Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

Abstract

Abstract Background Justicia is the largest genus in Acanthaceae and widely distributed in Asia, Africa, Australia and South America. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp) genomes of twelve Asian plants and combined with the previously published cp genome of J. leptostachya for further comparative genomics and phylogenetic analyses.Results All the cp genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739 bp, including a large single copy (LSC, 81,434–83,676 bp), a small single copy (SSC, 16,833–17,507 bp) and two inverted repeats (IR, 24,947–25,549 bp). GC contents range from 38.1–38.4%. All the plastomes contain 114 genes, containing 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for Justicia phylogeny. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with morphology evolution of inflorescence position from terminal to axillary and spikes gradually shorten into cymes.Conclusion Our study not only elucidates basic features of Justicia whole plastomes, but also first sheds light on interspecific relationships of Asian Justicia plants.