Complete chloroplast genome of Salvia plebeia: organization, specific barcode and phylogenetic analysis

The complete chloroplast genome of Lindernia crustacea (L.) F. Muell 1882 (Linderniaceae) and its phylogenetic analysis

Lindernia crustacea (L.) F. Muell 1882, a species in the Linderniaceae family, holds traditional medicinal value in China. To investigate its genetic diversity, we assembled, annotated, and characterized the first complete chloroplast genome of L. crustacea using Illumina sequencing data and various bioinformatics tools. The genome is 153,647 bp in length, with a GC content of 37.6%. It exhibits a typical quadripartite structure, consisting of a large single-copy region (LSC) of 85,411 bp, a small single-copy region (SSC) of 18,724 bp, and two inverted repeat sequences (IRa and IRb) of 25,816 bp each. The genome was predicted to contain 131 genes, including 87 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenomic analysis indicated that L. crustacea is closely related to L. stricta. These findings provide a foundation for further research on the evolution and potential medicinal applications of the Linderniaceae family.

The complete chloroplast genome sequence of leibnitzia anandria (linnaeus) turczaninow

Leibnitzia anandria is a perennial herbaceous plant with medicinal properties, and the entire plant can be used in traditional medicine. Leibnitzia anandria was once classified under the genus Gerbera Cass., but was reclassified under Leibnitzia Cass. recently. In this study, using the GeneLab M sequencing technology of the Genemind platform, we have sequenced, assembled, and analyzed the complete chloroplast genome of Leibnitzia anandria for the first time. The genome is 154168 bp in length, consisting of a large single-copy region(LSC, 80166 bp), a small single-copy region(SSC, 18202 bp), and a pair of inverted repeat sequences(IR, 27900 bp). We have predicted and annotated a total of 133 genes, including 88 protein-coding genes, 37 tRNA-coding genes, and 8 rRNA-coding genes. The results of the phylogenetic analysis indicate that Leibnitzia anandria and Leibnitzia nepalensis, as well as the closely related Gerbera plant, clustered into a separate clade, rather than grouping together with the other plants belonging to the tribe Mutisieae. This study provides new information for the phylogeny research of Leibnitzia anandria, contributing to a better understanding of its taxonomy and evolution.

Comparative chloroplast genomes and phylogenetic analyses of Pinellia

Background

Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear.

Methods and results

We sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68–111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be.

Conclusions

The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia.

Supplementary Information

The online version of this article (10.1007/s11033-022-07617-5) contains supplementary material, which is available to authorized users.

The complete chloroplast genome and phylogenetic analysis of Salvia oxyphora Briq. 1896 (Nepetoideae, Lamiaceae)

Salvia oxyphora Briq. 1896 is a perennial herb in the family Lamiaceae native to Central Bolivia. In this study, the chloroplast genome of S. oxyphora was sequenced using the Illumina platform and was assembled for the first time. The complete plastid genome of S. oxyphora was 151,014 bp in length including a large single-copy (LSC) region of 82,293 bp, a small single-copy (SSC) region of 17,531 bp, and a pair of inverted repeats (IR) regions of 25,595 bp. The total GC content of this genome was 38.04%, and that of LSC, SSC and IR regions was 36.21%, 31.80% and 43.13%, respectively. A total of 114 unique genes of this genome have been annotated, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The maximum likelihood phylogenetic tree was constructed with 51 complete chloroplast genomes, illustrating the close relationship of S. oxyphora to the Brazil’s native medicinal species S. splendens. The chloroplast genome of S. oxyphora provides a foundation for further studies on the adaptive evolution and genetic diversity of the genus Salvia.

Complete sequence of Cynanchum rostellatum (Apocynaceae: Asclepiadoideae) chloroplast genome and its phylogenetic analysis

Cynanchum rostellatum (Turcz.) Liede and Khanum 2016 is a perennial herbaceous twining vine that is widely distributed in Japan, South Korea, the United States of America, and China. In this study, the complete chloroplast (cp) genome of C. rostellatum was sequenced using the Illumina platform and assembled for the first time. This plastome has a circular structure with a length of 160,641 bp. The GC content of the plastome was 37.82%. The cp genome contained 113 unique genes, including 79 protein-coding, 30 transfer RNA, and four ribosomal RNA genes. Phylogenetic analysis based on the complete cp genome sequences of the Asclepiadoideae subfamily showed that C. rostellatum was closely related to C. bungei in the genus Cynanchum. These results provide useful information for both phylogenetic research and the utilization of C. rostellatum.

The complete chloroplast genome and phylogenetic analysis of Smilax moranensis (Liliales: Smilacaceae)

Smilax moranensis M.Martens & Galeotti 1842 is an important medicinal plant widely distributed in warm and temperate climates. In this paper, the complete chloroplast (cp) genome of S. moranensis was sequenced using the Illumina platform and assembled for the first time. This plastome is a circular structure of 157,907 bp in length. The GC content of the plastome was 37.16%. A total of 112 unique genes in this genome have been annotated, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. Phylogenetic analysis based on complete cp genome sequences of Smilacaceae family showed that Smilax is monophyletic. The position of S. moranensis was positioned as the sister to the other seven Smilax species. These results provide an important basis for future species identification and taxonomic determinations, as well as the phylogenetic reconstruction of the family Smilacaceae.

The complete chloroplast genome and phylogenetic analysis of Salvia karwinskii (Lamiaceae)

Salvia karwinskii Benth. 1835 is a perennial herb in the Lamiaceae family native in Mexico and Central America. The complete chloroplast (cp) genome of S. karwinskii was sequenced using the Illumina platform and assembled for the first time. The complete plastid genome of S. karwinskii was 150,907 bp in length including a large single-copy (LSC) region of 82,205 bp, a small single-copy (SSC) region of 17,538 bp, and a pair of inverted repeat (IR) regions of 25,582 bp. The total GC content of this genome was 38.05%, and that of LSC, SSC, and IR regions was 36.22%, 31.77%, and 43.14%, respectively. The cp genome contained 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The maximum-likelihood phylogenetic tree was constructed with 38 complete cp genomes, supporting a close relationship between S. karwinskii and a 10 species lineage, all of which belong to the subg. Calosphace of Salvia. The cp genome of S. karwinskii provides a foundation for further studies on genetic diversity and improving the classification system of Salvia.

The biology of medicinal resource substitution in Salvia

BACKGROUND

The decrease of wild reserves and the sharp increase of market demand have led to resource substitution, but it is still not clear how to discover medicinal alternative resources. Here we reveal the biology of medicinal resource substitution in the case of Salvia.

METHODS

A hypothesis was put forward that phylogeny and ecology were the main factors which determined alternative species selection. Phylogenetic analysis was performed based on chloroplast genomes. Spatial climatic pattern was assessed through three mathematical models.

RESULTS

Salvia miltiorrhiza and alternative species were mainly located in Clade 3 in topology, and their growth environment was clustered into an independent group 3 inferred from principal component analysis. Correlation and Maxent major climate factor analyses showed that the ecological variations within each lineage were significantly smaller than the overall divergent between any two lineages. Mantel test reconfirmed the inalienability between phylogeny and ecology (P = 0.002). Only the species that are genetically and ecologically related to S. miltiorrhiza can form a cluster with it.

CONCLUSIONS

Phylogenetic relationship and geographical climate work together to determine which species has the potential to be selected as substitutes. Other medicinal plants can learn from this biology towards developing alternative resources.

Comparative genomic study on the complete plastomes of four officinal Ardisia species in China

Ardisia Sw. (Primulaceae) is naturally distributed in tropical and subtropical areas. Most of them possess edible and medicinal values and are popular in clinical and daily use in China. However, ambiguous species delineation and genetic information limit the development and utilization of this genus. In this study, the chloroplast genomes of four Ardisia species, namely A. gigantifolia Stapf, A. crenata Sims, A. villosa Roxb. and A. mamillata Hance, were sequenced, annotated, and analyzed comparatively. All the four chloroplast genomes possess a typical quadripartite structure, and each of the genomes is about 156 Kb in size. The structure and gene content of the Ardisia plastomes were conservative and showed low sequence divergence. Furthermore, we identified five mutation hotspots as candidate DNA barcodes for Ardisia, namely, trnT-psbD, ndhF-rpl32, rpl32-ccsA, ccsA-ndhD and ycf1. Phylogenetic analysis based on the whole-chloroplast genomes data showed that Ardisia was sister to Tapeinosperma Hook. f. In addition, the results revealed a great topological profile of Ardisia's with strong support values, which matches their geographical distribution patterns. Summarily, our results provide useful information for investigations on taxonomic differences, molecular identification, and phylogenetic relationships of Ardisia plants.

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae)

Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species—Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.

Characterization of the complete chloroplast genome of Murraya exotica (Rutaceae) from Yunnan Province, China

Murraya exotica L. (Rutaceae) has important horticultural and medicinal values. Here, we reported the complete chloroplast (cp) genome of M. exotica using the next-generation sequencing method. The cp genome is 160,179 bp in length, including a large single-copy region (LSC, 87,726 bp), a small single-copy region (SSC, 18,465 bp), and a pair of inverted repeats (IR) regions 26,994 bp. A maximum-likelihood phylogenomic analysis showed that M. exotica was sister to Murraya paniculate. These findings will provide useful information for further investigation of cp genome evolution in Murraya.