A complete chloroplast genome of a traditional Chinese medicine herb, Rubia podantha, and phylogenomics of Rubiaceae.

Rubia podantha Diels is endemic to southwestern China and belongs to the family Rubiaceae. It is used in traditional Chinese medicines. To enrich the genetic data and resolve Rubiaceae's phylogeny, we assembled a complete chloroplast (cp) genome of R. podantha using Illumina HiSeq reads. The whole length of the cp genome was 154,866 bp. Annotation using PGA software found 113 genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. The large single-copy region was 84,717 bp, the inverted repeat B (IRa) region was 26,516 bp, the small single copy was 17,117 bp, and the inverted repeats B (IRb) region was 26,516 bp. Moreover, 64 SSRs were identified. Phylogenomic analysis using cp genomes of 109 Rubiaceae species found that R. podantha is closely related to R. cordifola. Rubiaceae was separated into three subfamilies: Ixoroideae, Cinchonoideae, and Rubiodeae. The genus Saprosma was not imbedded within the Spermacoceae alliance as reported in previous studies. Instead, it was imbedded within the Psychotrieae alliance. Divergence time estimation indicated that R. podantha split from its relative R. cordifolia around 1.25 million years ago. The assembled chloroplast genome in this study provided useful molecular information about the evolution of R. podantha and was a basis for phylogenetic analyses of Rubiaceae. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01302-y.

A complete chloroplast genome of Rubia yunnanensis Diels (Rubiaceae), a traditional Chinese herb endemic to China.

Rubia yunnanensis Diels 1912 (Rubiaceae) is a plant used in traditional Chinese medicine. We here assembled a complete chloroplast (cp) genome for R. yunnanensis using Illumina HiSeq reads. The genome is 155,108 bp in length. The genome contains 113 genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. The large single-copy (LSC) region is 84,848 bp, inverted repeat A (IRa) region is 26,573 bp, small single-copy (SSC) region is 17,114 bp, and inverted repeat B (IRb) region is 26,573 bp. A phylogenomic analysis found that R. yunnanensis is close to R. cordifolia. The assembled cp genome in this study provided a basis for the conservation and phylogenetic studies of R. yunnanensis.

Distribution pattern and habitat preference for Lobelia species (Campanulaceae) in five countries of East Africa.

East Africa is one of the centres of distribution and diversity for Lobelia L. (Campanulaceae, sub-family Lobelioideae). Lobelia habitats in East Africa have been facing habitat fragmentation and loss, which are recognised as a major threat to biodiversity. However, previous plant conservation studies in East Africa only focused on protected areas and ignored unprotected areas. Future conservation strategies of plants, such as Lobelia, will depend on knowledge of their distribution patterns and habitat preference in East Africa. To understand the distribution pattern and the habitat preference of Lobelia in five countries (Kenya, Uganda, Tanzania, Rwanda and Burundi) of East Africa, we conducted a literature review in the seven major vegetation regions (afro-alpine, afro-montane forest, drier savannah, grasslands, wetter savannah, Zambezian woodland and semi-desert and desert). We also employed meander and patterned searches, which allowed greater opportunities for recording Lobelia species. Our results showed that the genus is distributed in all of the seven regions of the five countries with 54 taxa. The afro-montane forest region, with 41 taxa, is the richest in species diversity, followed by the Zambezian woodland region with 18 taxa. The semi-desert and desert region has the lowest number with only four taxa. The afro-alpine region has 15 taxa, although the region is the smallest by area. The herbaceous type was found in all regions, while the giant type has a clear preference for the afro-alpine and afro-montane forest regions. Future conservation for Lobelia should consider its habitat preference by, for example, focusing on the afro-alpine and afro-montane forest regions. This study will facilitate the setting of future conservation strategies for Lobelia.

Genetic Adaptation of Giant Lobelias (Lobelia aberdarica and Lobelia telekii) to Different Altitudes in East African Mountains.

The giant lobelias in East African mountains are good models for studying molecular mechanisms of adaptation to different altitudes. In this study, we generated RNA-seq data of a middle-altitude species Lobelia aberdarica and a high-altitude species L. telekii, followed by selective pressure estimation of their orthologous genes. Our aim was to explore the important genes potentially involved in adaptation to different altitudes. About 9.3 Gb of clean nucleotides, 167,929-170,534 unigenes with total lengths of 159,762,099-171,138,936 bp for each of the two species were generated. OrthoMCL method identified 3,049 1:1 orthologous genes (each species was represented by one ortholog). Estimations of non-synonymous to synonymous rate were performed using an approximate method and a maximum likelihood method in PAML. Eighty-five orthologous genes were under positive selection. At least 8 of these genes are possibly involved in DNA repair, response to DNA damage and temperature stimulus, and regulation of gene expression, which hints on how giant lobelias adapt to high altitudinal environment that characterized by cold, low oxygen, and strong ultraviolet radiation. The negatively selected genes are over-represented in Gene Ontology terms of hydrolase, macromolecular complex assembly among others. This study sheds light on understanding the molecular mechanism of adaptation to different altitudes, and provides genomic resources for further studies of giant lobelias.