Chloroplast genomes reveal two major lineages in the plant genus Abutilon

Researchers have sequenced and assembled chloroplast genomes for a global sample of Abutilon, a genus of roughly 178 species in the mallow family that includes ornamental, economic, and medicinal plants. The study, published in BMC Plant Biology, combined newly sequenced herbarium specimens with publicly available raw data to build a genomic framework for a group whose taxonomic classification has long proved difficult.

Three previously reported chloroplast genomes were also incorporated, giving a total of nineteen genomes for analyses of genome structure, polymorphic loci, and phylogenetic relationships.

The assembled chloroplast genomes ranged from 159,458 to 160,454 base pairs in length and showed the typical quadripartite structure characteristic of chloroplast genomes. Each genome contained 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with conserved gene content and organisation across species.

Despite this overall conservation, the genomes were not identical. They showed high similarity in GC content, inverted repeat boundaries, relative synonymous codon usage, amino acid frequencies, and substitution patterns, but the total number of simple sequence repeats varied notably, from 70 to 97 per genome.

Selection analyses indicated predominant purifying selection across the chloroplast genes. However, the analysis also detected evidence of episodic positive selection in three genes: rpoC2, rbcL, and ycf1. Two codons in rbcL were found to be clade-specific, providing phylogenetic signal that distinguishes Australian species from Old World pantropical species.

Searching for regions useful for species identification, the researchers analysed nucleotide diversity across the genomes and identified six highly polymorphic intergenic spacers: trnH-psbA, rps19-rpl2, psbT-pbf1, psaC-ndhD, trnR-atpA, and ndhJ-ndhK. The authors suggest these loci may be suitable for taxonomic studies within the genus.

Phylogenetic analyses using both maximum likelihood and Bayesian inference resolved two major clades within Abutilon. One clade comprises an exclusively Australian lineage, occurring predominantly in arid and semi-arid environments, while the other is a pantropical lineage spanning multiple continents.

The analyses also recovered Abutilon grandifolium as sister to the remaining sampled Abutilon taxa in both the maximum likelihood and Bayesian trees. The authors caution, however, that no biogeographic origin can be inferred from this placement, pending broader taxon sampling and the integration of nuclear genomic data.

Overall, the study documents the evolutionary dynamics of the chloroplast genome in Abutilon and offers a foundational genomic framework for refining the taxonomy of the genus. In this study, the authors sequenced six species from herbarium specimens and assembled the chloroplast genomes of ten additional species from publicly available raw data.

Subject of Research: Chloroplast genome evolution and phylogeny of the plant genus Abutilon

Article Title: Evolutionary dynamics of the chloroplast genome in Abutilon (Malvoideae, Malvaceae)

Article References: Abdullah, Yan, R., Sammad, A., Vallada, A., & Tian, X. (2026). Evolutionary dynamics of the chloroplast genome in Abutilon (Malvoideae, Malvaceae). BMC Plant Biology, 26(1), Article 1557. https://doi.org/10.1186/s12870-026-09885-w

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09885-w

Keywords: Abutilon, chloroplast genome, Malvaceae, phylogenetics, herbarium specimens, simple sequence repeats, purifying selection, nucleotide diversity, biogeography, taxonomy, BMC Plant Biology, Evolutionary