Repetitive Regions Research Articles

Has recombination changed during the recent evolution of the guppy Y chromosome?

Genome sequencing and genetic mapping of molecular markers have demonstrated nearly complete Y-linkage across much of the guppy (Poecilia reticulata) XY chromosome pair. Predominant Y-linkage of factors controlling visible male-specific coloration traits also suggested that these polymorphisms are sexually antagonistic (SA). However, occasional exchanges with the X are detected, and recombination patterns also appear to differ between natural guppy populations, suggesting ongoing evolution of recombination suppression under selection created by partially sex-linked SA polymorphisms. We used molecular markers to directly estimate genetic maps in sires from 4 guppy populations. The maps are very similar, suggesting that their crossover patterns have not recently changed. Our maps are consistent with population genomic results showing that variants within the terminal 5 Mb of the 26.5 Mb sex chromosome, chromosome 12, are most clearly associated with the maleness factor, albeit incompletely. We also confirmed occasional crossovers proximal to the male-determining region, defining a second, rarely recombining, pseudo-autosomal region, PAR2. This fish species may therefore have no completely male-specific region (MSY) more extensive than the male-determining factor. The positions of the few crossover events suggest a location for the male-determining factor within a physically small repetitive region. A sex-reversed XX male had few crossovers in PAR2, suggesting that this region's low crossover rate depends on the phenotypic, not the genetic, sex. Thus, rare individuals whose phenotypic and genetic sexes differ, and/or occasional PAR2 crossovers in males can explain the failure to detect fully Y-linked variants.

Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration

Sciaenops ocellatus is among the most important artificially introduced farmed fish across 11 countries and regions. However, the frequent occurrence of extreme weather events and breeding escapes have placed great pressure on local marine biodiversity and ecosystems. We reported the de novo assembly and annotation with a contig N50 of 28.30 Mb using PacBio HiFi sequencing and Hi-C technologies, which resulted in a 283-fold increase in contig N50 length and improvement in continuity and quality in complex repetitive region for S. ocellatus compared to the previous version. In total, 257.36 Mb of repetitive sequences accounted for 35.48% of the genome, and 22,845 protein-coding genes associated with a BUSCO value of 98.32%, were identified by genome annotation. Moreover, 54 hub genes rapidly responding to hypoosmotic stress were identified by WGCNA. The high-quality chromosome-scale S. ocellatus genome and candidate resistance-related gene sets will not only provide a genomic basis for genetic improvement via molecular breeding, but will also lay an important foundation for investigating the molecular regulation of rapid responses to stress.

A cuticular protein, BgCPLCP1, contributes to insecticide resistance by thickening the cockroach endocuticle

Overuse of insecticides has led to severe environmental problems. Insect cuticle, which consists mainly of chitin, proteins and a thin outer lipid layer, serves multiple functions. Its prominent role is as a physical barrier that impedes the penetration of xenobiotics, including insecticides. Blattella germanica (L.) is a major worldwide indoor pest that causes allergic disease and asthma. Extensive use of pyrethroid insecticides, including β-cypermethrin, has selected for the rapid and independent evolution of resistance in cockroach populations on a global scale. We demonstrated that BgCPLCP1, the first CPLCP (cuticular proteins of low complexity with a highly repetitive proline-rich region) family cuticular protein in order Blattodea, contributes to insecticide penetration resistance. Silencing BgCPLCP1 resulted in 85.0 %–85.7 % and 81.0 %–82.0 % thinner cuticle (and especially thinner endocuticle) in the insecticide-susceptible (S) and β-cypermethrin-resistant (R) strains, respectively. The thinner and more permeable cuticles resulted in 14.4 % and 20.0 % lower survival of β-cypermethrin-treated S- and R-strain cockroaches, respectively. This study advances our understanding of cuticular penetration resistance in insects and opens opportunities for the development of new efficiently and environmentally friendly insecticides targeting the CPLCP family of cuticular proteins.

Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms

Improvements in long read DNA sequencing and related techniques facilitated the generation of complex eukaryotic genomes. Despite these advances, the quality of constructed plant reference genomes remains relatively poor due to the large size of genomes, high content of repetitive sequences, and wide variety of ploidy. Here, we developed the de novo sequencing and assembly of high polyploid plant genome, Hibiscus syriacus, a flowering plant species of the Malvaceae family, using the Oxford Nanopore Technologies and Pacific Biosciences Sequel sequencing platforms. We investigated an efficient combination of high-quality and high-molecular-weight DNA isolation procedure and suitable assembler to achieve optimal results using long read sequencing data. We found that abundant ultra-long reads allow for large and complex polyploid plant genome assemblies with great recovery of repetitive sequences and error correction even at relatively low depth Nanopore sequencing data and polishing compared to previous studies. Collectively, our combination provides cost effective methods to improve genome continuity and quality compared to the previously reported reference genome by accessing highly repetitive regions. The application of this combination may enable genetic research and breeding of polyploid crops, thus leading to improvements in crop production.

DNA Damage Atlas: an atlas of DNA damage and repair.

DNA damage and its improper repair are the major source of genomic alterations responsible for many human diseases, particularly cancer. To aid researchers in understanding the underlying mechanisms of genome instability, a number of genome-wide profiling approaches have been developed to monitor DNA damage and repair events. The rapid accumulation of published datasets underscores the critical necessity of a comprehensive database to curate sequencing data on DNA damage and repair intermediates. Here, we present DNA Damage Atlas (DDA, http://www.bioinformaticspa.com/DDA/), the first large-scale repository of DNA damage and repair information. Currently, DDA comprises 6,030 samples from 262 datasets by 59 technologies, covering 16 species, 10 types of damage and 135 treatments. Data collected in DDA was processed through a standardized workflow, including quality checks, hotspots identification and a series of feature characterization for the hotspots. Notably, DDA encompasses analyses of highly repetitive regions, ribosomal DNA and telomere. DDA offers a user-friendly interface that facilitates browsing, searching, genome browser visualization, hotspots comparison and data downloading, enabling convenient and thorough exploration for datasets of interest. In summary, DDA will stand as a valuable resource for research in genome instability and its association with diseases.

Immunoinformatic Approach for Rational Identification of Immunogenic Peptides Against Host Entry and/or Exit Mpox Proteins and Potential Multiepitope Vaccine Construction.

COVID-19 has intensified humanity's concern about the emergence of new pandemics. Since 2018, epidemic outbreaks of the mpox virus have become worrisome. In June 2022, the World Health Organization declared the disease a global health emergency, with 14 500 cases reported by the Centers for Disease Control and Prevention in 60 countries. Therefore, the development of a vaccine based on the current virus genome is paramount in combating new cases. In view of this, we hypothesized the obtainment of rational immunogenic peptides predicted from proteins responsible for entry of the mpox virus into the host (A17L, A26L/A30L, A33R, H2R, L1R), exit (A27L, A35R, A36R, C19L), and both (B5R). To achieve this, we aligned the genome sequencing data of mpox virus isolated from an infected individual in the United States in June 2022 (ON674051.1) with the reference genome dated 2001 (NC_003310.1) for conservation analysis. The Immune Epitope Database server was used for the identification and characterization of the epitopes of each protein related to major histocompatibility complex I or II interaction and recognition by B-cell receptors, resulting in 138 epitopes for A17L, 233 for A28L, 48 for A33R, 77 for H2R, 77 for L1R, 270 for A27L, 72 for A35R, A36R, 148 for C19L, and 276 for B5R. These epitopes were tested in silico for antigenicity, physicochemical properties, and allergenicity, resulting in 51, 40, 10, 34, 38, 57, 25, 7, 47, and 53 epitopes, respectively. Additionally, to select an epitope with the highest promiscuity of binding to major histocompatibility complexes and B-cell receptor simultaneously, all epitopes of each protein were aligned, and the most repetitive and antigenic regions were identified. By classifying the results, we obtained 23 epitopes from the entry proteins, 16 from the exit proteins, and 7 from both. Subsequently, 1 epitope from each protein was selected, and all 3 were fused to construct a chimeric protein that has potential as a multiepitope vaccine. The constructed vaccine was then analyzed for its physicochemical, antigenic, and allergenic properties. Protein modeling, molecular dynamics, and molecular docking were performed on Toll-like receptors 2, 4, and 8, followed by in silico immune simulation of the vaccine. Finally, the results indicate an effective, stable, and safe vaccine that can be further tested, especially in vitro and in vivo, to validate the findings demonstrated in silico.

Structural genomic variation and migratory behavior in a wild songbird.

Structural variants (SVs) are a major source of genetic variation; and descriptions in natural populations and connections with phenotypic traits are beginning to accumulate in the literature. We integrated advances in genomic sequencing and animal tracking to begin filling this knowledge gap in the Eurasian blackcap. Specifically, we (a) characterized the genome-wide distribution, frequency, and overall fitness effects of SVs using haplotype-resolved assemblies for 79 birds, and (b) used these SVs to study the genetics of seasonal migration. We detected >15 K SVs. Many SVs overlapped repetitive regions and exhibited evidence of purifying selection suggesting they have overall deleterious effects on fitness. We used estimates of genomic differentiation to identify SVs exhibiting evidence of selection in blackcaps with different migratory strategies. Insertions and deletions dominated the SVs we identified and were associated with genes that are either directly (e.g., regulatory motifs that maintain circadian rhythms) or indirectly (e.g., through immune response) related to migration. We also broke migration down into individual traits (direction, distance, and timing) using existing tracking data and tested if genetic variation at the SVs we identified could account for phenotypic variation at these traits. This was only the case for 1 trait-direction-and 1 specific SV (a deletion on chromosome 27) accounted for much of this variation. Our results highlight the evolutionary importance of SVs in natural populations and provide insight into the genetic basis of seasonal migration.

Range-Ambiguous Sea Clutter Suppression for Multichannel Spaceborne Radar Applications Via Alternating APC Processing

In this article, a novel range ambiguous cluter suppression method, i.e., alternating azitmuth phase coding (AAPC), based on azimuth phase coding (APC) is proposed, where the blind areas of target detection are solved. Based on the motion model of spaceborne radar (SBR) system, the sea clutter motion property is analyzed, and a multichannel sea clutter signal model with the consideration of range ambiguity is established. After that, the novel method AAPC is proposed. Finally, a time-domain sliding window projection method with the consideration of clutter internal motions is proposed to realize the sea clutter rejection. Compared with the current range-ambiguous sea clutter suppression algorithms, the improvements of this method are: 1) the range-ambiguous clutter can be separated and most of the clutter components in the main-lobe region can be rejected; and 2) the repetitive detection blind regions can be avoided by applying the proposed AAPC technique. Simulation results are presented to validate the feasibility of the proposed algorithm.

High levels of intra-strain structural variation in Drosophila simulans X pericentric heterochromatin.

Large genome structural variations can impact genome regulation and integrity. Repeat-rich regions like pericentric heterochromatin are vulnerable to structural rearrangements although we know little about how often these rearrangements occur over evolutionary time. Repetitive genome regions are particularly difficult to study with genomic approaches, as they are missing from most genome assemblies. However, cytogenetic approaches offer a direct way to detect large rearrangements involving pericentric heterochromatin. Here, we use a cytogenetic approach to reveal large structural rearrangements associated with the X pericentromeric region of Drosophila simulans. These rearrangements involve large blocks of satellite DNA-the 500-bp and Rsp-like satellites-which colocalize in the X pericentromeric heterochromatin. We find that this region is polymorphic not only among different strains, but between isolates of the same strain from different labs, and even within individual isolates. On the one hand, our observations raise questions regarding the potential impact of such variation at the phenotypic level and our ability to control for such genetic variability. On the other hand, this highlights the very rapid turnover of the pericentric heterochromatin most likely associated with genomic instability of the X pericentromere. It represents a unique opportunity to study the dynamics of pericentric heterochromatin, the evolution of associated satellites on a very short time scale, and to better understand how structural variation arises.

Disrupting the Repeat Domain of Premelanosome Protein (PMEL) Produces Dysamyloidosis and Dystrophic Ocular Pigment Reflective of Pigmentary Glaucoma.

Pigmentary glaucoma has recently been associated with missense mutations in PMEL that are dominantly inherited and enriched in the protein's fascinating repeat domain. PMEL pathobiology is intriguing because PMEL forms functional amyloid in healthy eyes, and this PMEL amyloid acts to scaffold melanin deposition. This is an informative contradistinction to prominent neurodegenerative diseases where amyloid formation is neurotoxic and mutations cause a toxic gain of function called "amyloidosis". Preclinical animal models have failed to model this PMEL "dysamyloidosis" pathomechanism and instead cause recessively inherited ocular pigment defects via PMEL loss of function; they have not addressed the consequences of disrupting PMEL's repetitive region. Here, we use CRISPR to engineer a small in-frame mutation in the zebrafish homolog of PMEL that is predicted to subtly disrupt the protein's repetitive region. Homozygous mutant larvae displayed pigmentation phenotypes and altered eye morphogenesis similar to presumptive null larvae. Heterozygous mutants had disrupted eye morphogenesis and disrupted pigment deposition in their retinal melanosomes. The deficits in the pigment deposition of these young adult fish were not accompanied by any detectable glaucomatous changes in intraocular pressure or retinal morphology. Overall, the data provide important in vivo validation that subtle PMEL mutations can cause a dominantly inherited pigment pathology that aligns with the inheritance of pigmentary glaucoma patient pedigrees. These in vivo observations help to resolve controversy regarding the necessity of PMEL's repeat domain in pigmentation. The data foster an ongoing interest in an antithetical dysamyloidosis mechanism that, akin to the amyloidosis of devastating dementias, manifests as a slow progressive neurodegenerative disease.

A hybrid RNA FISH immunofluorescence protocol on Drosophila polytene chromosomes

ObjectivesInvestigating protein-DNA interactions is imperative to understanding fundamental concepts such as cell growth, differentiation, and cell development in many systems. Sequencing techniques such as ChIP-seq can yield genome-wide DNA binding profiles of transcription factors; however this assay can be expensive, time-consuming, may not be informative for repetitive regions of the genome, and depend heavily upon antibody suitability. Combining DNA fluorescence in situ hybridization (FISH) with immunofluorescence (IF) is a quicker and inexpensive approach which has historically been used to investigate protein-DNA interactions in individual nuclei. However, these assays are sometimes incompatible due to the required denaturation step in DNA FISH that can alter protein epitopes, hindering primary antibody binding. Additionally, combining DNA FISH with IF may be challenging for less experienced trainees. Our goal was to develop an alternative technique to investigate protein-DNA interactions by combining RNA FISH with IF.ResultsWe developed a hybrid RNA FISH-IF protocol for use on Drosophila melanogaster polytene chromosome spreads in order to visualize colocalization of proteins and DNA loci. We demonstrate that this assay is sensitive enough to determine if our protein of interest, Multi sex combs (Mxc), localizes to single-copy target transgenes carrying histone genes. Overall, this study provides an alternative, accessible method for investigating protein-DNA interactions at the single gene level in Drosophila melanogaster polytene chromosomes.

Transformer‐based DNA methylation detection on ionic signals from Oxford Nanopore sequencing data

Transformer is an algorithm that adopts self‐attention architecture in the neural networks and has been widely used in natural language processing. In the current study, we apply Transformer architecture to detect DNA methylation on ionic signals from Oxford Nanopore sequencing data. We evaluated this idea using real data sets (Escherichia coli data and the human genome NA12878 sequenced by Simpson et al.) and demonstrated the ability of Transformers to detect methylation on ionic signal data.BackgroundOxford Nanopore long‐read sequencing technology addresses current limitations for DNA methylation detection that are inherent in short‐read bisulfite sequencing or methylation microarrays. A number of analytical tools, such as Nanopolish, Guppy/Tombo and DeepMod, have been developed to detect DNA methylation on Nanopore data. However, additional improvements can be made in computational efficiency, prediction accuracy, and contextual interpretation on complex genomics regions (such as repetitive regions, low GC density regions).MethodIn the current study, we apply Transformer architecture to detect DNA methylation on ionic signals from Oxford Nanopore sequencing data. Transformer is an algorithm that adopts self‐attention architecture in the neural networks and has been widely used in natural language processing.ResultsCompared to traditional deep‐learning method such as convolutional neural network (CNN) and recurrent neural network (RNN), Transformer may have specific advantages in DNA methylation detection, because the self‐attention mechanism can assist the relationship detection between bases that are far from each other and pay more attention to important bases that carry characteristic methylation‐specific signals within a specific sequence context.ConclusionWe demonstrated the ability of Transformers to detect methylation on ionic signal data.

Droplet digital PCR is a cost-effective method for analyzing long cell-free DNA in maternal plasma: Application in preeclampsia.

Long cell-free DNA (cfDNA) can be found in the plasma of pregnant women and cancer patients. We investigated if droplet digital PCR (ddPCR) can analyze such molecules for diagnostic purposes using preeclampsia as a model. Plasma samples from ten preeclamptic and sixteen normal pregnancies were analyzed. Two ddPCR assays targeting a single-copy gene, VCP, and one ddPCR assay targeting LINE-1 repetitive regions were used to measure the percentages of long cfDNA >533, 1001, and 170 bp, respectively. The LINE-1 assay was developed as guided by in silico PCR analyses to better differentiate preeclamptic and normal pregnancies. Preeclamptic patients had a significantly lower median percentage of long cfDNA than healthy pregnant controls, as determined by the LINE-1 170 bp assay (28.9% vs. 35.1%, p<0.0001) and the VCP 533 bp assay (6.6% vs. 8.7%, p=0.014). The LINE-1 assay provided a better differentiation than the VCP 533 bp assay (area under ROC curves, 0.94 vs. 0.79). ddPCR is a cost-effective approach for unlocking diagnostic information carried by long cfDNA in plasma and may have applications for the detection of preeclampsia. Further longitudinal studies with larger cohorts are required to assess the clinical utility of this test.

De novo assembled mitogenome analysis of Trichuris trichiura from Korean individuals using nanopore-based long-read sequencing technology.

Knowledge about mitogenomes has been proven to be essential in human parasite diagnostics and understanding of their diversity. However, the lack of substantial data for comparative analysis is still a challenge in Trichuris trichiura research. To provide high quality mitogenomes, we utilized long-read sequencing technology of Oxford Nanopore Technologies (ONT) to better resolve repetitive regions and to construct de novo mitogenome assembly minimizing reference biases. In this study, we got three de novo assembled mitogenomes of T. trichiura isolated from Korean individuals. These circular complete mitogenomes of T. trichiura are 14,508 bp, 14,441 bp, and 14,440 bp in length. A total of 37 predicted genes were identified consisting of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs) genes, two ribosomal RNA (rRNA) genes (rrnS and rrnL), and two non-coding regions. Interestingly, the assembled mitogenome has up to six times longer AT-rich regions than previous reference sequences, thus proving the advantage of long-read sequencing in resolving unreported non-coding regions. Furthermore, variant detection and phylogenetic analysis using concatenated protein coding genes, cox1, rrnL, and nd1 genes confirmed the distinct molecular identity of this newly assembled mitogenome while at the same time showing high genetic relationship with sequences from China or Tanzania. Our study provided a new set of reference mitogenome with better contiguity and resolved repetitive regions that could be used for meaningful phylogenetic analysis to further understand disease transmission and parasite biology.

First comparative analysis of complete chloroplast genomes among six Hedysarum (Fabaceae) species.

Hedysarum is one of the largest genera in the Fabaceae family, mainly distributed in the Northern Hemisphere. Despite numerous molecular studies on the genus Hedysarum, there is still a lack of research aimed at defining the specific characteristics of the chloroplast genome (cp genome) of the genus. Furthermore, the interrelationships between sections in the genus based on the cp genome have not yet been studied. In this study, comprehensive analyses of the complete cp genomes of six Hedysarum species, corresponding to sections Multicaulia, Hedysarum, and Stracheya were conducted. The complete cp genomes of H. drobovii, H. flavescens, and H. lehmannianum were sequenced for this study. The cp genomes of six Hedysarum species showed high similarity with regard to genome size (except for H. taipeicum), gene sequences, and gene classes, as well as the lacking IR region. The whole cp genomes of the six species were found to contain 110 genes ranging from 121,176 bp to 126,738 bp in length, including 76 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. In addition, chloroplast SSRs and repetitive sequence regions were reported for each species. The six Hedysarum species shared 7 common SSRs and exhibited 14 unique SSRs. As well, three highly variable genes (clpP, accD, and atpF) with high Pi values were detected among protein-coding genes. Furthermore, we conducted phylogenetic analyses using the complete cp genomes and 76 protein-coding genes of 14 legume species, including the seven Hedysarum species. The results showed that the Hedysarum species form a monophyletic clade closely related to the genera Onobrychis and Alhagi. Furthermore, both of our phylogenetic reconstructions showed that section Stracheya is more closely related to section Hedysarum than to section Multicaulia. This study is the first comprehensive work to investigate the genome characteristics of the genus Hedysarum, which provides useful genetic information for further research on the genus, including evolutionary studies, phylogenetic relationships, population genetics, and species identification.

Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia.

The suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods. For this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL. Both the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions. The filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL.

Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism

Chia (Salvia hispanica) is an emerging crop considered a functional food containing important substances with multiple potential applications. However, the molecular basis of some relevant chia traits, such as seed mucilage and polyphenol content, remains to be discovered. This study generates an improved chromosome-level reference of the chia genome, resolving some highly repetitive regions, describing methylation patterns, and refining genome annotation. Transcriptomic analysis shows that seeds exhibit a unique expression pattern compared to other organs and tissues. Thus, a metabolic and proteomic approach is implemented to study seed composition and seed-produced mucilage. The chia genome exhibits a significant expansion in mucilage synthesis genes (compared to Arabidopsis), and gene network analysis reveals potential regulators controlling seed mucilage production. Rosmarinic acid, a compound with enormous therapeutic potential, was classified as the most abundant polyphenol in seeds, and candidate genes for its complex pathway are described. Overall, this study provides important insights into the molecular basis for the unique characteristics of chia seeds.

Single-worm long-read sequencing reveals genome diversity in free-living nematodes.

Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.

Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

BackgroundThe development of cotton fiber is regulated by the orchestrated binding of regulatory proteins to cis-regulatory elements associated with developmental genes. The cis–trans regulatory dynamics occurred throughout the course of cotton fiber development are elusive. Here we generated genome-wide high-resolution DNase I hypersensitive sites (DHSs) maps to understand the regulatory mechanisms of cotton ovule and fiber development.ResultsWe generated DNase I hypersensitive site (DHS) profiles from cotton ovules at 0 and 3 days post anthesis (DPA) and fibers at 8, 12, 15, and 18 DPA. We obtained a total of 1185 million reads and identified a total of 199,351 DHSs through ~ 30% unique mapping reads. It should be noted that more than half of DNase-seq reads mapped multiple genome locations and were not analyzed in order to achieve a high specificity of peak profile and to avoid bias from repetitive genomic regions. Distinct chromatin accessibilities were observed in the ovules (0 and 3 DPA) compared to the fiber elongation stages (8, 12, 15, and 18 DPA). Besides, the chromatin accessibility during ovules was particularly elevated in genomic regions enriched with transposable elements (TEs) and genes in TE-enriched regions were involved in ovule cell division. We analyzed cis-regulatory modules and revealed the influence of hormones on fiber development from the regulatory divergence of transcription factor (TF) motifs. Finally, we constructed a reliable regulatory network of TFs related to ovule and fiber development based on chromatin accessibility and gene co-expression network. From this network, we discovered a novel TF, WRKY46, which may shape fiber development by regulating the lignin content.ConclusionsOur results not only reveal the contribution of TEs in fiber development, but also predict and validate the TFs related to fiber development, which will benefit the research of cotton fiber molecular breeding.

Gene amplifications and extrachromosomal circular DNAs: function and biogenesis.

Gene amplification is an increase in the copy number of restricted chromosomal segments that contain gene(s) and frequently results in the over-expression of the corresponding gene(s). Amplification may be found in the form of extrachromosomal circular DNAs (eccDNAs) or as linear repetitive amplicon regions that are integrated into chromosomes, which may form cytogenetically observable homogeneously staining regions or may be scattered throughout the genome. eccDNAs are structurally circular and in terms of their function and content, they can be classified into various subtypes. They play pivotal roles in many physiological and pathological phenomena such as tumor pathogenesis, aging, maintenance of telomere length and ribosomalDNAs (rDNAs), and gain of resistance against chemotherapeutic agents. Amplification of oncogenes is consistently seen in various types of cancers and can be associated with prognostic factors. eccDNAs are known to be originated from chromosomes as a consequence of various cellular events such as repair processes of damaged DNA or DNA replication errors. In this review, we highlighted the role of gene amplification in cancer, the functional aspects of eccDNAs subtypes, the proposed biogenesis mechanisms, and their role in gene or segmental-DNA amplification.