Characterization of the complete chloroplast genome of Emmenopterys henryi (Gentianales: Rubiaceae), an endangered relict tree species endemic to China

Complete chloroplast genome sequence of the medicinal plant Oxyceros horridus (Rubiaceae) and phylogenetic analysis

Oxyceros horridus Lour. 1790, valued for ornamental and medicinal properties, has been extensively utilized in traditional medicinal in Vietnam. This study assembled and characterized the first chloroplast of Oxyceros horridus, consisted of 155,333 bp with a GC content of 37.5%. The genome included 130 annotated genes (including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes), exhibited a typical quadripartite structure consistent with those found in other members of the Rubiaceae family. Phylogenetic analysis placed O. horridus in Ixoroideae subfamily, closely related to Fosergia shweliensis and Gardenia tenophylla. This study enriches cp genome data and phylogenetic insights within Rubiaceae.

The complete chloroplast genome of Gardenia stenophylla Merr (Rubiaceae) and its phylogenetic analysis

Gardenia stenophylla Merr, a member of the genus Gardenia in the family Rubiaceae, possesses significant medicinal and ornamental value and is widely distributed in China. This study reports the newly sequenced chloroplast genome of Gardenia stenophylla Merr. The complete chloroplast genome of Gardenia stenophylla Merr (155,109 bp, GC content of 37.5%) was shown to have a typical quadripartite structure, containing a pair of inverted repeat regions (IRs) of 28,802 bp separated by a large single-copy (LSC) region of 85,396 bp and a small single-copy (SSC) region of 18,109 bp. The chloroplast genome contained 151 genes encoding 106 proteins, 37 tRNAs, and eight rRNAs. The Gardenia stenophylla Merr chloroplast genome displayed the closest phylogenetic relationship to Gardenia jasminoides and Gardenia jasminoides var. grandiflora. These data will assist in future molecular phylogenetics of the Rubiaceae.

The complete chloroplast genome sequence of Nostolachma jenkinsii (Hook.f.) Deb & J.Lahiri, an endangered coffeeae plant

Nostolachma jenkinsii (Hook.f.) Deb & J.Lahiri, a member of the Rubiaceae family, is an endangered wild plant species with potential economic value. In this research, the complete chloroplast genome of N. jenkinsii was sequenced to gain insight into its genome feature and better understand the phylogenetic relationships among the Rubiaceae species. The chloroplast genome, with a total length of 155,036 bp, comprises two inverted repeats (IR) regions spanning 25,692 bp each, a large single-copy (LSC) region measuring 85,437 bp, and a short single-copy (SSC) region measuring 18,215 bp. There is an overall 37% GC content in the chloroplast genome. By annotation analysis,. 54 tRNA genes, 10 rRNA genes, and 107 protein-coding genes were all annotated in N. jenkinsii. Furthermore, we applied phylogenetic analysis that revealed a close relationship between N. jenkinsii, D. fruticosa and D. dubia, placing them together within the Rubiaceae family.

The complete chloroplast genome of Mussaenda pubescens and phylogenetic analysis

The chloroplast (cp) genome sequence of Mussaenda pubescens, a promising resource that is used as a traditional medicine and drink, is important for understanding the phylogenetic relationships among the Mussaenda family and genetic improvement and reservation. This research represented the first comprehensive description of the morphological characteristics of M. pubescens, as well as an analysis of the complete cp genome and phylogenetic relationship. The results indicated a close relationship between M. pubescens and M. hirsutula based on the morphological characteristics of the flower and leaves. The cp was sequenced using the Illumina NovaSeq 6000 platform. The results indicated the cp genome of M. pubescens spanned a total length of 155,122 bp, including a pair of inverted repeats (IRA and IRB) with a length of 25,871 bp for each region, as well as a large single-copy (LSC) region and a small single-copy (SSC) region with lengths of 85,370 bp and 18,010 bp, respectively. The results of phylogenetic analyses demonstrated that species within the same genus displayed a tendency to group closely together. It was suggested that Antirhea, Cinchona, Mitragyna, Neolamarckia, and Uncaria might have experienced an early divergence. Furthermore, M. hirsutula showed a close genetic connection to M. pubescens, with the two species having partially overlapping distributions in China. This study presents crucial findings regarding the identification, evolution, and phylogenetic research on Mussaenda plants, specifically targeting M. pubescens.

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

Uncaria, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four Uncaria species mentioned in the Chinese Pharmacopoeia and Uncaria scandens (an easily confused counterfeit) were sequenced and annotated. The findings demonstrated that the whole chloroplast genome of Uncaria genus is 153,780–155,138 bp in full length, encoding a total of 128–131 genes, containing 83–86 protein-coding genes, eight rRNAs and 37 tRNAs. These regions, which include eleven highly variable loci and 31–49 SSRs, can be used to create significant molecular markers for the Uncaria genus. The phylogenetic tree was constructed according to protein-coding genes and the whole chloroplast genome sequences of five Uncaria species using four methods. The topology of the two phylogenetic trees showed no difference. The sequences of U. rhynchophylla and U. scandens are clustered in one group, while the U. hirsuta and U. macrophylla are clustered in another group. U. sessilifructus is clustered together with the above two small clades. New insights on the relationship were revealed via phylogenetic research in five Uncaria species. This study will provide a theoretical basis for identifying U. rhynchophylla and its counterfeits, as well as the species of the Uncaria genus. This research provides the initial chloroplast genome report of Uncaria, contributes to elucidating the chloroplast genome evolution of Uncaria in China.

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from the department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct libraries. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotides (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that C. spruceanum is a sister species to Emmenopterys henryi and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.

Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae

In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.

Analysis of Poncirus polyandra (Rutaceae) chloroplast genome and its phylogenetic implications

Poncirus polyandra is a threatened plant in China Now, the complete chloroplast (cp) genome of P. polyandra was assembled. The cp genome of P. polyandra was 160,212 bp in length, it consists of a pair of inverted repeats ((IRa and IRb) regions (27,016 bp) separated by the large single-copy (LSC, 87,407 bp) and small single-copy (SSC, 18,775 bp) regions. The cp genome encodes 105 unique genes, including 70 protein-coding genes, 30 transfer RNA genes, 4 ribosomal RNA genes, and 1 pseudogene. The phylogenetic tree of Rutaceae showed that P. polyandra was clustered together with genus Citrus and Poncirus.