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. 2024 Apr 24:9:229.
doi: 10.12688/wellcomeopenres.21191.1. eCollection 2024.

The genome sequence of lesser trefoil or Irish shamrock, Trifolium dubium Sibth. (Fabaceae)

Markus Ruhsam  1 , Peter M Hollingsworth  1 , Ann M Mc Cartney  2 , Katie E Herron  3 , Graham M Hughes  3 , Maarten J M Christenhusz  4   5 , Michael F Fay  4 , Ilia J Leitch  4 ; Royal Botanic Garden Edinburgh 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 lesser trefoil or Irish shamrock, Trifolium dubium Sibth. (Fabaceae)

Markus Ruhsam et al. Wellcome Open Res. .

Abstract
in English, Irish

We present a genome assembly from an individual Trifolium dubium (lesser trefoil; Tracheophyta; Magnoliopsida; Fabales; Fabaceae) as part of a collaboration between the Darwin Tree of Life and the European Reference Genome Atlas. The genome sequence is 679.1 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The two mitochondrial genomes have lengths of 133.86 kb and 182.32 kb, and the plastid genome assembly has a length of 126.22 kilobases.

Cuirimid i láthair geanóm tionól ó an dhuine aonair seamróg na hÉireann mar chuid de a comhoibriú idir an Darwin Crann na Beatha agus an Atlas Géanóm Tagartha na hEorpa. Is an geanóm sheicheamhú 679.1megabases fad. An chuid is mó den tionól scafall isteach 15 crómasómach pseudomolecules. Ta an dhá mitochondrial geanóm tá faid de 133.86 kb agus 182.32 kb, agus an plastid geanóm tionól tá fad de 126.22 kb.

Keywords: Fabales; Trifolium dubium; chromosomal; genome sequence; lesser trefoil.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.
Photographs of Trifolium dubium ( a and b are representative images for the species, but not the specimen pr population used for genome sequencing, c is a representative plant from the population that was used for genome sequencing). a) https://commons.wikimedia.org/wiki/User:Rasbak b) https://commons.wikimedia.org/wiki/User:Kenraiz c) Markus Ruhsam.
Figure 2.
Figure 2.. Genome assembly of Trifolium dubium, drTriDubi3.1: 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 679,499,717 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 (64,644,275 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (46,006,535 and 34,190,264 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 fabales_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/drTriDubi3_1/dataset/drTriDubi3_1/snail.
Figure 3.
Figure 3.. Genome assembly of Trifolium dubium, drTriDubi3.1: BlobToolKit GC-coverage plot.
Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/drTriDubi3_1/dataset/drTriDubi3_1/blob.
Figure 4.
Figure 4.. Genome assembly of Trifolium dubium, drTriDubi3.1: 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/drTriDubi3_1/dataset/drTriDubi3_1/cumulative.
Figure 5.
Figure 5.. Genome assembly of Trifolium dubium, drTriDubi3.1: Hi-C contact map of the drTriDubi3.1 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=F0MkUMXRRMqAc9HJXoQ8LA.
See this image and copyright information in PMC

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