![]() This chapter will illustrate how to compare the chromatin interactome in different experimental conditions, starting from pre-computed Hi-C contact matrices, how to visualize the results, and how to correlate the observed variations in chromatin interaction strength with changes in gene expression. In particular, Hi-C has the potential to achieve the most comprehensive characterization of chromatin 3D interactions, as it is theoretically able to detect any pair of restriction fragments connected as a result of ligation by proximity. The widespread availability of Chromosome Conformation Capture (3C)-based high-throughput techniques has been instrumental in advancing our knowledge of chromatin nuclear organization. This is true at multiple levels of resolution: on a large scale, with chromosomes occupying distinct volumes (chromosome territories) at the level of individual chromatin fibers, which are organized into compartmentalized domains (e.g., Topologically Associating Domains-TADs), and at the level of short-range chromatin interactions between functional elements of the genome (e.g., enhancer-promoter loops). The exceptional rate of structural evolution of aphid autosomes renders them an important emerging model system for studying the role of large-scale genome rearrangements in evolution.The 3D organization of chromatin within the nucleus enables dynamic regulation and cell type-specific transcription of the genome. Despite being more diverged, the blood-feeding hemipterans have conserved synteny and we detect only two chromosome fusion or fission events. To test whether rapid evolution of genome structure is a hallmark of Hemiptera, we compared our aphid assemblies to chromosome-level assemblies of two blood-feeding Hemiptera (Rhodnius prolixus and Triatoma rubrofasciata). In contrast, gene content of the aphid sex (X) chromosome remained unchanged despite rapid sequence evolution, low gene expression and high transposable element load. We find that aphid autosomes have undergone dramatic reorganisation over the last 30 million years, to the extent that chromosome homology cannot be determined between aphids from the tribes Macrosiphini (M. Here, we investigate chromosome evolution in aphids -an important group of hemipteran plant pests -using newly generated chromosome-scale genome assemblies of the green peach aphid (Myzus persicae) and the pea aphid (Acyrthosiphon pisum), and a previously published chromosome-scale assembly of the corn-leaf aphid (Rhopalosiphum maidis). Whether this truly reflects the diversity of insect genome evolution is questionable given that many species exhibit rapid karyotype evolution. In insects, Diptera (flies and mosquitoes) and Lepidoptera (butterflies and moths) have high levels of chromosome conservation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. Large-scale chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. The completeness of the genome will provide high‐quality genomic knowledge on breeding and reveal genetic variation in L. cylindrica. cylindrica, and it demonstrated a high degree of conserved gene order in these three species. ![]() Genome collinearity analysis was performed in Cucurbita moschata, Cucumis sativus and L. According to the phylogenetic analysis, L. cylindrica is closely related to Cucurbita and Cucumis species and diverged from their common ancestor ~28.6–67.1 million years ago. In addition, 27,552 protein‐coding genes (87.02%) were annotated in five databases. Subsequently, 31,661 protein‐coding genes with an average of 5.69 exons per gene were identified in the L. cylindrica genome using de novo methods, transcriptome data and homologue‐based approaches. After removing redundant sequences, 416.31 Mb (62.18% of the genome) of repeat sequences was detected. Thirteen scaffolds corresponding to the 13 chromosomes were assembled from 1,156 contigs to a final size of 669 Mb with a contig N50 size of 5 Mb and a scaffold N50 size of 53 Mb. We combined Hi‐C data with a draft genome assembly to generate chromosome‐length scaffolds. To address the limited knowledge of the genome of Luffa species, the chromosome‐level genome of L. cylindrica was assembled and analysed using PacBio long reads and Hi‐C data. Sponge gourd (Luffa cylindrica (L.) Roem.) or luffa is a diploid herbaceous plant with 26 chromosomes (2n = 26) and belongs to the family Cucurbitaceae.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |