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. 2025 May 27;25(1):710.
doi: 10.1186/s12870-025-06711-7.

Conserved genome structure and phylogenetic insights for the heterogeneous subfamily of Convallarioideae (Asparagaceae) revealed from plastome data

Shao-De Wu  1 , Ran Meng  1 , Ze-Long Nie  1 , Ming-Yang Song  1 , Xing-Ru Chen  1 , Jun Wen  2 , Ying Meng  3
Affiliations

Conserved genome structure and phylogenetic insights for the heterogeneous subfamily of Convallarioideae (Asparagaceae) revealed from plastome data

Shao-De Wu et al. BMC Plant Biol. .

Abstract

Background: Convallarioideae, a subfamily of Asparagaceae, encompasses a wide range of morphologically diverse lineages previously classified under different traditional families and holds significant economic value. Despite its importance, chloroplast genome data for Convallarioideae remain limited, hindering a comprehensive understanding of their genome structural evolution and phylogenetic relationships. This study aims to provide a detailed characterization of chloroplast genome features and to conduct robust phylogenetic analyses of this subfamily using an expanded dataset of chloroplast genomes.

Results: The plastomes of the subfamily exhibit a typical circular quadripartite structure with conserved genomic organization and gene content. However, variations were observed in genome size, SSRs, and codon usage across the subfamily. Nine highly variable regions and positive selection genes were identified. Phylogenetic analyses based on complete plastid genomes resolved the non-monophyly of Polygonateae. Compared to Eriospermum mackenii, the chloroplast genomes of tribe Rusceae, tribe Dracaeneae, and the Polygonatum-Disporopsis lineage showed significant size reduction.

Conclusions: Chloroplast genomes across Convallarioideae exhibit remarkable structural conservation. The phylogenetic analyses revealed weakly resolved backbone relationships among core members of this subfamily. Indels in the LSC region and gene loss were identified as key drivers of structural divergence in plastome size. These results clarify the interplay between genomic architecture and phylogenetic discordance, advancing our understanding of genomic evolution within Convallarioideae.

Keywords: Convallarioideae; Genomic evolution; Phylogenetic; Plastid genomes.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: Experimental research and field studies on plants complies with relevant institutional, national, and international guidelines and legislation. All plant species are not rare species for protection. We have the permission to collect the plant samples by the local government. Our work reported here complies with the IUCN Policy Statement on Research Involving Species at Risk of Extinction. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Comparative analysis of gene order and junction sites of the 34 plastomes from Convallarioideae, showing connection sites of LSC, IRb, SSC, and IRa. The T bars above or below the genes indicate the extent of their parts with their corresponding values in the base pair. The plotted genes and distances in the vicinity of the junction sites are the scaled projection of the genome. JLB (IRb/LSC), JSB (IRb/SSC), JSA (SSC/IRa), and JLA (IRa/ LSC) represent the junction sites between two adjacent regions in the genome
Fig. 2
Fig. 2
Length variation of chloroplast genomes (A), insertions (B), and deletions (C) of the Convallarioideae taxa compared with Eriospermum mackenii
Fig. 3
Fig. 3
Nucleotide diversity (Pi) values of different regions of 34 plastomes. A Pi values of PCG regions; B Pi values of non-coding regions
Fig. 4
Fig. 4
Pairwise Ka/Ks ratios of 34 species from subfamily Convallarioideae in different genes with Eriospermum mackenii as a reference. The color closer to green represents the gene has a higher Ka/Ks ratio
Fig. 5
Fig. 5
Phylogenetic trees of Convallarioideae using the Bayesian inference method based on CGS (A) and PCG data (B). Numbers above branches indicate posterior probability (PP)
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References

    1. Chase MW, Reveal JL, Fay MF. A subfamilial classification for the expanded asparagalean families Amaryllidaceae, Asparagaceae and Xanthorrhoeaceae. Bot J Linn Soc. 2009;161(2):132–6.
    1. Tanaka N, Nguyen KS. Nolinoideae (Asparagaceae) in APG III needs replacing with Convallarioideae. Phytotaxa. 2023;583(3):297–9.
    1. Ji Y, Landis JB, Yang J, Wang S, Zhou N, Luo Y, Liu H. Phylogeny and evolution of Asparagaceae subfamily Nolinoideae: new insights from plastid phylogenomics. Ann Bot. 2023;131(2):301–12. - PMC - PubMed
    1. Group TAP, Chase MW, Christenhusz MJM, Fay MF, Byng JW, Judd WS, Soltis DE, Mabberley DJ, Sennikov AN, Soltis PS, et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc. 2016;181(1):1–20.
    1. Yamashita J, Tamura MN. Molecular phylogeny of the Convallariaceae (Asparagales). In: Wilson KL, DA M, editors. Monocots: systematics and evolution. Melbourne: CSIRO Publishing; 2000. p. 387–400.

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