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. 2024 Oct 7:9:570.
doi: 10.12688/wellcomeopenres.23137.1. eCollection 2024.

The genome sequence of the common alder, Alnus glutinosa (L.) Gaertn. (Betulaceae)

Maarten J M Christenhusz  1 , Zoë Goodwin  2 , David G Bell  2 , Claudia A Martin  2   3 ; Royal Botanic Gardens Kew Genome Acquisition Lab; Royal Botanic Garden Edinburgh Genome Acquisition Lab; Darwin Tree of Life Barcoding collective; Plant Genome Sizing 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 the common alder, Alnus glutinosa (L.) Gaertn. (Betulaceae)

Maarten J M Christenhusz et al. Wellcome Open Res. .

Abstract

We present a genome assembly of a diploid specimen of Alnus glutinosa (the common alder; Streptophyta; Magnoliopsida; Fagales; Betulaceae). The genome sequence has a total length of 456.80 megabases. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome assemblies have lengths of 505.23 and 155.85 kilobases and the plastid genome is 160.82 kilobases long. Gene annotation of this assembly on Ensembl identified 23,728 protein-coding genes.

Keywords: Alnus glutinosa; Fagales; chromosomal; common alder; genome sequence.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Photographs of the Alnus glutinosa (dhAlnGlut1) specimen used for genome sequencing.
a) Habitat along River Thames in Canbury Gardens. b) leaves. c) female fruits (white arrows) and young male catkins (blue arrows).
Figure 2.
Figure 2.. Genome assembly of Alnus glutinosa, dhAlnGlut1.1: 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 457,583,206 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 (53,352,176 bp, shown in red). . Orange and pale-orange arcs show the N50 and N90 scaffold lengths (30,513,540 and 25,901,623 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/dhAlnGlut1_1/dataset/dhAlnGlut1_1/snail.
Figure 3.
Figure 3.. Genome assembly of Alnus glutinosa, dhAlnGlut1.1: Blob plot of base coverage against GC proportion for sequences in the assembly.
Sequences are coloured by phylum. Circles are sized in proportion to sequence length. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/dhAlnGlut1_1/dataset/dhAlnGlut1_1/blob.
Figure 4.
Figure 4.. Genome assembly of Alnus glutinosa dhAlnGlut1.1: 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/dhAlnGlut1_1/dataset/dhAlnGlut1_1/cumulative.
Figure 5.
Figure 5.. Genome assembly of Alnus glutinosa, dhAlnGlut1.1: Hi-C contact map of the dhAlnGlut1.1 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=ewauaBn_S4-EMrvmkdS1-g.
See this image and copyright information in PMC

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