The formation and evolution of centromeric satellite repeats in Saccharum species

Integrated multi-omics analysis unravels the floral scent characteristics and regulation in "Hutou" multi-petal jasmine

The multi-petal "Hutou" jasmine (Jasminum sambac var. Trifoliatum) is highly valued for bonsai cultivation and landscape design, however, the aroma profile and mechanisms underlying floral scent formation remain elusive. In this study, we generate a nearly complete telomere-to-telomere (T2T) genome assembly of "Hutou" jasmine (487.45 Mb with contig N50 of 38.93 Mb). Metabolomic profiling unveils that 16 significantly differential volatiles (SDVs) may play a crucial role in the formation of flower aroma. Among them, five scented SDVs, particularly α-farnesene and pentanoic acid 1-ethenyl-1,5-dimethyl-4-hexenyl ester, contribute to the characteristic aroma profile of "Hutou" jasmine flowers. Weighted gene co-expression network analysis (WGCNA) identifies HTWRKY41, HTWRKY53, and HTHSP90 as the hub genes potentially regulating the production of these 16 metabolites. The expression of selected genes and duplication events drive the increased relative content of major sesquiterpenoids in terpenoid biosynthetic pathway. Four structural genes (BEAT3, BSMT1, BPBT2, and BPBT3) are potentially implicated in the emission of downstream key volatile esters (benzyl acetate, methyl benzoate, and benzyl benzoate) in the phenylpropanoids synthesis. Our integrated dataset of genomics, transcriptomics, and metabolomics present here provides a theoretical basis for the practical utilization of fragrance and genetic improvement in horticultural applications of "Hutou" jasmine.

A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites

We systematically examine the application of different phasing strategies to decrypt strawberry genome organization and produce a fully phased and accurate reference genome for Fragaria x ananassa cv. "EA78" (2n = 8x = 56). We identify 147 bp canonical centromeric repeats across 50 strawberry chromosomes and uncover the formation of six neocentromeres through centromere turnover. Our findings indicate strawberry genomes have diverged centromeric satellite arrays among chromosomes, particularly across homoeologs, while maintaining high sequence similarity between homologs. We trace the evolutionary dynamics of centromeric repeats and find substantial centromere size expansion in wild and cultivated octoploids compared to the diploid ancestor, F. vesca.

Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis

Phragmites australis is a globally distributed grass species (Poaceae) recognized for its vast biomass and exceptional environmental adaptability, making it an ideal model for studying wetland ecosystems and plant stress resilience. However, genomic resources for this species have been limited. In this study, we assembled a chromosome-level reference genome of P. australis containing one B chromosome. An explosion of LTR-RTs, centered on the Copia family, occurred during the late Pleistocene, driving the expansion of P. australis genome size and subgenomic differentiation. Comparative genomic analysis showed that P. australis underwent two whole gene duplication events, was segregated from Cleistogenes songorica at 34.6 Mya, and that 41.26% of the gene families underwent expansion. Based on multi-tissue transcriptomic data, we identified structural genes in the biosynthetic pathway of pharmacologically active Phragmitis rhizoma polysaccharides with essential roles in rhizome development. This study deepens our understanding of Arundinoideae evolution, genome dynamics, and the genetic basis of key traits, providing essential data and a genetic foundation for wetland restoration, bioenergy development, and plant stress.

A cost-effective oligo-based barcode system for chromosome identification in longan and lychee

Oligonucleotide (Oligo)-based fluorescence in situ hybridization (FISH) represents a highly effective methodology for identifying plant chromosomes. Longan is a commercially significant fruit species, yet lacking basic chromosomal markers has hindered its cytogenetic research. In this study, we developed a cost-effective oligo-based system for distinguishing chromosomes of longan (Dimocarpus longan Lour., 2n = 2x = 30). For this system, each synthesized oligo contained two chromosome-specific sequences that spanned a distance of over 200 kb, and a PCR-based flexible amplification method coupled with nested primers was used for probe labeling. The use of these oligo-based barcodes enabled the marking of 36 chromosomal regions, which allowed for the unambiguous distinction of all 15 chromosomes in both longan and lychee (Litchi chinensis Sonn., 2n = 2x = 30) species. Based on the identification of individual chromosomes, we constructed karyotypes and detected genome assembly errors involving the 35S ribosomal RNA gene (35S rDNA) in longan and lychee. Developing oligo-based barcodes offers considerable promise for advancing cytogenetic research in longan, lychee, and their related species. Furthermore, this cost-effective synthesis system can be referred to the development of new oligo libraries among other species.

Chromosome-specific barcode system with centromeric repeat in cultivated soybean and wild progenitor

Wild soybean Glycine soja is the progenitor of cultivated soybean Glycine max Information on soybean functional centromeres is limited despite extensive genome analysis. These species are an ideal model for studying centromere dynamics for domestication and breeding. We performed a detailed chromatin immunoprecipitation analysis using centromere-specific histone H3 protein to delineate two distinct centromeric DNA sequences with unusual repeating units with monomer sizes of 90-92 bp (CentGm-1) and 413-bp (CentGm-4) shorter and longer than standard nucleosomes. These two unrelated DNA sequences with no sequence similarity are part of functional centromeres in both species. Our results provide a comparison of centromere properties between a cultivated and a wild species under the effect of the same kinetochore protein. Possible sequence homogenization specific to each chromosome could highlight the mechanism for evolutionary conservation of centromeric properties independent of domestication and breeding. Moreover, a unique barcode system to track each chromosome is developed using CentGm-4 units. Our results with a unifying centromere composition model using CentGm-1 and CentGm-4 superfamilies could have far-reaching implications for comparative and evolutionary genome research.

Extrachromosomal circular DNA containing DTX1 promotes cell growth in hydroquinone-induced malignantly transformed cells by regulating the transcription of DTX1

BACKGROUND

Extrachromosomal circular DNA (eccDNA), a novel class of DNA with a circular topological structure, is present in a variety of cancer cells and tissues and may play broad roles in processes ranging from aging to cancer cell heterogeneity through multiple mechanisms. EccDNA has been characterized by profile, structure and function in several prominent studies but its effect on hydroquinone (HQ)-induced malignantly transformed cells (TK6-HQ) is still elusive.

METHODS

Circle-seq was applied to determine the eccDNA counts and characteristics of TK6-HQ cells. DNA-fluorescence in situ hybridization was used to measure the abundance of eccDNA_DTX1. Differential gene expression analysis was carried out by RNA-seq. Gene expression was quantified by wertern blot and qPCR. Decircularization of eccDNA_DTX1 was achieved by CRISPR/Cas9. Tumorigenicity was evaluated by xenograft assay in BALB/c nude mice.

RESULTS

In this study, we characterized the structure of eccDNAs and the function of DTX1-containing eccDNA (eccDNA_DTX1) in TK6-HQ cells. A total of 669,179 eccDNAs were identified, including 901 eccDNAs with different counts. Most of the eccDNAs were < 1000 bp in length and were enriched in four periodic peaks starting at 186 bp with an interval of ~ 180 bp. The genomic distribution of eccDNAs confirmed that eccDNAs could be observed across all chromosomes and had greater enrichment on chromosomes 17, 19, 20, and 22, with abundant Alu repeat elements, introns and CpG islands. By combining the results of the integrated circle-seq analysis of eccDNAs with those from the RNA-seq analysis (differentially expressed genes, 1064 upregulated and 427 downregulated), the authors showed that the transcription of 20 potential coding genes might be driven by eccDNAs. Finally, the knockdown of eccDNA_DTX1 by CRISPR/Cas9 inhibited the growth of TK6-HQ cells in vitro and in vivo by inhibiting the transcription of DTX1 and promoting ferroptosis, and ferroptosis inhibior, Ferrostatin-1, abrogated the proliferation inhibition of eccDNA_DTX1 knockdown.

CONCLUSIONS

EccDNA_DTX1 promotes cell growth in hydroquinone-induced malignantly transformed cells by regulating the transcription of DTX1 and ferroptosis. This study profiles eccDNA characteristics and defines the role and mechanism of eccDNA_DTX1 for the first time, shedding new light on the relationship between eccDNAs and carcinogenesis.

Plant kinetochore complex: composition, function, and regulation

The kinetochore complex, an important protein assembly situated on the centromere, plays a pivotal role in chromosome segregation during cell division. Like in animals and fungi, the plant kinetochore complex is important for maintaining chromosome stability, regulating microtubule attachment, executing error correction mechanisms, and participating in signaling pathways to ensure accurate chromosome segregation. This review summarizes the composition, function, and regulation of the plant kinetochore complex, emphasizing the interactions of kinetochore proteins with centromeric DNAs (cenDNAs) and RNAs (cenRNAs). Additionally, the applications of the centromeric histone H3 variant (the core kinetochore protein CENH3, first identified as CENP-A in mammals) in the generation of ploidy-variable plants and synthesis of plant artificial chromosomes (PACs) are discussed. The review serves as a comprehensive roadmap for researchers delving into plant kinetochore exploration, highlighting the potential of kinetochore proteins in driving technological innovations in synthetic genomics and plant biotechnology.

Cytoplasmic genomes of Jasminum sambac reveal divergent sub-mitogenomic conformations and a large nuclear chloroplast-derived insertion

BACKGROUND

Jasminum sambac, a widely recognized ornamental plant prized for its aromatic blossoms, exhibits three flora phenotypes: single-petal ("SP"), double-petal ("DP"), and multi-petal ("MP"). The lack of detailed characterization and comparison of J. sambac mitochondrial genomes (mitogenomes) hinders the exploration of the genetic and structural diversity underlying the varying floral phenotypes in jasmine accessions.

RESULTS

Here, we de novo assembled three mitogenomes of typical phenotypes of J. sambac, "SP", "DP", and "MP-hutou" ("HT"), with PacBio reads and the "HT" chloroplast (cp) genome with Illumina reads, and verified them with read mapping and fluorescence in situ hybridization (FISH). The three mitogenomes present divergent sub-genomic conformations, with two, two, and four autonomous circular chromosomes ranging in size from 35.7 kb to 405.3 kb. Each mitogenome contained 58 unique genes. Ribosome binding sites with conserved AAGAAx/AxAAAG motifs were detected upstream of uncanonical start codons TTG, CTG and GTG. The three mitogenomes were similar in genomic content but divergent in structure. The structural variations were mainly attributed to recombination mediated by a large (~ 5 kb) forward repeat pair and several short repeats. The three jasmine cp. genomes showed a well-conserved structure, apart from a 19.9 kb inversion in "HT". We identified a 14.3 kb "HT"-specific insertion on Chr7 of the "HT" nuclear genome, consisting of two 7 kb chloroplast-derived fragments with two intact ndhH and rps15 genes, further validated by polymerase chain reaction (PCR). The well-resolved phylogeny suggests faster mitogenome evolution in J. sambac compared to other Oleaceae species and outlines the mitogenome evolutionary trajectories within Lamiales. All evidence supports that "DP" and "HT" evolved from "SP", with "HT" being the most recent derivative of "DP".

CONCLUSION

The comprehensive characterization of jasmine organelle genomes has added to our knowledge of the structural diversity and evolutionary trajectories behind varying jasmine traits, paving the way for in-depth exploration of mechanisms and targeted genetic research.

A telomere-to-telomere gap-free reference genome assembly of avocado provides useful resources for identifying genes related to fatty acid biosynthesis and disease resistance

Avocado (Persea americana Mill.) is an economically valuable plant because of the high fatty acid content and unique flavor of its fruits. Its fatty acid content, especially the relatively high unsaturated fatty acid content, provides significant health benefits. We herein present a telomere-to-telomere gapless genome assembly (841.6 Mb) of West Indian avocado. The genome contains 40 629 predicted protein-coding genes. Repeat sequences account for 57.9% of the genome. Notably, all telomeres, centromeres, and a nucleolar organizing region are included in this genome. Fragments from these three regions were observed via fluorescence in situ hybridization. We identified 376 potential disease resistance-related nucleotide-binding leucine-rich repeat genes. These genes, which are typically clustered on chromosomes, may be derived from gene duplication events. Five NLR genes (Pa11g0262, Pa02g4855, Pa07g3139, Pa07g0383, and Pa02g3196) were highly expressed in leaves, stems, and fruits, indicating they may be involved in avocado disease responses in multiple tissues. We also identified 128 genes associated with fatty acid biosynthesis and analyzed their expression patterns in leaves, stems, and fruits. Pa02g0113, which encodes one of 11 stearoyl-acyl carrier protein desaturases mediating C18 unsaturated fatty acid synthesis, was more highly expressed in the leaves than in the stems and fruits. These findings provide valuable insights that enhance our understanding of fatty acid biosynthesis in avocado.

Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae

BACKGROUND

Centromeres play a crucial and conserved role in cell division, although their composition and evolutionary history in green algae, the evolutionary ancestors of land plants, remains largely unknown.

RESULTS

We constructed near telomere-to-telomere (T2T) assemblies for two Trebouxiophyceae species, Chlorella sorokiniana NS4-2 and Chlorella pyrenoidosa DBH, with chromosome numbers of 12 and 13, and genome sizes of 58.11 Mb and 53.41 Mb, respectively. We identified and validated their centromere sequences using CENH3 ChIP-seq and found that, similar to humans and higher plants, the centromeric CENH3 signals of green algae display a pattern of hypomethylation. Interestingly, the centromeres of both species largely comprised transposable elements, although they differed significantly in their composition. Species within the Chlorella genus display a more diverse centromere composition, with major constituents including members of the LTR/Copia, LINE/L1, and LINE/RTEX families. This is in contrast to green algae including Chlamydomonas reinhardtii, Coccomyxa subellipsoidea, and Chromochloris zofingiensis, in which centromere composition instead has a pronounced single-element composition. Moreover, we observed significant differences in the composition and structure of centromeres among chromosomes with strong collinearity within the Chlorella genus, suggesting that centromeric sequence evolves more rapidly than sequence in non-centromeric regions.

CONCLUSIONS

This study not only provides high-quality genome data for comparative genomics of green algae but gives insight into the composition and evolutionary history of centromeres in early plants, laying an important foundation for further research on their evolution.

The evolution and formation of centromeric repeats analysis in Vitis vinifera

MAIN CONCLUSION

Six grape centromere-specific markers for cytogenetics were mined by combining genetic and immunological assays, and the possible evolution mechanism of centromeric repeats was analyzed. Centromeric histone proteins are functionally conserved; however, centromeric repetitive DNA sequences may represent considerable diversity in related species. Therefore, studying the characteristics and structure of grape centromere repeat sequences contributes to a deeper understanding of the evolutionary process of grape plants, including their origin and mechanisms of polyploidization. Plant centromeric regions are mainly composed of repetitive sequences, including SatDNA and transposable elements (TE). In this research, the characterization of centromere sequences in the whole genome of grapevine (Vitis vinifera L.) has been conducted. Five centromeric tandem repeat sequences (Vv1, Vv2, Vv5, Vv6, and Vv8) and one long terminal repeat (LTR) sequence Vv24 were isolated. These sequences had different centromeric distributions, which indicates that grape centromeric sequences may undergo rapid evolution. The existence of extrachromosomal circular DNA (eccDNA) and gene expression in CenH3 subdomain region may provide various potential mechanisms for the generation of new centromeric regions.

Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus)

BACKGROUND

Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes.

RESULTS

In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA.

CONCLUSIONS

Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.

Polyploid Genome Assembly Provides Insights into Morphological Development and Ascorbic Acid Accumulation of Sauropus androgynus

Sauropus androgynus (S. androgynus) (2n = 4x = 52) is one of the most popular functional leafy vegetables in South and Southeast Asia. With its rich nutritional and pharmaceutical values, it has traditionally had widespread use for dietary and herbal purposes. Here, the genome of S. androgynus was sequenced and assembled, revealing a genome size of 1.55 Gb with 26 pseudo-chromosomes. Phylogenetic analysis traced back the divergence of Sauropus from Phyllanthus to approximately 29.67 million years ago (Mya). Genome analysis revealed that S. androgynus polyploidized around 20.51 Mya and shared a γ event about 132.95 Mya. Gene function analysis suggested that the expansion of pathways related to phloem development, lignin biosynthesis, and photosynthesis tended to result in the morphological differences among species within the Phyllanthaceae family, characterized by varying ploidy levels. The high accumulation of ascorbic acid in S. androgynus was attributed to the high expression of genes associated with the L-galactose pathway and recycling pathway. Moreover, the expanded gene families of S. androgynus exhibited multiple biochemical pathways associated with its comprehensive pharmacological activity, geographic adaptation and distinctive pleasurable flavor. Altogether, our findings represent a crucial genomic asset for S. androgynus, casting light on the intricate ploidy within the Phyllanthaceae family.

Gene duplications facilitate C4-CAM compatibility in common purslane

Common purslane (Portulaca oleracea) integrates both C4 and crassulacean acid metabolism (CAM) photosynthesis pathways and is a promising model plant to explore C4-CAM plasticity. Here, we report a high-quality chromosome-level genome of nicotinamide adenine dinucleotide (NAD)-malic enzyme (ME) subtype common purslane that provides evidence for 2 rounds of whole-genome duplication (WGD) with an ancient WGD (P-β) in the common ancestor to Portulacaceae and Cactaceae around 66.30 million years ago (Mya) and another (Po-α) specific to common purslane lineage around 7.74 Mya. A larger number of gene copies encoding key enzymes/transporters involved in C4 and CAM pathways were detected in common purslane than in related species. Phylogeny, conserved functional site, and collinearity analyses revealed that the Po-α WGD produced the phosphoenolpyruvate carboxylase-encoded gene copies used for photosynthesis in common purslane, while the P-β WGD event produced 2 ancestral genes of functionally differentiated (C4- and CAM-specific) beta carbonic anhydrases involved in the C4 + CAM pathways. Additionally, cis-element enrichment analysis in the promoters showed that CAM-specific genes have recruited both evening and midnight circadian elements as well as the Abscisic acid (ABA)-independent regulatory module mediated by ethylene-response factor cis-elements. Overall, this study provides insights into the origin and evolutionary process of C4 and CAM pathways in common purslane, as well as potential targets for engineering crops by integrating C4 or CAM metabolism.

Pan-centromere reveals widespread centromere repositioning of soybean genomes

Centromere repositioning refers to a de novo centromere formation at another chromosomal position without sequence rearrangement. This phenomenon was frequently encountered in both mammalian and plant species and has been implicated in genome evolution and speciation. To understand the dynamic of centromeres on soybean genome, we performed the pan-centromere analysis using CENH3-ChIP-seq data from 27 soybean accessions, including 3 wild soybeans, 9 landraces, and 15 cultivars. Building upon the previous discovery of three centromere satellites in soybean, we have identified two additional centromere satellites that specifically associate with chromosome 1. These satellites reveal significant rearrangements in the centromere structures of chromosome 1 across different accessions, consequently impacting the localization of CENH3. By comparative analysis, we reported a high frequency of centromere repositioning on 14 out of 20 chromosomes. Most newly emerging centromeres formed in close proximity to the native centromeres and some newly emerging centromeres were apparently shared in distantly related accessions, suggesting their emergence is independent. Furthermore, we crossed two accessions with mismatched centromeres to investigate how centromere positions would be influenced in hybrid genetic backgrounds. We found that a significant proportion of centromeres in the S9 generation undergo changes in size and position compared to their parental counterparts. Centromeres preferred to locate at satellites to maintain a stable state, highlighting a significant role of centromere satellites in centromere organization. Taken together, these results revealed extensive centromere repositioning in soybean genome and highlighted how important centromere satellites are in constraining centromere positions and supporting centromere function.

A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis

JUJUNCAO (Cenchrus fungigraminus; 2n = 4x = 28) is a Cenchrus grass with the highest biomass production among cultivated plants, and it can be used for mushroom cultivation, animal feed, and biofuel production. Here, we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated ∼2.7 million years ago (mya). Its genome consists of two subgenomes, and subgenome A shares high collinear synteny with pearl millet. We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO. Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes, which was a further indication of asymmetric DNA methylation. The three types of centromeric repeat in the JUJUNCAO genome (CEN137, CEN148, and CEN156) may have evolved independently within each subgenome, with some introgressions of CEN156 from the B to the A subgenome. We investigated the photosynthetic characteristics of JUJUNCAO, revealing its typical C4 Kranz anatomy and high photosynthetic efficiency. NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO, which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield. Taken together, our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies, as well as genetic improvement of Cenchrus grasses.

Centromere Plasticity With Evolutionary Conservation and Divergence Uncovered by Wheat 10+ Genomes

Centromeres (CEN) are the chromosomal regions that play a crucial role in maintaining genomic stability. The underlying highly repetitive DNA sequences can evolve quickly in most eukaryotes, and promote karyotype evolution. Despite their variability, it is not fully understood how these widely variable sequences ensure the homeostasis of centromere function. In this study, we investigated the genetics and epigenetics of CEN in a population of wheat lines from global breeding programs. We captured a high degree of sequences, positioning, and epigenetic variations in the large and complex wheat CEN. We found that most CENH3-associated repeats are Cereba element of retrotransposons and exhibit phylogenetic homogenization across different wheat lines, but the less-associated repeat sequences diverge on their own way in each wheat line, implying specific mechanisms for selecting certain repeat types as functional core CEN. Furthermore, we observed that CENH3 nucleosome structures display looser wrapping of DNA termini on complex centromeric repeats, including the repositioned CEN. We also found that strict CENH3 nucleosome positioning and intrinsic DNA features play a role in determining centromere identity among different lines. Specific non-B form DNAs were substantially associated with CENH3 nucleosomes for the repositioned centromeres. These findings suggest that multiple mechanisms were involved in the adaptation of CENH3 nucleosomes that can stabilize CEN. Ultimately, we proposed a remarkable epigenetic plasticity of centromere chromatin within the diverse genomic context, and the high robustness is crucial for maintaining centromere function and genome stability in wheat 10+ lines as a result of past breeding selections.

A chromosome-level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation

High-quality radish (Raphanus sativus) genome represents a valuable resource for agronomical trait improvements and understanding genome evolution among Brassicaceae species. However, existing radish genome assembly remains fragmentary, which greatly hampered functional genomics research and genome-assisted breeding. Here, using a NAU-LB radish inbred line, we generated a reference genome of 476.32 Mb with a scaffold N50 of 56.88 Mb by incorporating Illumina, PacBio and BioNano optical mapping techniques. Utilizing Hi-C data, 448.12 Mb (94.08%) of the assembled sequences were anchored to nine radish chromosomes with 40 306 protein-coding genes annotated. In total, 249.14 Mb (52.31%) comprised the repetitive sequences, among which long terminal repeats (LTRs, 30.31%) were the most abundant class. Beyond confirming the whole-genome triplication (WGT) event in R. sativus lineage, we found several tandem arrayed genes were involved in stress response process, which may account for the distinctive phenotype of high disease resistance in R. sativus. By comparing against the existing Xin-li-mei radish genome, a total of 2 108 573 SNPs, 7740 large insertions, 7757 deletions and 84 inversions were identified. Interestingly, a 647-bp insertion in the promoter of RsVRN1 gene can be directly bound by the DOF transcription repressor RsCDF3, resulting into its low promoter activity and late-bolting phenotype of NAU-LB cultivar. Importantly, introgression of this 647-bp insertion allele, RsVRN1^In-536 , into early-bolting genotype could contribute to delayed bolting time, indicating that it is a potential genetic resource for radish late-bolting breeding. Together, this genome resource provides valuable information to facilitate comparative genomic analysis and accelerate genome-guided breeding and improvement in radish.

A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus

A diploid genome in the Saccharum complex facilitates our understanding of evolution in the highly polyploid Saccharum genus. Here we have generated a complete, gap-free genome assembly of Erianthus rufipilus, a diploid species within the Saccharum complex. The complete assembly revealed that centromere satellite homogenization was accompanied by the insertions of Gypsy retrotransposons, which drove centromere diversification. An overall low rate of gene transcription was observed in the palaeo-duplicated chromosome EruChr05 similar to other grasses, which might be regulated by methylation patterns mediated by homologous 24 nt small RNAs, and potentially mediating the functions of many nucleotide-binding site genes. Sequencing data for 211 accessions in the Saccharum complex indicated that Saccharum probably originated in the trans-Himalayan region from a diploid ancestor (x = 10) around 1.9-2.5 million years ago. Our study provides new insights into the origin and evolution of Saccharum and accelerates translational research in cereal genetics and genomics.

Characterization of centromeric DNA of Gossypium anomalum reveals sequence-independent enrichment dynamics of centromeric repeats

Centromeres in eukaryotes are composed of highly repetitive DNAs, which evolve rapidly and are thought to achieve a favorable structure in mature centromeres. However, how the centromeric repeat evolves into an adaptive structure is largely unknown. We characterized the centromeric sequences of Gossypium anomalum through chromatin immunoprecipitation against CENH3 antibodies. We revealed that the G. anomalum centromeres contained only retrotransposon-like repeats but were depleted in long arrays of satellites. These retrotransposon-like centromeric repeats were present in the African-Asian and Australian lineage species, suggesting that they might have arisen in the common ancestor of these diploid species. Intriguingly, we observed a substantial increase and decrease in copy numbers among African-Asian and Australian lineages, respectively, for the retrotransposon-derived centromeric repeats without apparent structure or sequence variation in cotton. This result indicates that the sequence content is not a decisive aspect of the adaptive evolution of centromeric repeats or at least retrotransposon-like centromeric repeats. In addition, two active genes with potential roles in gametogenesis or flowering were identified in CENH3 nucleosome-binding regions. Our results provide new insights into the constitution of centromeric repetitive DNA and the adaptive evolution of centromeric repeats in plants.

Investigating the Origin and Evolution of Polyploid Trifolium medium L. Karyotype by Comparative Cytogenomic Methods

Trifolium medium L. is a wild polyploid relative of the agriculturally important red clover that possesses traits promising for breeding purposes. To date, T. medium also remains the only clover species with which agriculturally important red clover has successfully been hybridized. Even though allopolyploid origin has previously been suggested, little has in fact been known about the T. medium karyotype and its origin. We researched T. medium and related karyotypes using comparative cytogenomic methods, such as fluorescent in situ hybridization (FISH) and RepeatExplorer cluster analysis. The results indicate an exceptional karyotype diversity regarding numbers and mutual positions of 5S and 26S rDNA loci and centromeric repeats in populations of T. medium ecotypes and varieties. The observed variability among T. medium ecotypes and varieties suggests current karyotype instability that can be attributed to ever-ongoing battle between satellite DNA together with genomic changes and rearrangements enhanced by post-hybridization events. Comparative cytogenomic analyses of a T. medium hexaploid variety and diploid relatives revealed stable karyotypes with a possible case of chromosomal rearrangement. Moreover, the results provided evidence of T. medium having autopolyploid origin.

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

Long terminal repeat retrotransposons (LTR retrotransposons) are the most abundant group of mobile genetic elements in eukaryotic genomes and are essential in organizing genomic architecture and phenotypic variations. The diverse families of retrotransposons are related to retroviruses. As retrotransposable elements are dispersed and ubiquitous, their "copy-out and paste-in" life cycle of replicative transposition leads to new genome insertions without the excision of the original element. The overall structure of retrotransposons and the domains responsible for the various phases of their replication is highly conserved in all eukaryotes. The two major superfamilies of LTR retrotransposons, Ty1/Copia and Ty3/Gypsy, are distinguished and dispersed across the chromosomes of higher plants. Members of these superfamilies can increase in copy number and are often activated by various biotic and abiotic stresses due to retrotransposition bursts. LTR retrotransposons are important drivers of species diversity and exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution. Additionally, LTR retrotransposons influence the gene expression patterns of adjacent genes by modulating potential small interfering RNA (siRNA) and RNA-directed DNA methylation (RdDM) pathways. Furthermore, comparative and evolutionary analysis of the most important crop genome sequences and advanced technologies have elucidated the epigenetics and structural and functional modifications driven by LTR retrotransposon during speciation. However, mechanistic insights into LTR retrotransposons remain obscure in plant development due to a lack of advancement in high throughput technologies. In this review, we focus on the key role of LTR retrotransposons response in plants during heat stress, the role of centromeric LTR retrotransposons, and the role of LTR retrotransposon markers in genome expression and evolution.

Extrachromosomal circular DNA: A neglected nucleic acid molecule in plants

Throughout the years, most plant genomic studies were focused on nuclear chromosomes. Extrachromosomal circular DNA (eccDNA) has largely been neglected for decades since its discovery in 1965. While initial research showed that eccDNAs can originate from highly repetitive sequences, recent findings show that many regions of the genome can contribute to the eccDNA pool. Currently, the biological functions of eccDNAs, if any, are a mystery but recent studies have indicated that they can be regulated by different genomic loci and contribute to stress response and adaptation. In this review, we outline current relevant technological developments facilitating eccDNA identification and the latest discoveries about eccDNAs in plants. Finally, we explore the probable functions and future research directions that could be undertaken with respect to different eccDNA sources.

Extrachromosomal circular DNA (eccDNA): an emerging star in cancer

Extrachromosomal circular DNA (eccDNA) is defined as a type of circular DNA that exists widely in nature and is independent of chromosomes. EccDNA has attracted the attention of researchers due to its broad, random distribution, complex biogenesis and tumor-relevant functions. EccDNA can carry complete gene information, especially the oncogenic driver genes that are often carried in tumors, with increased copy number and high transcriptional activity. The high overexpression of oncogenes by eccDNA leads to malignant growth of tumors. Regardless, the exact generation and functional mechanisms of eccDNA in disease progression are not yet clear. There is, however, an emerging body of evidence characterizing that eccDNA can be generated from multiple pathways, including DNA damage repair pathways, breakage-fusion-bridge (BFB) mechanisms, chromothripsis and cell apoptosis, and participates in the regulation of tumor progression with multiplex functions. This up-to-date review summarizes and discusses the origins, biogenesis and functions of eccDNA, including its contribution to the formation of oncogene instability and mutations, the heterogeneity and cellular senescence of tumor cells, and the proinflammatory response of tumors. We highlight the possible cancer-related applications of eccDNA, such as its potential use in the diagnosis, targeted therapy and prognostic assessment of cancer.

Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum

Saccharum spontaneum is a founding Saccharum species and exhibits wide variation in ploidy levels. We have assembled a high-quality autopolyploid genome of S. spontaneum Np-X (2n = 4x = 40) into 40 pseudochromosomes across 10 homologous groups, that better elucidates recent chromosome reduction and polyploidization that occurred circa 1.5 million years ago (Mya). One paleo-duplicated chromosomal pair in Saccharum, NpChr5 and NpChr8, underwent fission followed by fusion accompanied by centromeric split around 0.80 Mya. We inferred that Np-X, with x = 10, most likely represents the ancestral karyotype, from which x = 9 and x = 8 evolved. Resequencing of 102 S. spontaneum accessions revealed that S. spontaneum originated in northern India from an x = 10 ancestor, which then radiated into four major groups across the Indian subcontinent, China, and Southeast Asia. Our study suggests new directions for accelerating sugarcane improvement and expands our knowledge of the evolution of autopolyploids.

Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae)

Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31 Medicago taxa we detected exceptionally high post-IGT amplification of mitochondrial (mt) DNA sequences containing rps10 in the nuclear genome of Medicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in the M. polymorpha nuclear genome. The mt rps10-like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6-3.0% of total genomic DNA, a value approximately three-fold greater than the entire mitogenome in M. polymorpha. Compared to a typical mt gene, the mt rps10-like sequence coverage level was 691.5-7198-fold higher in M. polymorpha and closely related species. In addition to the post-IGT amplification, our analysis identified the canonical telomeric repeat and the species-specific satellite arrays that are likely attributable to an ancestral chromosomal fusion in M. polymorpha. A possible relationship between chromosomal instability and the mt rps10-like tandem repeat family in the M. polymorpha clade is discussed.

A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars

Modern sugarcane cultivars are derived from the hybridization of Saccharum officinarum (2n = 80) and S. spontaneum (2n = 40-128), leading to a variety of complex genomes with highly polyploid and varied chromosome structures. These complex genomes have hindered deciphering the genome structure and marker-assisted selection in sugarcane breeding. Ten cultivars were analyzed by fluorescence in situ hybridization adopting chromosome painting and S. spontaneum-specific probes. The results showed six types of chromosomes in the studied cultivars, including S. spontaneum or S. officinarum chromosomes, interspecific recombinations from homoeologous or nonhomoeologous chromosomes, and translocations of S. spontaneum or S. officinarum chromosomes. The results showed unexpectedly high proportions of interspecific recombinations in these cultivars (11.9-40.9%), which renew our knowledge that less than 13% of chromosomes result from interspecific exchanges. Also, the results showed a high frequency of translocations (an average of 2.15 translocations per chromosome) between S. officinarum chromosomes. The diverse types of chromosomes in cultivars imply that hybrid gametes of S. spontaneum and S. officinarum may form unusual chromosome pairs, including homoeologous or nonhomoeologous chromosomes either between or within S. spontaneum and S. officinarum. Moreover, we consistently observed 11 or 12 copies for the four studied chromosomes, i.e., chromosomes 1, 2, 7, and 8, suggesting steady transmission during the breeding program. By comparison, we found a relatively fewer copies of S. spontaneum chromosome 1 than those of S. spontaneum chromosomes 2, 7, and 8. These results provide deep insights into the structure of cultivars and may facilitate chromosome-assisted selection in sugarcane breeding.

Chromosome-scale assembly and population diversity analyses provide insights into the evolution of Sapindus mukorossi

Sapindus mukorossi is an environmentally friendly plant and renewable energy source whose fruit has been widely used for biomedicine, biodiesel, and biological chemicals due to its richness in saponin and oil contents. Here, we report the first chromosome-scale genome assembly of S. mukorossi (covering ~391 Mb with a scaffold N50 of 24.66 Mb) and characterize its genetic architecture and evolution by resequencing 104 S. mukorossi accessions. Population genetic analyses showed that genetic diversity in the southwestern distribution area was relatively higher than that in the northeastern distribution area. Gene flow events indicated that southwest species may be the donor population for the distribution areas in China. Genome-wide selective sweep analysis showed that a large number of genes are involved in defense responses, growth and development, including SmRPS2, SmRPS4, SmRPS7, SmNAC2, SmNAC23, SmNAC102, SmWRKY6, SmWRKY26, and SmWRKY33. We also identified several candidate genes controlling six agronomic traits by genome-wide association studies, including SmPCBP2, SmbHLH1, SmCSLD1, SmPP2C, SmLRR-RKs, and SmAHP. Our study not only provides a rich genomic resource for further basic research on Sapindaceae woody trees but also identifies several economically significant genes for genomics-enabled improvements in molecular breeding.

Complete Genome Sequences and Genome-Wide Characterization of Trichoderma Biocontrol Agents Provide New Insights into their Evolution and Variation in Genome Organization, Sexual Development, and Fungal-Plant Interactions

Trichoderma spp. represent one of the most important fungal genera to mankind and in natural environments. The genus harbors prolific producers of wood-decaying enzymes, biocontrol agents against plant pathogens, plant-growth-promoting biofertilizers, as well as model organisms for studying fungal-plant-plant pathogen interactions. Pursuing highly accurate, contiguous, and chromosome-level reference genomes has become a primary goal of fungal research communities. Here, we report the chromosome-level genomic sequences and whole-genome annotation data sets of four strains used as biocontrol agents or biofertilizers (Trichoderma virens Gv29-8, Trichoderma virens FT-333, Trichoderma asperellum FT-101, and Trichoderma atroviride P1). Our results provide comprehensive categorization, correct positioning, and evolutionary detail of both nuclear and mitochondrial genomes, including telomeres, AT-rich blocks, centromeres, transposons, mating-type loci, nuclear-encoded mitochondrial sequences, as well as many new secondary metabolic and carbohydrate-active enzyme gene clusters. We have also identified evolutionarily conserved core genes contributing to plant-fungal interactions, as well as variations potentially linked to key behavioral traits such as sex, genome defense, secondary metabolism, and mycoparasitism. The genomic resources we provide herein significantly extend our knowledge not only of this economically important fungal genus, but also fungal evolution and basic biology in general. IMPORTANCE Telomere-to-telomere and gapless reference genome assemblies are necessary to ensure that all genomic variants are studied and discovered, including centromeres, telomeres, AT-rich blocks, mating type loci, biosynthetic, and metabolic gene clusters. Here, we applied long-range sequencing technologies to determine the near-completed genome sequences of four widely used biocontrol agents or biofertilizers: Trichoderma virens Gv29-8 and FT-333, Trichoderma asperellum FT-101, and Trichoderma atroviride P1. Like those of three Trichoderma reesei wild isolates [QM6a, CBS999.97(MAT1-1) and CBS999.97(MAT1-2)] we reported previously, these four biocontrol agent genomes each contain seven nuclear chromosomes and a circular mitochondrial genome. Substantial intraspecies and intragenus diversities are also discovered, including single nucleotide polymorphisms, chromosome shuffling, as well as genomic relics derived from historical transposition events and repeat-induced point (RIP) mutations.

Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer

Extrachromosomal circular DNA (eccDNA) refers to a type of circular DNA that originate from but are likely independent of chromosomes. Due to technological advancements, eccDNAs have recently emerged as multifunctional molecules with numerous characteristics. The unique topological structure and genetic characteristics of eccDNAs shed new light on the monitoring, early diagnosis, treatment, and prediction of cancer. EccDNAs are commonly observed in both normal and cancer cells and function via different mechanisms in the stress response to exogenous and endogenous stimuli, aging, and carcinogenesis and in drug resistance during cancer treatment. The structural diversity of eccDNAs contributes to the function and numerical diversity of eccDNAs and thereby endows eccDNAs with powerful roles in evolution and in cancer initiation and progression by driving genetic plasticity and heterogeneity from extrachromosomal sites, which has been an ignored function in evolution in recent decades. EccDNAs show great potential in cancer, and we summarize the features, biogenesis, evaluated functions, functional mechanisms, related methods, and clinical utility of eccDNAs with a focus on their role in evolution and cancer.

Chromosomal Characterization of Tripidium arundinaceum Revealed by Oligo-FISH

Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum. Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum, even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum. Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding.

Using carrot centromeric repeats to study karyotype relationships in the genus Daucus (Apiaceae)

Background

In the course of evolution, chromosomes undergo evolutionary changes; thus, karyotypes may differ considerably among groups of organisms, even within closely related taxa. The genus Daucus seems to be a promising model for exploring the dynamics of karyotype evolution. It comprises some 40 wild species and the cultivated carrot, a crop of great economic significance. However, Daucus species are very diverse morphologically and genetically, and despite extensive research, the taxonomic and phylogenetic relationships between them have still not been fully resolved. Although several molecular cytogenetic studies have been conducted to investigate the chromosomal structure and karyotype evolution of carrot and other Daucus species, detailed karyomorphological research has been limited to carrot and only a few wild species. Therefore, to better understand the karyotype relationships within Daucus, we (1) explored the chromosomal distribution of carrot centromeric repeats (CentDc) in 34 accessions of Daucus and related species by means of fluorescence in situ hybridization (FISH) and (2) performed detailed karyomorphological analysis in 16 of them.

Results

We determined the genomic organization of CentDc in 26 accessions of Daucus (belonging to both Daucus I and II subclades) and one accession of closely related species. The CentDc repeats were present in the centromeric regions of all chromosomes of 20 accessions (representing 11 taxa). In the other Daucus taxa, the number of chromosome pairs with CentDc signals varied depending on the species, yet their centromeric localization was conserved. In addition, precise chromosome measurements performed in 16 accessions showed the inter- and intraspecific karyological relationships among them.

Conclusions

The presence of the CentDc repeats in the genomes of taxa belonging to both Daucus subclades and one outgroup species indicated the ancestral status of the repeat. The results of our study provide useful information for further evolutionary, cytotaxonomic, and phylogenetic research on the genus Daucus and may contribute to a better understanding of the dynamic evolution of centromeric satellites in plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07853-2.