Guang-Wan Hu

The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection.

Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

Cremastra malipoensis (Orchidaceae), a New Species from Yunnan, China

Abstract Cremastra malipoensis G. W. Hu, a new rare species of Orchidaceae, is described and illustrated, and a taxonomic key to the species of the genus is provided. It occurs in southeastern Yunnan, China, near the border of Vietnam. It is most similar to C. appendiculata, but its inflorescences have fewer flowers (only 4–7), its flowers are positioned horizontally and become slightly pendulous, the lateral lobes of the lip are geniculate and twisted 90° at the base, and the mid-lobe of the lip is somewhat reflexed, rhombic to broadly ovoid, and 9–10 × 8–9 mm. The new species is known only from a single population and categorized under the ICUN criteria as critically endangered. Formal recognition is required for protecting this species, which grows sympatrically with more common species that are harvested as medicinal herbs.

Development of microsatellite markers in Hagenia abyssinica (Bruce) J.F. Gmel, an endangered tropical tree of eastern Africa, using next-generation sequencing.

Hagenia abyssinica (Bruce) J.F. Gmel is an endangered tree species endemic to the high mountains of tropical Africa. We used Illumina paired-end technology to sequence its nuclear genome, aiming at creating the first genomic data library and developing the first set of genomic microsatellites. Seventeen microsatellite markers were validated in 24 individuals. The average number of alleles per locus was 7.6, while the observed and expected heterozygosities ranged from 0.000 to 0.958 and from 0.354 to 0.883, respectively. These polymorphic markers will be used as tools for further molecular studies to facilitate formulation of appropriate conservation strategies for this species.

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.

Lobelia hongiana (Campanulaceae), a new species from Guangxi, China

Abstract Lobelia hongiana, a new species of Campanulaceae from Guangxi, South China, is described and illustrated here. This new species is most similar to L. chinensis and L. loochooensis, but differs by its elliptic-obovate or oblanceolate leaf, 2.5–3 mm long greenish-carmine hypanthium, 5 or 6 calyx lobes, purplish-white corolla, with yellowish-green blotches at the base of lower lobes, glabrous filaments, 7–8 mm long broadly obconic capsule. Molecular phylogenetic analysis has been conducted based on ITS and two chloroplast sequences (atpB and rbcL) and 14 taxa in Lobelia are included. L. hongiana is well supported as a new species by the evidence from both morphology and molecular phylogeny.

Species richness and phylogenetic diversity of seed plants across vegetation zones of Mount Kenya, East Africa

Abstract Mount Kenya is of ecological importance in tropical east Africa due to the dramatic gradient in vegetation types that can be observed from low to high elevation zones. However, species richness and phylogenetic diversity of this mountain have not been well studied. Here, we surveyed distribution patterns for a total of 1,335 seed plants of this mountain and calculated species richness and phylogenetic diversity across seven vegetation zones. We also measured phylogenetic structure using the net relatedness index (NRI) and the nearest species index (NTI). Our results show that lower montane wet forest has the highest level of species richness, density, and phylogenetic diversity of woody plants, while lower montane dry forest has the highest level of species richness, density, and phylogenetic diversity in herbaceous plants. In total plants, NRI and NTI of four forest zones were smaller than three alpine zones. In woody plants, lower montane wet forest and upper montane forest have overdispersed phylogenetic structures. In herbaceous plants, NRI of Afro‐alpine zone and nival zone are smaller than those of bamboo zone, upper montane forest, and heath zone. We suggest that compared to open dry forest, humid forest has fewer herbaceous plants because of the closed canopy of woody plants. Woody plants may have climate‐dominated niches, whereas herbaceous plants may have edaphic and microhabitat‐dominated niches. We also proposed lower and upper montane forests with high species richness or overdispersed phylogenetic structures as the priority areas in conservation of Mount Kenya and other high mountains in the Eastern Afro‐montane biodiversity hotspot regions.

Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae)

Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively. The chloroplast genome was observed to contain 116 unique genes, of which 80 are protein-coding, 32 are transfer RNAs, and four are ribosomal RNAs. In addition, a total of 196 SSR markers were detected in the chloroplast genome of Streptocarpus teitensis with mononucleotides (57.1%) being the majority, followed by trinucleotides (33.2%) and dinucleotides and tetranucleotides (both 4.1%), and pentanucleotides being the least (1.5%). Genome alignment indicated that this genome was comparable to other sequenced members of order Lamiales. The phylogenetic analysis suggested that Streptocarpus teitensis is closely related to Lysionotus pauciflorus and Dorcoceras hygrometricum.

Components and Anti-HepG2 Activity Comparison of Lycopodium Alkaloids from Four Geographic Origins

Lycopodium japonicum Thunb. has attracted great interests due to its rich alkaloids with significant anticancer activity. However, significant chemical differences often exist in a plant species from different geographic origins and affect its quality and bioactivities. Thus, it is urgent to reveal their chemical and biological distinctions at the molecular level. In this context, a comparative chemical analysis of LAs using HPLC-UV-ESI-MS/MS was firstly conducted and resulted in the detection of 46 LAs, 28 of which were identified, and a series of unique LAs markers, such as peaks 2, 9, 10, and 11, were further found to be characteristic LAs and selected as markers from four different origins for their quality control. In parallel, the comparative bioactivity assay revealed that the total LAs from Hubei province exhibited much higher inhibitory rate at 65.95% against HepG2 cells than those at 26.72%, 20.26%, and 33.62% for Kenya, Guangxi province, and Zhejiang province in China, respectively. To this end, significant chemical fingerprinting differences and discrepancies in bioactivity of LAs were explored firstly, which could provide valuable information for quality control and further activity studies on LAs from different sources and promote their better pharmaceutical applications in the future as well.