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. 2024 Oct 15:9:508.
doi: 10.12688/wellcomeopenres.23015.2. eCollection 2024.

The genome sequence of fat-hen, Chenopodium album L

Sahr Mian  1 , Maarten J M Christenhusz  1   2 ; Royal Botanic Gardens Kew Genome Acquisition Lab; Plant Genome Sizing collective; Darwin Tree of Life Barcoding collective; 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 fat-hen, Chenopodium album L

Sahr Mian et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual Chenopodium album (fat-hen; Streptophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence has a total length of 1,593.80 megabases. Most of the assembly (99.61%) is scaffolded into 27 chromosomal pseudomolecules suggesting the individual is an allohexaploid (2 n = 6 x = 54). The mitochondrial and plastid genome assemblies have lengths of 312.95 kilobases and 152.06 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 50,077 protein-coding genes.

Keywords: Caryophyllales; Chenopodium album; chromosomal; fat-hen; genome sequence.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Photograph of the Chenopodium album (dcCheAlbu1) specimen used for genome sequencing.
Figure 2.
Figure 2.. Genome assembly of Chenopodium album, dcCheAlbu1.1: 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 1,594,308,297 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 (91,301,842 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (60,299,674 and 39,868,957 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 eudicots_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAOKFF01/dataset/CAOKFF01/snail.
Figure 3.
Figure 3.. Genome assembly of Chenopodium album, dcCheAlbu1.1: Distribution plot of base coverage in ERR10677843 against position for sequences along each of the 27 assembled chromosomes in the assembly CAOKFF01.
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 Chenopodium album, dcCheAlbu1.1: 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/CAOKFF01/dataset/CAOKFF01/cumulative.
Figure 5.
Figure 5.. Genome assembly of Chenopodium album, dcCheAlbu1.1: Hi-C contact map of the dcCheAlbu1.1 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=QH1Co6i1RL6k53dsnNEL-A.
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. Oxford University Press,2020;36(1):311–316. 10.1093/bioinformatics/btz540 - DOI - PMC - PubMed
    1. Aken BL, Ayling S, Barrell D, et al. : The ensembl gene annotation system. Database (Oxford). 2016;2016: baw093. 10.1093/database/baw093 - DOI - PMC - PubMed
    1. Alanko T, Oinonen M, Schulman L: Plant remains from the early modern garden of the manor of Kumpula, Helsinki, Finland: an alternative sampling method for macrofossil analysis. Veget Hist Archaeobot. 2015;24:571–585. 10.1007/s00334-015-0517-z - DOI
    1. Amjad L, Shafighi M: The effect of air pollution on Chenopodium album L. pollen structure. J Agric Sci Technol. 2012;2(1A):143–148. Reference Source
    1. Bajwa AA, Zulfiqar U, Sadia S, et al. : A global perspective on the biology, impact and management of Chenopodium album and Chenopodium murale: two troublesome agricultural and environmental weeds. Environ Sci Pollut Res Int. 2019;26(6):5357–5371. 10.1007/s11356-018-04104-y - DOI - PubMed

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