Repetitive Sequences Research Articles

Chromosome-level genome assembly of starry flounder (Platichthys stellatus).

Starry flounder (Platichthys stellatus) is widely distributed along the coastlines of the North Pacific. As an euryhaline flatfish, it can adapt to a wide range of environmental salinity ranging from freshwater to seawater, and is a promising aquaculture flatfish species in Korea and North China. However, no high-quality starry flounder reference genome has been reported to date, which greatly limits the studies of genetics and functional genomics. Here, we obtained a high-quality chromosome-level starry flounder genome assembly with alength of 643.56 Mb (scaffold N50: 26.19 Mb, contig N50: 10.00 Mb) combining short-reads sequencing, PacBio HiFi sequencing, and Hi-C sequencing. Approximately 94.02% of assembled sequences were anchored into 24 pseudochromosomes, and a total of 18 telomeres were detected. Totally 22,835 protein-coding genes and 227.87 Mb repetitive sequences were identified. In summary, the high-quality chromosome-level genome assembly not only provides valuable resources for genetic research in starry flounder, but also advances the development of molecular breeding technology of starry flounder.

Long telomere inheritance through budding yeast sexual cycles.

The ends of linear eukaryotic chromosomes are protected from being recognized as DNA double-strand breaks by telomeres, containing repetitive DNA sequences which bind specific proteins. In humans, mutations in telomere regulatory genes lead to short or long telomere syndromes. These syndromes often show genetic anticipation, where disease has earlier onset and a more severe manifestation in each new generation. Later generations inherit not only the mutation affecting telomere length, but also abnormal length telomeres. Many aspects of telomere length homeostasis are conserved between mammals and yeast. Here we explored telomere length inheritance patterns through the sexual cycle in yeast. Analysis of single telomeres, rather than bulk telomeres, shows that if haploid yeast with short telomeres mate with wild-type yeast creating diploids, short telomere lengths rapidly normalize (within 30 cell divisions). However, long telomeres inherited from one parent can persist for more than 200 mitotic cell divisions. Long telomere can also be transmitted through more than one round of meiosis, independently of mutations that cause long telomeres. These patterns, along with haploinsufficiency effects, show that even in yeast there is a complex relationship between telomere length, telomere length inheritance, and mutations that affect telomere length. Our findings may have implications for families affected by telomere syndromes.

A telomere-to-telomere gap-free genome assembly of the endangered humphead wrasse (Cheilinus undulatus)

Humphead wrasse, Cheilinus undulatus, is an endangered fish species with high economic and ecological value as well as natural sex change from female to male, while sexual selection occurs in breeding aggregations. In our present study, we constructed the first gap-free telomere-to-telomere (T2T) genome assembly for humphead wrasse, by integration of PacBio HiFi, ONT Ultra-long and Hi-C sequencing techniques. With 99% of the entire sequences anchored into 24 chromosomes, this haplotypic genome assembly spans approximately 1.25 Gb and presents a complete set of 48 telomeres and 24 centromeres. In terms of correctness (quality value QV: 53.447) and completeness (BUSCO score: 99.3%), this chromosome-scale assembly is indeed of high quality. We predicted 658.03 Mb of repetitive sequences and annotated 26,609 protein-coding genes in the assembled genome. This high-quality T2T genome assembly not only facilitates the genetic conservation of humphead wrasse, but also offers fundamental genomic data for supporting in-depth investigations on functional genomics, genetic diversity, and selective breeding for this economically important teleost.

A chromosome-level genome assembly and annotation of Cercis chuniana (Fabaceae)

The genus Cercis L., at the base of the subfamily Cercidoideae of Fabaceae, is known for its ecological adaptability and significant medicinal, ornamental, and economic value. However, the lack of a high-quality genome hinders the understanding of the evolution of Cercis and Fabaceae. In this study, we present a chromosome-level genome of Cercis chuniana by combining Illumina short reads, PacBio HiFi long reads, and Hi-C data. The final genome size is 355.53 Mb, consisting of 12 contigs with a N50 of 42.34 Mb. Notably, 344.24 Mb, corresponding to 96.82% of the genome, was anchored to seven chromosomes. The assembly comprises 24.83% repetitive sequences, including 19.32% long terminal repeats. Additionally, a total of 33,837 protein-coding genes were predicted in the genome, with 32,709 (96.67%) genes successfully annotated. The high-quality genome assembly of C. chuniana not only bridges the existing gap in genomic data and offers important resources for molecular studies of this species, but also provides essential insights for future studies on speciation, functional and comparative genomics within the Fabaceae family.

PCR-Free Site-Directed Mutagenesis on Repetitive Sequences Using Single-Stranded DNA-Assisted Double-Stranded DNA Nicking by DNAzymes.

Site-directed mutagenesis (SDM) is a key driver for many biochemical investigations and biotechnological applications. Despite decades of development, it is still difficult to perform SDM on some sequences, including highly repetitive ones, because polymerase chain reaction (PCR) is often used as the most effective method for SDM, but results in complicated products with these sequences. To overcome this limitation, we report herein a PCR-free SDM method that uses DNA-cleaving DNAzymes. Since these DNAzymes lack the capability of cleaving double-stranded DNA, we employed single-stranded DNAs as assisting DNAs to open superhelical plasmids, allowing the DNA-cleaving DNAzymes to cleave the plasmid. Such a system, named single-stranded DNA-assisted double-stranded DNA nicking by DNAzymes (DANDA), expanded the substrate scope of DNAzymes to double-stranded, superhelical plasmids. We showed that DANDA is highly customizable and target-specific, which allows successful generation of mutations on a plasmid containing PCR-incompatible repetitive sequences. By using solely unmodified DNA oligos that are more cost-effective and easier to prepare than other systems that employ either PNA or restriction enzymes, this DANDA system further expands the applications of DNA-cleaving DNAzymes in synthetic biology for different biochemical and biotechnological applications.

Chromosome-level genome assembly of Nothapodytes nimmoniana

Nothapodytes nimmoniana is a plant species belonging to the genus Nothapodytes in the family Icacinaceae. This species holds significant medicinal value due to its camptothecin content. In this study, we present the first chromosome-level genome assembly of N. nimmoniana constructed using NGS, Hi-C, and HiFi sequencing technologies. The assembled genome spans 3.53 Gb across 14 chromosomes, with an N50 length of 248.74 Mb. Genome annotation revealed that repetitive sequences constitute 80.82% of the genome size, and 83,269 protein-coding genes were predicted. Additionally, 4,360,538 bp of non-coding RNA were annotated. This genomic resource provides a foundation for further investigation into camptothecin biosynthesis pathways and plant phylogeny in N. nimmoniana.

The Complete Chloroplast Genome of Purdom’s Rhododendron (Rhododendron purdomii Rehder & E. H. Wilson): Genome Structure and Phylogenetic Analysis

Rhododendron purdomii Rehder & E. H. Wilson (Ericaceae) is a threatened ornamental and medicinal shrub or small tree species primarily distributed in the Qinling-Daba Mountains of Central China. To facilitate its conservation and utilization, the complete chloroplast genome of Rh. purdomii was sequenced, assembled, and characterized. The cp genome exhibited a typical quadripartite structure with a total length of 208,062 bp, comprising a large single copy (LSC) region of 110,618 bp, a small single copy (SSC) region of 2606 bp, and two inverted repeat (IR) regions of 47,419 bp each. The overall GC content was 35.81%. The genome contained 146 genes, including 96 protein-coding genes, 42 transfer RNA genes, and 8 ribosomal RNA genes. Structure analysis identified 67,354 codons, 96 long repetitive sequences, and 171 simple sequence repeats. Comparative genomic analysis across Rhododendron species revealed hypervariable coding regions (accD, rps9) and non-coding regions (trnK-UUU-ycf3, trnI-CAU-rpoB, trnT-GGU-accD, rpoA-psbL, rpl20-trnC-GCA, trnI-CAU-rrn16, and trnI-CAU-rps16), which may serve as potential molecular markers for genetic identification. Phylogenetic reconstruction confirmed the monophyly of Rhododendron species and highlighted a close relationship between Rh. purdomii and Rh. henanense subsp. lingbaoense. These results provide essential genomic resources for advancing taxonomic, evolutionary, conservation, and breeding studies of Rh. purdomii and other species within the genus Rhododendron.

Comprehensive analysis of repetitive extragenic palindrome sequences identified in bacteria and archaea using a new web-based tool, RepRanger.

Repetitive extragenic palindromic (REP) sequences were first discovered in the intergenic regions of Escherichia coli and later found in phylogenetically distinct bacterial species. However, their biological roles and sequence conservation remain unclear. Considering the growing number of microbial genome sequencing and annotation projects, along with the lack of online tools for REP identification, we developed a new web-based platform, RepRanger, to rapidly identify and annotate putative palindromic elements, including REPs. Using RepRanger, we identified >4,000 REPs in the E. coli MG1655 genome. Moreover, 81 (~52%) of its 157 small noncoding RNAs (sRNAs; known to regulate gene expression) contain REPs. Further analysis using RepRanger, alongside other bioinformatics tools, yielded 10 REP consensus motifs. Notably, REPs potentially involved in translational control (i.e., located within 15 nucleotides downstream of an open reading frame) primarily host motif 4, whereas REPs present in sRNAs predominantly encoded motif 9. Putative targets of REP-containing sRNAs include genes that rewire metabolic pathways in response to environmental changes, indicating that REPs likely contribute to bacterial adaptation. We also reveal that REP consensus motifs are similar across pathogenic and environmental E. coli strains but not commensal and laboratory ones. We employed RepRanger to search for REPs and confirm that they are present across bacteria and archaea. Furthermore, we uncovered similarities in REP sequences between bacterial and archaeal genomes. Thus, we demonstrate that RepRanger represents a versatile tool for discovering REPs in bacteria and archaea, providing new insights into their functions and sequence diversity.IMPORTANCERepetitive extragenic palindromic (REP) sequences were first discovered in Escherichia coli, but their biological roles, diversity, and sequence conservation remain unclear. We have developed a web-based tool, RepRanger, to identify and annotate putative palindromic elements, including REPs. Using RepRanger, we identified approximately 4,000 REPs in the E. coli MG1655 genome. We show that >50% of small noncoding RNAs (sRNAs) contain REPs. The predicted functions of REP-containing sRNAs indicate that REPs likely contribute to bacterial environmental adaptability. In addition, we have discovered REPs in pathogenic, environmental, and commensal E. coli, allowing us to assess their sequence similarity. We show that REPs are widely present in bacterial and archaeal genomes and share some sequence similarities. Our comparison of REPs in annotated genomes broadens the current understanding of REP sequence diversity, conservation, and function.

A Study on the Diagnostic and Prognostic Value of Extrachromosomal Circular DNA in Breast Cancer

Objectives: To investigate the clinical diagnostic and prognostic value of extrachromosomal circular DNA (eccDNA) in breast cancer, eccDNA profiles were constructed for 81 breast cancer tumor tissues and 33 adjacent non-tumor tissues. Methods: The distribution characteristics of eccDNA across functional genomic elements and repetitive sequences were systematically analyzed. Furthermore, a diagnostic model for differentiating malignant and normal breast tissues, as well as a prognostic prediction model, was developed using a random forest algorithm. Results: EccDNA in breast cancer tissues harbor a higher proportion of functional elements and repetitive sequences, with their annotated genes significantly enriched in tumor- and immune-related pathways. However, no significant differences in eccDNA features were observed across breast cancer subtypes or pathological stages. In the validation cohort, the eccDNA-based diagnostic model achieved an AUC of 0.83, with repetitive elements and enhancer-associated features contributing the most to diagnostic performance. The prognostic model achieved an AUC of 0.78, with repetitive element annotations also showing strong prognostic relevance. Conclusions: These findings highlight the promising potential of eccDNA in the development of precision diagnostics and prognostic systems for breast cancer.

Volcano: a pipeline to characterize long terminal repeat-retrotransposons families in plants

Abstract Motivation Long Terminal Repeat Retrotransposons (LTR-RTs) comprise a significant portion of repetitive sequences in numerous plant species. LTR-RTs hold considerable functional significance, as they can impact gene family functionality and contribute to the formation of new genes. Investigating the quantities and activities of LTR-RTs is essential for understanding species’ evolutionary dynamics and the foundational mechanisms driving genome evolution. While current softwares can predict and initially classify LTR-RTs, there is a high need for more comprehensive and efficient software to fully characterize and quantify LTR-RTs during burst events and in subsequent detailed classification and quantification, especially given the surged demands of genome annotation. Results In this study, we have developed a pipeline called Volcano to accurately classify LTR-RTs and characterize burst families in plants. To distinguish different clades of LTR-RTs, we have implemented an improved depth-first search algorithm. Volcano can also quantify LTR-RT expression using RNA-seq data. By analyzing LTR-RTs in three genomes from the Asteraceae family, we observed that larger genomes tend to contain a greater number of LTR-RTs, and our software effectively categorizes them at the clade level. Availability The proposed Volcano compressor can be downloaded from https://github.com/Suosihe/volcano_LTR Supplementary information Supplementary data are available at Bioinformatics online.

Chromosome-level genome assembly of the ornamental plant Alcea rosea

Alcea rosea, a member of the Malvaceae family, is celebrated for its rich floral palette and global horticultural significance. Here, we present a high-quality reference genome for A. rosea, achieving a genome assembly size of 1.01 Gbp, with a Contig N50 length of 36.61 Mbp. The genome sequence was successfully mapped to 21 chromosomes, and the scaffold N50 length reached 52.57 Mbp, with a scaffold genome completeness of 99.6%. A total of 565.84 Mbp (comprising 56% of the genome) of repetitive sequences were identified, with transposable elements being predominant, particularly long terminal repeat (LTR) elements, which accounted for 48.44% of the genome. 51,436 genes were annotated. Among these predicted genes, the average gene length and coding sequence (CDS) length were 2739.92 bp and 1242.54 bp, respectively.

Chromosome-level genome assembly and annotation of Spinibarbus caldwelli

Spinibarbus caldwelli is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in southern China, the lack of genomic resources has hampered the genetic breeding and conservation. Here, we release a chromosome-level genome assembly for S. caldwelli using PacBio HiFi long-reads, Illumina short-reads, and Hi-C sequencing data. The final genome assembly is 1.77 Gb in size, with a contig N50 of 24.27 Mb. Using Hi-C scaffolding, 99.14% of the contigs were successfully anchored to 50 chromosomes, resulting in a scaffold N50 of 35.29 Mb. The final genome assembly shows a BUSCO completeness of 98.27%. The assembled genome contains 49.41% repetitive sequences and 51,505 predicted genes, 90.83% of which have been functionally annotated. This genome provides a genetic basis for S. caldwelli, facilitating the exploration of Cyprinid phylogeny, genetic improvement, and conservation efforts.

Exploring genetic diversity and genomic insights of Bacillus subtilis isolates from cassava rhizosphere using molecular barcoding and whole genome sequencing

Bacillus subtilis plays a significant role in both agriculture and industry. It is commonly isolated from agricultural environments, particularly various soil types. This study aimed to investigate DNA barcoding and whole-genome sequencing of B. subtilis strains, focusing on those specific to the cassava rhizosphere. Genetic identification and diversity of B. subtilis strains isolated from the rhizosphere of the Piroon 2 cassava cultivar were initially characterized using 16 S rDNA, a molecular marker for species-level identification. To explore strain-specific biodiversity within B. subtilis, repetitive DNA elements—specifically extragenic palindromic and BOX sequences—were analyzed across the genomes of the isolated strains. These repetitive sequences revealed two main structural patterns, providing clear and distinct genomic fingerprints for biodiversity analysis. The results showed that both REP and BOX sequences were highly conserved within specific regions of the B. subtilis genome, resulting in reliable and reproducible DNA patterns suitable for whole-genome phylogenetic analysis. While the 16 S rDNA approach showed a high sequence similarity among the B. subtilis strains (99.98%), whole-genome analysis using repetitive sequences allowed for clearer differentiation, with phylogenetic distances exceeding 97%. Whole-genome sequencing of the elite strain BsPr8 was performed using the Illumina MiSeq platform. The sequencing results yielded 56 contigs, with an average GC content of 43.67% and a total genome size of approximately 4,050 Kbp. Genome annotation identified 3,575 proteins with functional assignments, including 1,055 enzymes classified by Enzyme Commission numbers. The PATRIC database further annotated 3,937 genus-specific protein families. Additionally, 45 genes homologous to known antibiotic resistance genes were identified within the BsPr8 genome. These findings have important implications for sustainable agricultural practices and cassava cultivation. By elucidating the genetic diversity and genomic characteristics of B. subtilis strains, this study facilitates the identification of beneficial traits—such as plant growth promotion, pathogen suppression, and improved nutrient uptake. These strains hold potential for development as biofertilizers or biopesticides, offering an environmentally friendly alternative to conventional chemical inputs.

Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art

Short tandem repeats (STRs) are repetitive DNA sequences that contribute to genetic diversity and play a significant role in disease susceptibility. The human genome contains approximately 1.5 million STR loci, collectively covering around 3% of the total sequence. Certain repeat expansions can significantly impact cellular function by altering protein synthesis, impairing DNA repair, and leading to neurodegenerative and neuromuscular diseases. Traditional short-read sequencing struggles to accurately characterize STRs due to its limited read length, which limits the ability to resolve repeat expansions, increases mapping errors, and reduces sensitivity for detecting large insertions or interruptions. This review examines how long-read sequencing technologies, particularly Oxford Nanopore and PacBio, overcome these limitations by enabling direct sequencing of full STR regions with improved accuracy. We discuss challenges in sequencing, bioinformatics workflows, and the latest computational tools for STR detection. Additionally, we highlight the strengths and limitations of different methods, providing deeper insight into the future of STR genotyping.

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.

Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses with minimal accuracy loss compared to alignment-based methods. However, applying pseudoalignment to large genomic references, like chromosomes, is challenging due to their size and repetitive sequences. We introduce a new and modified pseudoalignment scheme that partitions each reference into "virtual colors." These are essentially overlapping bins of fixed maximal extent on the reference sequences that are treated as distinct "colors" from the perspective of the pseudoalignment algorithm. We apply this modified pseudoalignment procedure to process and map single-cell ATAC-seq data in our new tool alevin-fry-atac. We compare alevin-fry-atac to both Chromap and Cell Ranger ATAC. Alevin-fry-atac is highly scalable and, when using 32 threads, is 2.8 times faster than Chromap (the second fastest approach) while using only 33% of the memory required by Chromap. The resulting peaks and clusters generated from alevin-fry-atac show high concordance with those obtained from both Chromap and the Cell Ranger ATAC pipeline, demonstrating that virtual color-enhanced pseudoalignment directly to the genome provides a fast, memory-frugal, and accurate alternative to existing approaches for single-cell ATAC-seq processing. The development of alevin-fry-atac brings single-cell ATAC-seq processing into a unified ecosystem with single-cell RNA-seq processing (via alevin-fry) to work toward providing a truly open alternative to many of the varied capabilities of CellRanger. Alevin-fry-atac is written in Rust and C++17, and is freely-available under a BSD 3-clause license. It is integrated into piscem (https://github.com/COMBINE-lab/piscem) and alevin-fry (https://github.com/COMBINE-lab/alevin-fry), and is also supported directly as part of simpleaf (https://github.com/COMBINE-lab/simpleaf).

Assembly and comparative analysis of the complete mitochondrial genome of Cardiocrinum giganteum: a primitive Liliaceae group with significant scientific research value

Background Cardiocrinum giganteum, belonging to genus Cardiocrinum of family Liliaceae, is a genus endemic to East Asia and is considered one of the more primitive groups within the Liliaceae family. C. giganteum is the largest one among all the lily species in plant and flower size, and possesses high ornamental, medicinal, and scientific research value. However, due to its long-term wild status, its value has not been fully exploited and utilized, especially regarding the mitochondrial genome, which is crucial for plant growth activities, there have been no relevant studies and reports so far.ResultsIn this study, we sequenced and assembled the complete mitochondrial genome of C. giganteum and elucidated its evolutionary trajectory and phylogenetic relationships. The C. giganteum mitogenome has a multi-chromosomal structure containing 19 circular molecules. The assembled mitogenome has a total length of 2,066,679 bp and a GC content of 44.54%. A total of 37 unique protein-coding genes (PCGs), 16 tRNA, and three rRNA genes were annotated. Several repetitive sequences and sequence fragments homologous to chloroplasts have also been found in the C. giganteum mitogenome. To determine the evolutionary and taxonomic positions of C. giganteum, we constructed a phylogenetic tree using C. giganteum mitochondrial PCGs. Additionally, we analyzed the relatively synonymous codon usage of PCGs, identified RNA editing events, and conducted syntenic analysis with closely related species.ConclusionsThis study presents the first comprehensive mitochondrial genome (mtDNA) characterization of C. giganteum (Liliaceae), revealing its unique multi-chromosomal configuration. Our findings address the knowledge gap in mitochondrial research within the Cardiocrinum genus while enriching the mitochondrial genome database of Liliaceae. The assembled mtDNA provides critical insights into the phylogenetic relationships between Cardiocrinum and its allied genera, establishing essential genomic resources for evolutionary analyses, species identification, and genetic diversity studies across Liliaceae.

GenRepAI: Utilizing Artificial Intelligence to Identify Repeats in Genomic Suffix Trees

Background: The human genome is densely populated with repetitive DNA sequences that play crucial roles in genomic functions and structures but are also implicated in over 40 human diseases. The computational challenge of identifying and characterizing these repeats is significant due to the complexity and size of the genome, which are overwhelming traditional algorithms. Methods: To address these challenges, we propose GenRepAI, a deep learning framework to navigate and analyze genomic suffix trees. GenRepAI employs supervised machine learning classifiers trained on labeled datasets of repeat annotations and unsupervised anomaly detection to identify novel repeat sequences. The models are trained using convolutional neural networks (CNNs), long short-term memory networks (LSTMs), and vision transformers to classify and annotate repeats within the human genome. Results: GenRepAI is designed to comprehensively profile repeats that underlie various neurological diseases, allowing researchers to identify pathogenic expansions. The framework will integrate into existing genomic analysis pipelines, with the capability to screen patient genomes and highlight potential causal variants for further validation. Conclusion: GenRepAI is set to become a foundational tool in genomics, leveraging artificial intelligence to enhance the characterization of repetitive sequences. It promises significant advancements in the molecular diagnosis of repeat expansion disorders and contributes to a deeper understanding of genomic structure and function, with broad applications in personalized medicine.

Chromosome-level genome assembly and annotation of Pterygoplichthys pardalis

Suckermouth catfishes, with their evolved powerful features, have become notorious invasive species, causing significant damage to aquatic ecosystems. However, the lack of high-quality genomes severely restricts research on this group within the field. In this study, we de novo assembled the chromosome-level genome assembly of Pterygoplichthys pardalis using multiple platforms of sequencing data, including Illumina short reads, Nanopore long reads, and Hi-C sequencing reads, resulting in a 1.51 Gb genome assembly. Multiple evaluations, including read mapping ratio (98.52%), transcript mapping ratio (99.61%), conserved BUSCO gene set (98.8%), and N50 score (49.47 Mb), indicated the high continuity and accuracy of the genome assembly we generated. Genome annotation found that 0.97 Gb of genome sequences are repetitive sequences, accounting for 64.47% of the genome assembly. Further, 23,859 protein-coding genes were successfully predicted, 92.92% of which could be annotated in functional databases. This high-quality genome assembly of P. pardalis provides a valuable resource for understanding the genetic underpinnings of P. pardalis’s invasive success and offers critical data for future fisheries research and management.

Telomere Shortening in Interstitial Lung Disease: Challenges and Promises.

Interstitial lung disease (ILD) is a group of diseases involving diffuse pulmonary parenchymal lesions and alveolar inflammation and interstitial fibrosis. Telomeres are repetitive DNA sequences at the end of chromosomes to maintain structural integrity and telomerase can prevent telomere shortening. Telomerase abnormalities such as related gene mutations lead to decrease in telomerase activity and telomere shortening. It has been proven that telomere shortening and telomerase abnormalities are related to the occurrence and development of ILD. Telomere shortening occurs in different types of ILD patients and is associated with prognosis. Gene therapy targeting telomerase exhibits therapeutic potential. The paper elaborates on the progress of telomere shortening in the diagnosis, differential diagnosis, treatment, and prognosis of ILD in recent years, in order to demonstrate its potential and promises and to be helpful for clinical diagnosis and treatment.

A high-quality chromosome-level genome assembly of Eucalyptus globulus Labill.

Eucalyptus globulus Labill. is the primary plant material used for the extraction of eucalyptus oil. For this study, we generated a chromosome-level genome assembly of E. globulus using a combination of HiFi long-reads, Illumina short-reads and Hi-C data. The assembled genome size was 556.98 Mb, with a contig N50 of 37.93 Mb and scaffold N50 of 54.03 Mb. The completeness of the genome assembly was evaluated at 98.30% by BUSCO, and 99.05% of the genome sequence was anchored to 11 chromosomes. Additionally, 52.55% of repetitive sequences were identified in the genome, and 36,387 protein-coding genes were predicted, of which 96.80% were functionally annotated. Notably, a comparison of the genome of E. globulus with six other congeneric species revealed strong conservation, in terms of gene numbers and structures. Overall, we assembled the most complete E. globulus genome sequence to date. This will serve as a valuable resource toward the elucidation of the molecular kinetics behind the accumulation of eucalyptus oil in E. globulus leaves to facilitate further genetic improvements.