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. 2024 Nov 5:9:645.
doi: 10.12688/wellcomeopenres.23291.1. eCollection 2024.

The genome sequence of the white-throated dipper, Cinclus cinclus (Linnaeus, 1758)

Stuart P Sharp  1 ; Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team; Wellcome Sanger Institute Scientific Operations: Sequencing Operations; Wellcome Sanger Institute Tree of Life Core Informatics team; Tree of Life Core Informatics collective; Darwin Tree of Life Consortium
Affiliations

The genome sequence of the white-throated dipper, Cinclus cinclus (Linnaeus, 1758)

Stuart P Sharp et al. Wellcome Open Res. .

Abstract

We present a genome assembly from a juvenile male Cinclus cinclus (the white-throated dipper; Chordata; Aves; Passeriformes; Cinclidae). The genome sequence has a total length of 1,170.80 megabases. Most of the assembly (93.88%) is scaffolded into 39 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.67 kilobases in length.

Keywords: Cinclus cinclus; Passeriformes; chromosomal; genome sequence; white-throated dipper.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.
Photographs of Cinclus cinclus by Stuart Sharp: a) Adult, b) 9-day-old nestling and c) Juvenile.
Figure 2.
Figure 2.. Genome assembly of Cinclus cinclus, bCinCin1.1: 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 1,170,855,695 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 (152,364,536 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (74,357,285 and 8,299,355 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 passeriformes_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_963662255.1/dataset/GCA_963662255.1/snail.
Figure 3.
Figure 3.. Genome assembly of Cinclus cinclus assembly bCinCin1.1: BlobToolKit GC-coverage plot showing sequence coverage (vertical axis) and GC content (horizontal axis).
The circles represent scaffolds, with the size proportional to scaffold length and the colour representing phylum membership. The histograms along the axes display the total length of sequences distributed across different levels of coverage and GC content. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_963662255.1/dataset/GCA_963662255.1/blob.
Figure 4.
Figure 4.. Genome assembly of Cinclus cinclus bCinCin1.1: BlobToolKit cumulative sequence plot.
The grey line shows cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_963662255.1/dataset/GCA_963662255.1/cumulative.
Figure 5.
Figure 5.. Genome assembly of Cinclus cinclus bCinCin1.1: Hi-C contact map of the bCinCin1.1 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=Oxsf2F9DQzWyNREabxewqA.
See this image and copyright information in PMC

References

    1. Abdennur N, Mirny LA: Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. 10.1093/bioinformatics/btz540 - DOI - PMC - PubMed
    1. Allio R, Schomaker-Bastos A, Romiguier J, et al. : MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20(4):892–905. 10.1111/1755-0998.13160 - DOI - PMC - PubMed
    1. Altschul SF, Gish W, Miller W, et al. : Basic Local Alignment Search Tool. J Mol Biol. 1990;215(3):403–410. 10.1016/S0022-2836(05)80360-2 - DOI - PubMed
    1. Bateman A, Martin MJ, Orchard S, et al. : UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2023;51(D1):D523–D531. 10.1093/nar/gkac1052 - DOI - PMC - PubMed
    1. Bates A, Clayton-Lucey I, Howard C: Sanger Tree of Life HMW DNA fragmentation: diagenode Megaruptor ®3 for LI PacBio. protocols.io. 2023. 10.17504/protocols.io.81wgbxzq3lpk/v1 - DOI

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