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

Abstract

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.

Complete chloroplast genome sequences of the ornamental plant Prunus Cistena and comparative and phylogenetic analyses with its closely related species

“…2). Similar to the previous results for other study, most of the codons ending with A or T have RSCU values greater than 1, while, most of those ending with C or G have RSCU values of less than 1 [21][22][23].…”

Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily

“…Thus, we can assure that the difference among their chloroplast genomes is in their intergenic regions. However, for other Uncaria species, it has been previously reported a variation in the number of genes, with U. scandens presenting the lowest number of genes (128) within the genus so far 41 . From the comparative analysis among the species of this subfamily, we found an evolutionary conservation of these genomes’ quadripartite structure: a LSC, a SSC and two IRs regions.…”

“…Closely related species tend to have similar genomic characteristics and the difference in the size of the LSC, SSC and IR regions among the species can only explain 20% of the variation on cpDNA size 44 , 45 . Within Cinchonoideae, U. tomentosa was the species with the longest cpDNA sequence, 156,390 bp, even when compared to other asian Uncaria species 41 , while U. rhynchophylla showed the shortest, 154,605 bp, but U. scandens has the shortest cpDNA for the genus so far (153,780 bp)41 . We found that the difference in genome size can be related to non-coding sequences.…”

“…On GenBank, an NCBII database, there have been deposited 4650 chloroplast genomes of terrestrial plants. For the Uncaria genus, up to date, there are only five species with complete cpDNA deposited on NCBI, U. rhynchophylla 40, U. hirsuta , U. machrophylla , U. scandens and U. sessilifructus all occurring in Asian regions and so far no species occurring in America had their genomes deposited 40 , 41 .…”

The chloroplast genome of two medicinal species (Veronica anagallis-aquatica and Veronica unulata) and its comparative analysis with related Veronica species

“…Codon preferences are in uenced by natural selection, base mutations, and genetic drift, are the result of long-term evolution of species in response to environmental selection, and affect the expression of mRNA and protein levels in the genome [46][47][48][49][50] . The most abundant amino acid in both species is leucine (Leu), with an average of 2,279, which is also common in other angiosperm species 51,52 . Meanwhile, based on the results of other angiosperm cp genomes, our study demonstrated that most codons ending in A/U have RSCU values higher than 1, which may be caused by a composition bias towards high A/T ratios 53,54 .…”