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. 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.
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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. 17 Citations 4 Altmetric Part of the Methods in Molecular Biology book series (MIMB,volume 1861) Abstract Recent advances in next-generation sequencing (NGS) and chromosome conformation capture (3C) analysis have led to the development of Hi-C, a genome-wide version of the 3C method. To address this need, Juicebox.js can access hic files located at an arbitrary URL, downloading only the small portion of the file that is required to fulfill each user request. 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. Genome scaffolding with the Juicer, JuiceBox, 3D-DNA pipeline Here at the ISUGIF, we have used multiple different contig assemblers and had success with this pipeline. 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.
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cylindrica, and it demonstrated a high degree of conserved gene order in these three species. Hi-C Fruit Juice Box Orange Lavaburst - 10 CT 80 calories per box100 vitamin CMade with real fruit juice, UPC Code 025000013058 Manufactured by Coca-Cola.
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.
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We combined Hi‐C data with a draft genome assembly to generate chromosome‐length scaffolds. Each Hi-C drink box contains a full days supply of Vitamin C, is made with real fruit juice.
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. Several 3D genome browsers, including WashU Epigenome Browser (Zhou et al., 2013) and Juicebox (Durand et al., 2016), have been developed to visualize 3C-based. Sponge gourd (Luffa cylindrica (L.) Roem.) or luffa is a diploid herbaceous plant with 26 chromosomes (2n = 26) and belongs to the family Cucurbitaceae. Tools included in the comparison are Cooler /HiGlass, Juicer /Juicebox, HOMER, HiC-Pro, HiC-bench, TADbit, HiFive, HicDat, HiCInspector, HiCUP, HiCExplorer, and HiCeekR. Juicebox Web is an interactive contact map viewer app for. Table 1 Feature comparison of different Hi-C analysis tools.
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