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We present a genome assembly from an individual female Vanessa atalanta (the red admiral; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 370 megabases in span. The majority of the assembly (99.44%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. Gene annotation of this assembly o...
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... final assembly has a total length of 370 Mb in 142 sequence scaffolds with a scaffold N50 of 13 Mb (Table 1). Of the assembly sequence, 99.44% was assigned to 32 chromosomal-level scaffolds, representing 30 autosomes (numbered by sequence length), and the W and Z sex chromosome ( Figure 2- Figure 5; Table 2). ...Context 2
... ilVanAtal1.1 genome was annotated using the Ensembl annotation pipeline (Table 1; https://rapid.ensembl.org/Vanessa_ atalanta_GCA_905147765.1/). ...Context 3
... raw sequence data and the assembly have been deposited in INSDC databases. Raw data and assembly accession identifiers are reported in Table 1. ...Context 4
... final assembly has a total length of 370 Mb in 142 sequence scaffolds with a scaffold N50 of 13 Mb (Table 1). Of the assembly sequence, 99.44% was assigned to 32 chromosomal-level scaffolds, representing 30 autosomes (numbered by sequence length), and the W and Z sex chromosome ( Figure 2- Figure 5; Table 2). ...Context 5
... ilVanAtal1.1 genome was annotated using the Ensembl annotation pipeline (Table 1; https://rapid.ensembl.org/Vanessa_ atalanta_GCA_905147765.1/). ...Similar publications
We present a genome assembly from an individual male Caradrina kadenii (Clancy’s Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 426.0 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 ki...
We present a genome assembly from an individual female cranefly Tipula vernalis (Arthropoda; Insecta; Diptera; Tipulidae). The genome sequence has a total length of 1,272.30 megabases. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.01 kilobases in length. Gene annota...
We present a genome assembly from an individual female Othius punctulatus (a rove beetle; Arthropoda; Insecta; Coleoptera; Staphylinidae). The genome sequence is 870.5 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 20....
We present a genome assembly from an individual female Papilio machaon (the common yellow swallowtail; Arthropoda; Insecta; Lepidoptera; Papilionidae). The genome sequence is 252 megabases in span. The majority of the assembly (99.97%) is scaffolded into 31 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitocho...
We present a genome assembly from an individual male Rhingia rostrata (the Grey-backed Snout-hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 650.1 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and i...
Citations
... Outgroup data were taken from chromosome-resolved assemblies of other Nymphalid butterflies that were publicly available at the time of analysis: the Satyrini Pararge aegeria (80), Aphantopus hyperantus (81), and more distant outgroups Aglais urticae (82), Vanessa atalanta (83), and Vanessa cardui (84). To obtain single copy orthologs (SCOs) among all assemblies, each assembly including E. ligea was annotated with WebAugustus (85,86) in two steps: First, gene prediction was run using the standard Augustus species parameters for Heliconius melpomene. ...
The impact of large-scale chromosomal rearrangements, such as fusions and fissions, on speciation is a long-standing conundrum. We assessed whether bursts of change in chromosome numbers resulting from chromo-somal fusion or fission are related to increased speciation rates in Erebia, one of the most species-rich and karyotypically variable butterfly groups. We established a genome-based phylogeny and used state-dependent birth-death models to infer trajectories of karyotype evolution. We demonstrated that rates of anagenetic chro-mosomal changes (i.e., along phylogenetic branches) exceed cladogenetic changes (i.e., at speciation events), but, when cladogenetic changes occur, they are mostly associated with chromosomal fissions rather than fusions. We found that the relative importance of fusion and fission differs among Erebia clades of different ages and that especially in younger, more karyotypically diverse clades, speciation is more frequently associated with cladoge-netic chromosomal changes. Overall, our results imply that chromosomal fusions and fissions have contrasting macroevolutionary roles and that large-scale chromosomal rearrangements are associated with bursts of species diversification.
Larvae of caddisflies (Trichoptera) produce silk to build various underwater structures allowing them to exploit a wide range of aquatic environments. The silk adheres to various substrates underwater and has high tensile strength, extensibility, and toughness and is of interest as a model for biomimetic adhesives. As a step toward understanding how the properties of underwater silk evolved in Trichoptera, we used genomic data to identify full-length sequences and characterize the primary structure of the major silk protein, h-fibroin, across the order. The h-fibroins have conserved termini and basic motif structure with high variation in repeating modules and variation in the percentage of amino acids, mainly proline. This finding might be linked to differences in mechanical properties related to the different silk usage and sets a starting point for future studies to screen and correlate amino acid motifs and other sequence features with quantifiable silk properties.
Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble. Existing algorithms for identifying satellite repeats either require the complete assembly of satellites or only work for simple repeat structures without HORs. Here we describe Satellite Repeat Finder (SRF), a new algorithm for reconstructing satellite repeat units and HORs from accurate reads or assemblies without prior knowledge on repeat structures. Applying SRF to real sequence data, we showed that SRF could reconstruct known satellites in human and well-studied model organisms. We also found satellite repeats are pervasive in various other species, accounting for up to 12% of their genome contents but are often underrepresented in assemblies. With the rapid progress on genome sequencing, SRF will help the annotation of new genomes and the study of satellite DNA evolution even if such repeats are not fully assembled.
