Bougainvillea (Nyctaginaceae) is a popular ornamental plant group primarily grown for its striking colorful bracts. However, despite its established horticultural value, limited genomic resources and molecular studies have been reported for this genus. Thus, to address this existing gap, complete chloroplast genomes of four species (Bougainvillea glabra, Bougainvillea peruviana, Bougainvillea pachyphylla, Bougainvillea praecox) and one Bougainvillea cultivar were sequenced and characterized. The Bougainvillea cp genomes range from 153,966 bp to 154,541 bp in length, comprising a large single-copy region (85,159 bp–85,708 bp) and a small single-copy region (18,014 bp–18,078 bp) separated by a pair of inverted repeats (25,377–25,427 bp). All sequenced plastomes have 131 annotated genes, including 86 protein-coding, eight rRNA, and 37 tRNA genes. These five newly sequenced Bougainvillea cp genomes were compared to the Bougainvillea spectabilis cp genome deposited in GeBank. The results showed that all cp genomes have highly similar structures, contents, and organization. They all exhibit quadripartite structures and all have the same numbers of genes and introns. Codon usage, RNA editing sites, and repeat analyses also revealed highly similar results for the six cp genomes. The amino acid leucine has the highest proportion and almost all favored synonymous codons have either an A or U ending. Likewise, out of the 42 predicted RNA sites, most conversions were from serine (S) to leucine (L). The majority of the simple sequence repeats detected were A/T mononucleotides, making the cp genomes A/T-rich. The contractions and expansions of the IR boundaries were very minimal as well, hence contributing very little to the differences in genome size. In addition, sequence variation analyses showed that Bougainvillea cp genomes share nearly identical genomic profiles though several potential barcodes, such as ycf1, ndhF, and rpoA were identified. Higher variation was observed in both B. peruviana and B. pachyphylla cp sequences based on SNPs and indels analysis. Phylogenetic reconstructions further showed that these two species appear to be the basal taxa of Bougainvillea. The rarely cultivated and wild species of Bougainvillea (B. pachyphylla, B. peruviana, B. praecox) diverged earlier than the commonly cultivated species and cultivar (B. spectabilis, B. glabra, B. cv.). Overall, the results of this study provide additional genetic resources that can aid in further phylogenetic and evolutionary studies in Bougainvillea. Moreover, genetic information from this study is potentially useful in identifying Bougainvillea species and cultivars, which is essential for both taxonomic and plant breeding studies.

Bougainvillea Comm. ex Juss. is one of the renowned genera in the Nyctaginaceae, but despite its recognized horticultural value, the taxonomy and phylogeny of the genus is not well-studied. Phylogenetic reconstructions based on plastid genomes showed that B. pachyphylla and B. peruviana are basal taxa, while B. spinosa is sister to two distinct clades: the predominantly cultivated Bougainvillea clade (B. spectabilis, B. glabra, B. arborea, B. cultivar, B. praecox) and the clade containing wild species of Bougainvillea (B. berberidifolia, B. campanulata, B. infesta, B. modesta, B. luteoalba, B. stipitata, and B. stipitata var. grisebachiana). Early divergence of B. peruviana, B. pachyphylla and B. spinosa is highly supported, thus the previously proposed division of Bougainvillea into two subgenera (Bougainvillea and Tricycla) was not reflected in this study. Morphological analysis also revealed that leaf arrangement, size, and indumentum together with the perianth tube and anthocarp shape and indumentum are important characteristics in differentiating the species of Bougainvillea. In the present study, 11 species and one variety are recognized in Bougainvillea. Six names are newly reduced to synonymy, and lectotypes are designated for 27 names. In addition, a revised identification key and illustrations of the distinguishing parts are also provided in the paper.

Nepeta hemsleyana Oliver ex Prain (1891) is one of the aromatic Tibetan herbs used to treat convulsions. In this study, the complete chloroplast genome of N. hemsleyana was analyzed and is presented here for the first time. The assembled genome, 152,171 bp in length, contained a large single-copy region (82,214 bp) and a small single-copy region (17,605 bp) separated by a pair of inverted repeats (25,676 bp). A total of 131 genes were identified, including 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. The phylogenetic analysis also confirmed the early divergence of N. hemsleyana from other species in subtribe Nepetinae.

Gynochthodes cochinchinensis previously known as Morinda cochinchinensis is considered as potential medicinal plant in family Rubiaceae. In this paper, the complete chloroplast genome of G. cochinchinensis was sequenced and characterized for the first time. The cp genome of G. cochinchinensis was 153,022 bp in length containing a large single copy region (83,799 bp), a small single copy region (17,591 bp), and a pair of inverted repeat regions (25,816 bp). It has a total of 131 genes, comprising of 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Phylogenetic analysis revealed that Gynochthodes cochinchinensis together with Gynochthodes officinalis were closely related to genus Morinda.

Phlomoides rotata (Benth. ex Hook.f.) Mathiesen is a perennial herb endemic to Qinghai-Tibet Plateau with important medicinal properties. Here, we sequenced and analyzed the complete chloroplast (cp) genome of P. rotata and reconstructed the phylogeny of P. rotata based on 24 cp genomes. The genome of P. rotata is 151,825 bp in length, including a large single-copy (LSC) region of 83,129 bp and a small single-copy (SSC) region of 17,398 bp. A total of 131 genes were identified, of which 86 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Phylogenetic analyses revealed that the species P. rotata is closely related to Phlomoides alpina with bootstrap support (BS) values of 100%. Overall, the genomic resources presented in this study will be beneficial for further studies on evolutionary patterns of P. rotata and its closely related species.

Psychotria pendens from the lowland ultramafic forest of Mt. Victoria, Palawan Island, Philippines is herein described as a new species of Rubiaceae. The new species is morphologically similar to P. rubiginosa (Gitingensis species group) by having monochotomous inflorescence and oblanceolate to oblong-elliptic leaves but is distinguished by its large, leaf-like, valvate stipules with biattenuate to biacuminate tips, pendent inflorescence, glabrous abaxial leaf surface, narrowly triangular bracts, and glabrous calyx. Molecular analysis revealed that this newly discovered species belongs to the Pacific Psychotria clade, and is allied to the Philippine species P. luzoniensis and Hawaiian species P. mariniana. The species is assessed as Critically Endangered (CR) based on the IUCN Red List categories and criteria.