Chromosome-level genome assembly of Cylas formicarius provides insights into its adaptation and invasion mechanisms

Cylasformicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage.This study improved the effect of comprehensive management and understanding of genetic mechanisms by examining the functional genomics of C. formicarius.Using Illumina and PacBio sequencing, this study obtained a chromosome-level genome assembly of adult weevils from lines inbred for 15 generations.The high-quality assembly obtained was 338.84 Mb, with contig and scaffold N50 values of 14.97 and 34.23 Mb, respectively.In total, 157.51 Mb of repeat sequences and 11 907 protein-coding genes were predicted.A total of 337.06 Mb of genomic sequences was located on the 11 chromosomes, accounting for 99.03%of the total length of the associated chromosome.Comparative genomic analysis showed that C. formicarius was sister to Dendroctonus ponderosae, and C. formicarius diverged from D. ponderosae approximately 138.89 million years ago (Mya).Many important gene families expanded in the C. formicarius genome were involved in the detoxification of pesticides, tolerance to cold stress and chemosensory system.To further study the role of odorant-binding proteins (OBPs) in olfactory recognition of C. formicarius, the binding assay results indicated that Cfor OBP4–6 had strong binding affinities for sex pheromones and other ligands.The high-quality C. formicarius genome provides a valuable resource to reveal the molecular ecological basis, genetic mechanism, and evolutionary process of major agricultural pests;it also offers new ideas and new technologies for ecologically sustainable pest control.

Screening and functional analysis of the long-range interaction elements ofβ-globin genes

Objective:Studies have shown thatβ-globin gene presents a selective expression transformation mechanism during development,and its upstream locus control region(LCR)regulates the expression pattern ofβ-globin gene family.To further explore the molecular network ofβ-globin gene expression regulation,other long-range regulatory elements that may be involved in the regulation ofβ-globin gene expression were screened and the dynamic regulation and transformation mechanism ofβ-globin gene was deeply studied.Methods:Promyelocytic cells were induced to differentiate by all-trans retinoic acid.β-globin gene promoter region and LCR were used as the target sites for circular chromosome conformational capture(4C)analysis.Through sequencing and regulatory element analysis,the sites interacting withβ-globin family loci were screened in the whole genome.Results:According to the results of 4C sequencing,the sites that interact with HBD promoter region and LCR were screened.Verified by chromosome conformational capture(3C),the results were consistent with those of sequencing.The functional analysis of regulatory elements by formaldehyde-assisted separation regulatory elements and Epiregio online website showed that the screening sites AC105129.4,AL354707.17,AC078785.22 and AC021646.35 were all potential regulatory elements involved inβ-globin gene.Conclusion:The interaction between 4C screening site and anchor site showed the complex spatial organization ofβ-globin family loci in the nucleus.

Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo(Dendrocalamus latiflorus Munro)

Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot growth.Both genetic transformation and clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)gene editing techniques are available for D.latiflorus,enabling reverse genetic approaches.Thus,D.latiflorus has the potential to be a model bamboo species.However,the genome sequence of D.latiflorus has remained unreported due to its polyploidy and large genome size.Here,we sequenced the D.latiflorus genome and assembled it into three allele-aware subgenomes(AABBCC),representingthe largest genome of a major bamboo species.We assembled 70 allelic chromosomes(2,737 Mb)for hexaploid D.latiflorus using both singlemolecule sequencing from the Pacific Biosciences(Pac Bio)Sequel platform and chromosome conformation capture sequencing(Hi-C).Repetitive sequences comprised 52.65%of the D.latiflorus genome.We annotated 135231 protein-coding genes in the genome based on transcriptomes from eight different tissues.Transcriptome sequencing using RNA-Seq and Pac Bio singlemolecule real-time long-read isoform sequencing revealed highly differential alternative splicing(AS)between non-abortive and abortive shoots,suggesting that AS regulates the abortion rate of bamboo shoots.This high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using D.latiflorus as a model species.

Freeze substitution Hi-C,a convenient and cost-effective method for capturing the natural 3D chromatin conformation from frozen samples

Chromatin interactions functionally affect genome architecture and gene regulation,but to date,only fresh samples must be used in High-through chromosome conformation capture(Hi-C)to keep natural chromatin conformation intact.This requirement has impeded the advancement of 3 D genome research by limiting sample collection and storage options for researchers and severely limiting the number of samples that can be processed in a short time.Here,we develop a freeze substitution Hi-C(FS-Hi-C)technique that overcomes the need for fresh samples.FS-Hi-C can be used with samples stored in liquid nitrogen(LN2):the water in a vitreous form in the sample cells is replaced with ethanol via automated freeze substitution.After confirming that the FS step preserves the natural chromosome conformation during sample thawing,we tested the performance of FS-Hi-C with Drosophila melanogaster and Gossypium hirsutum.Beyond allowing the use of frozen samples and confirming that FS-Hi-C delivers robust data for generating contact heat maps and delineating A/B compartments and topologically associating domains,we found that FS-HiC outperforms the in situ Hi-C in terms of library quality,reproducibility,and valid interactions.Thus,FS-HiC will probably extend the application of 3D genome structure analysis to the vast number of experimental contexts in biological and medical research for which Hi-C methods have been unfeasible to date.

Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-order Genomic Interactions

Recent studies have characterized the genomic structures of many eukaryotic cells,often focusing on their relation to gene expression.However,these studies have largely investigated cells grown in 2D cultures,although the transcriptomes of 3D-cultured cells are generally closer to their in vivo phenotypes.To examine the effects of spatial constraints on chromosome conformation,we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C.Our results reveal significant differences in higher-order genomic interactions,notably in compartment identity and strength as well as in topologically associating domain(TAD)-TAD interactions,but only minor differences are found at the TAD level.Our RNA-seq analysis reveals up-regulated expression of genes involved in physiological hepatocyte functions in the 3D-cultured cells.These genes are associated with a subset of structural changes,suggesting that differences in genomic structure are critically important for transcriptional regulation.However,there are also many structural differences that are not directly associated with changes in gene expression,whose cause remains to be determined.Overall,our results indicate that growth in 3D significantly alters higher-order genomic interactions,which may be consequential for a subset of genes that are important for the physiological functioning of the cell.

3D genome organization in the central nervous system,implications for neuropsychological disorders

Chromosomes in eukaryotic cell nuclei are highly compacted and finely organized into hierarchical threedimensional(3 D) configuration. In recent years, scientists have gained deeper understandings of 3 D genome structures and revealed novel evidence linking 3 D genome organization to various important cell events on the molecular level. Most importantly, alteration of 3 D genome architecture has emerged as an intriguing higher order mechanism that connects disease-related genetic variants in multiple heterogenous and polygenic neuropsychological disorders, delivering novel insights into the etiology. In this review, we provide a brief overview of the hierarchical structures of 3 D genome and two proposed regulatory models,loop extrusion and phase separation. We then focus on recent Hi-C data in the central nervous system and discuss 3 D genome alterations during normal brain development and in mature neurons. Most importantly,we make a comprehensive review on current knowledge and discuss the role of 3 D genome in multiple neuropsychological disorders, including schizophrenia, repeat expansion disorders, 22 q11 deletion syndrome, and others.