Cordiaceae is a family comprising more than 400 species in the order Boraginales. The classification of this family has undergone changes over time, transitioning between family and subfamily status. In the present study, the complete chloroplast (cp) genomes of Cordia monoica and Cordia sinensis were sequenced, and their cp genomes were then characterized, analyzed, and compared to those of closely related taxa. The lengths of the cp genomes of C. monoica and C. sinensis were 151,813 bp and 152,050 bp, respectively. Both genomes consisted of 114 genes, divided into 4 ribosomal RNA genes, 30 transfer RNA genes, and 80 protein-coding genes. We observed a unique gene inversion in the trnM-rbcL region of both Cordia species. The long repeats analysis revealed that both species’ chloroplast genomes contained forward and palindromic repeats. The simple sequence repeats (SSRs) analysis detected 155 microsatellites in each genome, with the majority being mononucleotide repeats (A/T). Phylogenetic analysis based on maximum likelihood and Bayesian analyses confirmed two major clades in the order Boraginales: clade I comprised Boraginaceae, while clade II included Cordiaceae, Ehretiaceae, and Heliotropiaceae. This study expands our knowledge of the evolutionary relationships across the order Boraginales and offers useful genetic resources.

Ehretiaceae is a family in the order Boraginales. It contains more than 150 species. The Ehretiaceae classification has remained elusive and changed over time from subfamily to family, or vice versa. In this paper, we sequenced, characterized, and analyzed the complete chloroplast (cp) genomes of Ehretia cymosa and Ehretia obtusifolia, and their cp genomes were compared to those of related species. The length of the chloroplast genomes of E. cymosa was 156,328 bp, whereas that of E. obtusifolia was 155,961 bp. Each genome contained 114 genes, including 80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Repeat analysis revealed that complement, forward, palindromic, and reverse repeats were present in the chloroplast genomes of both species. Simple sequence repeat analysis showed that the chloroplast genomes of E. cymosa and E. obtusifolia comprise 141 and 139 microsatellites, respectively. Phylogenetic analysis based on Bayesian and maximum likelihood analyses divided the order Boraginales into two well-supported clades. The first clade includes a single family (Boraginaceae), and the second clade includes three families (Ehretiaceae, Cordiaceae, and Heliotropiaceae). This study provides valuable genomic resources and insights into the evolutionary relationships within Boraginales.

Background: Heliotropiaceae is a family of the order Boraginales and has over 450 species. The members of the family Heliotropiaceae have been widely reported to be used in traditional medicine Over time, the classification of Heliotropiaceae has remained uncertain and has moved from family to subfamily, or conversely. Results: In the present study, we sequenced, analyzed, and compared the complete plastomes of Euploca strigosa, Heliotropium arbainense, and Heliotropium longiflorum with the genomes of related taxa. The lengths of the plastomes of E. strigosa, H. arbainense, and H. longiflorum were 155,174 bp, 154,709 bp, and 154,496 bp, respectively. Each plastome consisted of 114 genes: 80 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The long repeats analysis indicated that reverse, palindromic, complement and forward repeats were all found in the three plastomes. The simple repeats analysis showed that the plastomes of E. strigosa, H. arbainense, and H. longiflorum contained 158, 165, and 151 microsatellites, respectively. The phylogenetic analysis confirmed two major clades in the Boraginales: clade I comprised Boraginaceae, while clade II included Heliotropiaceae, Ehretiaceae, Lennoaceae, and Cordiaceae. Inside the family Heliotropiaceae, E. strigosa is nested within the Heliotropium genus. Conclusions: This study expands our knowledge of the evolutionary relationships within Heliotropiaceae and offers useful genetic resources.

Background: Curcuma bakerii is a species of the family Zingiberaceae, endemic to Bangladesh. This genus of rhizomatous plants is widely distributed in tropical regions worldwide and is valued for its medicinal, aromatic, and culinary properties. Methods: The complete chloroplast (cp) genome of C. bakerii was reconstructed using high-throughput sequencing data. Subsequently, the genome was functionally annotated, assembled, and analyzed to clarify its evolutionary dynamics and structural organization. Results: The study’s findings indicate that the genome size is 162,189 base pairs (bp) and that it has a normal quadripartite structure with a large single-copy (LSC) region also comprises a small single-copy (SSC) region and two inverted repeats (IRa and IRb). The GC content of the genome was 36.18%, consisting of 135 genes: 88 protein-coding, 39 tRNA, and 8 rRNA. The codon usage analysis revealed 22 high-frequency and five optimal codons indicative of codon bias. Analysis of repetitive sequences revealed 213 Simple Sequence Repeats (SSRs), most of which were A/T. Additionally, seven mutation hotspots were reported, with 68.08% of single-nucleotide polymorphisms (SNPs) detected in the coding region and 31.91% in the noncoding region. Nonsynonymous substitutions accounted for 63.78%, while synonymous substitutions accounted for 36.11%. Conclusions: Based on this study, cp genome sequencing is a useful tool for understanding the intrageneric relationships among Curcuma species. The research presents a complete cp genome of C. bakerii from Bangladesh and provides a useful genomic resource for the molecular evolution, phylogeny, and genetic diversity study of the genus Curcuma.

Zingiber salarkhanii (Zingiberaceae family) is an endemic species of Bangladesh. It possesses biological effects, including analgesic, anxiolytic, cytotoxic, and antioxidant properties. Although genomic data on Zingiber is scarce, the entire chloroplast (cp) genome has been extensively used as a molecular marker to resolve phylogenetic issues. The genome size is 163,980 bp, and it has a standard quadripartite structure, with an average GC content of 36.91%. The genome contains 138 genes (113 unique), comprising 90 protein-coding genes, 79 unique genes, 48 noncoding genes (34 unique), 40 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). Codon usage analysis of the cp revealed 14 high-frequency codons besides 18 optimal codons in this species. A repetitive study revealed 211 simple sequence repeats (SSRs), predominantly A/T mononucleotide repeats. Sequence alignment indicated that variable regions were primarily located in the single-copy regions. Sequence comparison showed that most variable regions were located within the single-copy regions, and nucleotide diversity (π = 0–0.11289) indicated overall low divergence with 11 mutation hotspots. Phylogenetic investigations using both coding sequences and complete cp genomes indicated that Z. salarkhanii is most closely related to the Zingiber genus. Phylogenetic investigations using both coding genes and complete cp genomes placed Z. salarkhanii within the core Zingiber lineage, revealing its closest relationship to Z. recurvatum rather than to the genus. It conducted an extensive analysis of many cp genomic characteristics for phylogenetic significance, including overall genome architecture, codon usage bias, repetitive sequences, inverted repeat borders, and phylogenetic reconstruction. These findings provide a basis for further research to elucidate the molecular evolutionary dynamics of individual population variability within the species and genus. The plastome reported here also provides an essential genomic reference for future work on population variation and species differentiation within Zingiber.