Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jul 25:8:321.
doi: 10.12688/wellcomeopenres.19628.1. eCollection 2023.

The genome sequence of the tree of heaven, Ailanthus altissima (Mill.) Swingle, 1916

Rowan J Schley  1 , Ilia J Leitch  2 , Maarten J M Christenhusz  2 ; Royal Botanic Gardens Kew Genome Acquisition Lab; Darwin Tree of Life Barcoding collective; Plant Genome Sizing collective; Wellcome Sanger Institute Tree of Life programme; Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective; Tree of Life Core Informatics collective; Darwin Tree of Life Consortium
Affiliations

The genome sequence of the tree of heaven, Ailanthus altissima (Mill.) Swingle, 1916

Rowan J Schley et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual Ailanthus altissima (tree of heaven; Streptophyta; Magnoliopsida; Sapindales; Simaroubaceae). The genome sequence is 939 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies are 661.1 kilobases and 161.1 kilobases long, respectively.

Keywords: Ailanthus altissima; Simaroubaceae; chromosomal; genome sequence; tree of heaven.

PubMed Disclaimer

Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Ailanthus altissima (not the sampled specimen).
a) mature tree; b) young sapling, and c) new leaves in Nottinghamshire (photographs © Carlton Roberts); d) A. altissima fruits (photograph © Nicholas A. Tonelli).
Figure 2.
Figure 2.. Genome assembly of Ailanthus altissima, drAilAlti1.1: metrics.
The BlobToolKit Snailplot 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 939,218,608 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 (38,427,504 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (29,421,908 and 24,184,688 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/CAMPEX01/dataset/CAMPEX01/snail.
Figure 3.
Figure 3.. Genome assembly of Ailanthus altissima, drAilAlti1.1: GC coverage.
BlobToolKit GC-coverage plot. Chromosomes are coloured by phylum. Circles are sized in proportion to chromosome length. Histograms show the distribution of chromosome length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAMPEX01/dataset/CAMPEX01/blob.
Figure 4.
Figure 4.. Genome assembly of Ailanthus altissima, drAilAlti1.1: cumulative sequence.
BlobToolKit cumulative sequence plot. The grey line shows cumulative length for all chromosomes. Coloured lines show cumulative lengths of chromosomes assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAMPEX01/dataset/CAMPEX01/cumulative.
Figure 5.
Figure 5.. Genome assembly of Ailanthus altissima, drAilAlti1.1: Hi-C contact map.
Hi-C contact map of the drAilAlti1.1 assembly, visualised using HiGlass. Chromosomes are given in order of size from left to right and top to bottom. An interactive version of this figure is available at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=XyRKDNDOTHy19SzkZkKRWw.
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. Challis R, Richards E, Rajan J, et al. : BlobToolKit – interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g3.119.400908 - DOI - PMC - PubMed
    1. Cheng H, Concepcion GT, Feng X, et al. : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18(2):170–175. 10.1038/s41592-020-01056-5 - DOI - PMC - PubMed
    1. Chow W, Brugger K, Caccamo M, et al. : gEVAL – a web-based browser for evaluating genome assemblies. Bioinformatics. 2016;32(16):2508–2510. 10.1093/bioinformatics/btw159 - DOI - PMC - PubMed
    1. Dallas JF, Leitch M, Hulme PE: Microsatellites for tree of heaven ( Ailanthus altissima). Mol Ecol Notes. 2005;5(2):340–342. 10.1111/j.1471-8286.2005.00920.x - DOI

LinkOut - more resources