization of full-length ERVs (Fl-ERVs), and evaluated their impact on phenotypic variation to gain insights into the biological role of Fl-ERVs in pigs. Overall, 39 RIPs (insertions or deletions relative to the pig reference genome) generated by Fl-ERVs were predicted by comparative genomic analysis, and 18 of them were confirmed by PCR detection. Four RIP sites (D5, D14, D15, and D18) were further evaluated by population analysis, and all of them displayed polymorphisms in multiple breeds. The RIP site of ERV-D14, which is a Fl-ERV inserted in the STAB2-like gene, was further confirmed by sequencing. Population analysis of the polymorphic site of ERV-D14 reveals that it presents moderate polymorphism information in the Large White pig breed, and the association analysis reveals that the RIP of ERV-D14 is associated with age variations at 30 kg body weight (p < 0.05) and 100 kg body weight (p < 0.01) in the population of Large White pigs (N = 480). Furthermore, the ERV-D14 RIP is associated with changes in the expression of the target gene STAB2-like in the liver, backfat, and leaf fat in Sushan pigs. These data suggest that some Fl-ERVs are still mobilizing in the pig’s genome, and contribute to genomic and phenotypic variations. Full article

Terminal repeat retrotransposons in miniature (TRIMs) are short non-autonomous long terminal repeat (LTR) retrotransposons found from various eukaryotes. Cassandra is a unique TRIM lineage which contains a 5S rRNA-derived sequence in its LTRs. Here, two new groups of TRIMs, designated Helenus and Ajax, are reported based on bioinformatics analysis and the usage of Repbase. Helenus is found from fungi, animals, and plants, and its LTRs contain a tRNA-like sequence. It includes two LTRs and between them, a primer-binding site (PBS) and polypurine tract (PPT) exist. Fungal and plant Helenus generate 5 bp target site duplications (TSDs) upon integration, while animal Helenus generates 4 bp TSDs. Ajax includes a 5S rRNA-derived sequence in its LTR and is found from two nemertean genomes. Ajax generates 5 bp TSDs upon integration. These results suggest that despite their unique promoters, Helenus and Ajax are TRIMs whose transposition is dependent on autonomous LTR retrotransposon. These TRIMs can originate through an insertion of SINE in an LTR of TRIM. The discovery of Helenus and Ajax suggests the presence of TRIMs with a promoter for RNA polymerase III derived from a small RNA gene, which is here collectively termed TRIMp3. Full article

Transposable elements (TEs) significantly drive dynamic changes that characterize genome evolution. However, understanding the variability associated with TE insertions among different cultivars remains challenging. The pomegranate (Punica granatum L.) has yet to be extensively studied regarding the roles of TEs in the diversification of cultivars. Herein, we explored the genome distribution of TEs and its potential functional implications among four pomegranate cultivars, ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’ and ‘Tunisia’, whose genome sequences are available. A total of 8404 full-length TEs were isolated. The content of TEs varied among the cultivars, ranging from 41.67% of ‘Taishanhong’ to 52.45% of ‘Bhagwa’. In all cultivars, the Gypsy superfamily of retrotransposons accounted for a larger genome proportion than the Copia superfamily. Seventy-three full-length TEs were found at the same genomic loci in all four cultivars. By contrast, 947, 297, 311, and 874 TEs were found exclusively in ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’, and ‘Tunisia’ cultivars, respectively. Phylogenetic clustering based on the presence of TE insertions in specific loci reflected the geographic origins of the cultivars. The insertion time profiles of LTR-REs were studied in the four cultivars. Shared elements across the four cultivars exhibited, on average, a more ancient insertion date than those exclusive to three, two, or one cultivars. The majority of TEs were located within 1000 bp from the nearest gene. This localization was observed for 57% of DNA TEs and 55% of long-terminal repeat retrotransposons (LTR-RE). More than 10% of TEs resulted inserted within genes. Concerning DNA TEs, 3.91% of insertions occurred in introns, while 2.42% occurred in exons. As to LTR-REs, 4% of insertions occurred in exons and 1.98% in introns. Functional analysis of the genes lying close to TEs was performed to infer if differences in TE insertion can affect the fruit quality. Two TE insertions were found close to two genes encoding 4-coumarate--CoA ligase, an enzyme involved in the phenylpropanoid pathway. Moreover, a TIR/Mariner element was found within the exon of a gene encoding anthocyanidin reductase in the ‘Tunisia’ genotype, crucial in the biosynthesis of flavan-3-ols and proanthocyanidins, strictly correlated with the nutraceutical properties of pomegranate. Although functional and metabolomic studies are essential to elucidate the consequences of TE insertions, these results contribute to advancing our comprehension of the role of TEs in pomegranate genomics, providing insights for crop breeding. Full article

Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution. Full article

Background: Retrotransposons with long terminal repeats (LTR retrotransposons) are widespread in all groups of eukaryotes and are often both the cause of new mutations and the source of new sequences. Apart from their high activity in generative and differentiation-stage tissues, LTR retrotransposons also become more active in response to different stressors. The precise causes of LTR retrotransposons’ activation in response to stress, however, have not yet been thoroughly investigated. Methods: We used RT-PCR to investigate the transcriptional profile of LTR retrotransposons and piRNA clusters in response to oxidative and chronic heat stresses. We used Oxford Nanopore sequencing to investigate the genomic environment of new insertions of the retrotransposons. We used bioinformatics methods to find the stress-induced transcription factor binding sites in LTR retrotransposons. Results: We studied the transposition activity and transcription level of LTR retrotransposons in response to oxidative and chronic heat stress and assessed the contribution of various factors that can affect the increase in their expression under stress conditions: the state of the piRNA-interference system, the influence of the genomic environment on individual copies, and the presence of the stress-induced transcription factor binding sites in retrotransposon sequences. Conclusions: The main reason for the activation of LTR retrotransposons under stress conditions is the presence of transcription factor binding sites in their regulatory sequences, which are triggered in response to stress and are necessary for tissue regeneration processes. Stress-induced transposable element activation can function as a trigger mechanism, triggering multiple signal pathways and resulting in a polyvariant cell response. Full article