Comparative chloroplast genomics of Hibiscus (Hibisceae, Malvoideae, Malvaceae) and its phylogenetic implications
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Hibiscus L. (Hibisceae, Malvoideae, Malvaceae) is a globally distributed genus valued for its ornamental and medicinal significance, yet its taxonomy remains complex. Here, we de novo assembled the complete chloroplast (cp) genomes of 16 Hibiscus species and compared them with 13 published genomes. These genomes ranged from 159,125 to 163,360 base pairs and exhibited a conserved quadripartite structure, encoding 112 unique genes (78 protein-coding genes, 30 transfer RNAs, and 4 ribosomal RNAs). While codon usage, amino acid frequency, substitution patterns, and inverted repeats contraction and expansion revealed high similarity, the number of simple sequence repeats (SSRs) varied among species. Comparative analyses identified five highly polymorphic non-coding loci ( trnH-psbA , ndhF-rpl32 , rps19-rpl22 , trnR-atpA , and ndhD-ccsA ) and six coding loci ( rpl22 , ycf1 , matK , rpl32 , rbcL , and ndhF ) as suitable for DNA barcoding and phylogenetic studies. Phylogenomic analyses based on the cp genome confirmed the polyphyly of Hibiscus , with Urena Dill. ex L., Malvaviscus Fabr., Kosteletzkya C. Presl, and Kydia Roxb. nested within it. Three major clades were recovered (/Phylloglandula, /Trionum, /Euhibiscus). Hibiscus volkensii Gürke showed a long branch, suggesting a distinct evolutionary trajectory. Thepparatia scandens (Roxb. ex G.Don) Phuph. was resolved as sister to Hibiscus verdcourtii Craven. Incongruences were observed between the cp genome phylogeny and recent sectional classifications, based on phylogenetic analysis of a few cp markers, particularly for sections Hibiscus , Bombicella , and Lilibiscus . Overall, this study provides new insights into the cp genome evolution of Hibiscus and its implications for the phylogeny of this genus. However, these incongruences underscore the need for nuclear genomic data to clarify the taxonomy of this complex genus and other genera within the tribe Hibisceae.
