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The genome sequence of a ground beetle, Harpalus rufipes (DeGeer, 1774)

Maxwell V L Barclay et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual male Harpalus rufipes (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence spans 890.50 megabases. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,884 protein-coding genes.

Keywords: Coleoptera; Harpalus rufipes; chromosomal; genome sequence; ground beetle.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Photograph of the Harpalus rufipes (icHarRufp1) specimen used for genome sequencing.
Figure 2.
Figure 2.. Genome assembly of Harpalus rufipes, icHarRufp1.1: metrics.
The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 890,553,490 bp assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (90,524,188 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (52,722,989 and 28,314,201 bp), respectively. The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the endopterygota_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icHarRufp1_1/dataset/icHarRufp1_1/snail.
Figure 3.
Figure 3.. Genome assembly of Harpalus rufipes, icHarRufp1.1: Distribution plot of base coverage in ERR10812855 against position for sequences in the assembly.
Windows of 100kb are coloured by phylum. The assembly has been filtered to exclude sequences with length < 2,550,000 An interactive version of this figure is available here.
Figure 4.
Figure 4.. Genome assembly of Harpalus rufipes icHarRufp1.1: BlobToolKit cumulative sequence plot.
The grey line shows cumulative length for all sequences. Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icHarRufp1_1/dataset/icHarRufp1_1/cumulative.
Figure 5.
Figure 5.. Genome assembly of Harpalus rufipes icHarRufp1.1: Hi-C contact map of the icHarRufp1.1 assembly, visualised using HiGlass.
Chromosomes are shown in order of size from left to right and top to bottom. An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=HwBjO53IRuCb4qV63cwCyg.
See this image and copyright information in PMC

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