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. 2025 Sep 26;12(1):1563.
doi: 10.1038/s41597-025-05665-7.

Chromosome-level genome assembly of Bienertia sinuspersici, Single-cell-C4 plant

Kim Jung Sun  1 , Seung-Jae Lee  2 , Hoyoung Chung  3 , Inhwan Hwang  4 , Yoong-Jung Hwang  5 , Sung Yong Baek  2 , Sascha Offermann  6
Affiliations

Chromosome-level genome assembly of Bienertia sinuspersici, Single-cell-C4 plant

Kim Jung Sun et al. Sci Data. .

Abstract

Bienertia sinuspersici is a flowering plant currently classified under the family Amaranthaceae. It is an important C4 model plant with dimorphic chloroplast on single chlorenchyma cells. Subcellular-compartmentalization of peripheral compartment chloroplast (PCC) and central compartment chloroplast (CCC) in the single cell is utilized for carbon fixation in B. sinuspersici. The genome assembly and gene annotation were performed with PacBio long-read sequencing for contig-level assembly, barcoded linked reads for scaffolding and Hi-C sequencing technology to obtain high-quality of chromosome-level genome assembly. The final assembly analysis was resulted in a total of 7,031 scaffolds, a genome size of 3,608 Mbp and an N50 length of 360.8 Mbp. Nine scaffold that exceeded 100 Mbp were classified and confirmed as chromosome-level. The completeness of BUSCO rate was over 95%. A total gene set of 40,465 was annotated. This study provides a useful resource for the genomic analysis of B. sinuspersici as a Single Cell C4 plants.

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Conflict of interest statement

Competing interests: The authors declare no conflicts of interest.

Figures

Fig. 1
Fig. 1
Material and genome information of Bienertia sinuspersici. (a) Bienerta chlorenchyma cells were isolated and stained with Acridine orange (green nucleus). (b) Plant material management on this project. Several Bienerta seed are soiled and growing on the pot. Among them, Bienertia (R5-5) are selected (left). This plant performed vegetative cutting asexually into the magenta boxes. Multi-propagation of these plants by vegetative cutting asexually into the magenta boxes again several times. These cloned plants used the materials for genome sequencing as well as all experiments (right). (c) K-mer histogram was indicated K-mer species (blue) and K-mer individuals (red).
Fig. 2
Fig. 2
Genome assembly results of Bienertia sinuspersici. (a) Contact map. The Hi-C raw read pairs were aligned on the genome assembly sequences; the x and y axes indicate their positions; the red dots indicate the position of the read pairs, and a high density of red dots denotes that they are located on the same chromosome. (b) Overview of Bienertia sinuspersici genome assembly sequences. The features are arranged in chromosomes GC skew [a], GC contents [b], Copia density [c], Gypsy density [d], DNA element density [e] and gene density [f] at 1-Mbp intervals across the 9 chromosomes.
See this image and copyright information in PMC

References

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