The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences

- Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences.
- Background: As one of the largest genera in Apiaceae, Bupleurum L.
- In addition, few of the species are endemic to Southwest China, a distribution and diversity center of Chinese Bupleurum.
- Endemic species are key components of biodiversity and ecosystems, and investigation of the chloroplast genomes features of endemic species in Bupleurum will be helpful to develop a better understanding of evolutionary process and phylogeny of the genus.
- Bupleurum species to determine the evolutionary characteristics of the genus and the phylogenetic relationships of Asian Bupleurum..
- Results: The complete chloroplast genome sequences of the 4 endemic Bupleurum species are 155,025 bp to 155,323 bp in length including a SSC and a LSC region separated by a pair of IRs.
- Chloroplast genomes of the 21 Bupleurum species showed no rearrangements and a high sequence identity .
- 2 Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China Full list of author information is available at the end of the article.
- Conclusions: The chloroplast genome data of the four endemic Bupleurum species provide important insights into the characteristics and evolution of chloroplast genomes of this genu, and the phylogeny of Bupleurum..
- Bupleurum L., with more than 180 species, represents one of the largest genera of the family Apiaceae and is distributed in the north temperate zone (mainly in Eur- asia, the Mediterranean, North Africa, Asia and North America) [1, 2].
- Bupleurum is easily distinguished from other genera of the family for its simple and entire leaves as well as con- spicuous bracts and bracteoles, which are almost unique morphology characteristics in the family [1, 4].
- In spite of the efforts at phylogenetic analysis in previous studies, some essential problems concerning the phylogenetic re- lationship of Bupleurum based on nrDNA (ITS) and various plastid sequences (e.
- The understanding of the evolutionary connection among the plant species, the features they shared, and their differences from other taxonomic groups [20] all benefit from comparative analysis of whole chloroplast genomes that provide insights into the phylogenetic rela- tionships and species evolution in different taxa [21 – 28]..
- It is important to investigate chloroplast genomes of the taxonomically significant genera, for understand- ing how infrageneric species are linked, what features are shared among them, and how they are different from other taxonomic groups [20, 29].
- The advancement of the high-throughput sequencing technologies has dras- tically lowered the cost of analysis of the whole chloro- plast genome sequences.
- As a result, the evolution of chloroplast of the genus is poorly understood.
- [37], the chloroplast genomes of only five Bupleurum species were reported, but few of the species are endemic to Southwest China.
- Investi- gation of the chloroplast genome features of endemic Bupleurum species may provide important insights into the evolution and phylogeny of the genus, especially the endemic Bupleurum species, thus helping to clarify the phylogenetic relationships and evolutionary aspects in the genus..
- The sequence data of the chloroplast genomes provide a clue to the evolution and phylogeny of Bupleurum.
- The sequences of the 4 Bupleurum chloroplast genomes ranged from 154,925 bp (B.
- The chloroplast gene contents of the 4 Bupleurum species were identical (Table 1).
- The Mauve alignment analysis revealed that there was no rearrangement in coding and non-coding re- gions of the 21 Bupleurum chloroplast genomes.
- On the other side of the IRb/SSC was the gene ndhF, which was 15–39 bp away from the IRb/SSC junction.
- 1 Chloroplast genome map of the four Bupleurum species.
- Genes shown outside of the larger circle are transcribed clockwise, while genes shown inside are transcribed counterclockwise.
- Thick lines of the smaller circle indicate IRs and the inner circle represents the GC variation across the genic regions.
- Genome divergent hotspot regions in Bupleurum species Comparative sequence analysis of the 21 Bupleurum species using mVISTA revealed a high sequence identity across the 21 species (Additional file 1: Fig.
- The nucleotide diversity (Pi) of the chloroplast ge- nomes in the 21 Bupleurum species was also calculated to assess the sequence divergence level of these species..
- Most of the se- quences with high Pi values were spacer regions between genes.
- c means the incomplete copy located in the IR of the gene straddling the IR and LSC/SSC regions.
- At the species level, by con- catenating all of the 80 genes into a super-matrix, the Ka/Ks ratios ranged from 0.50 (B.
- The Ka/Ks ratios were also calculated for all the 80 protein-coding genes in the chloroplast genomes of the 21 Bupleurum species separately (Additional file 2: Fig..
- Within each of the alignments, local collinear blocks are represented by blocks of the same color and linked.
- After sorting the genes into functional categories and groups, Ka/Ks of the photosynthetic genes were lower than those of genes related to self-replication as well as other genes .
- Results of Bayesian and ML analyses of the 21 Bur- pleurum and 2 outgroup chloroplast genomes are pre- sented in Fig.
- 90%) and strong posterior probabilities (PP = 1) for most of the nodes.
- We for the first time described the chloroplast genomes of the 4 Bupleurum species endemic to Southwest.
- 3 Comparison of the LSC, SSC and IR junction among the 21 Bupleurum cp genomes.
- China, which provide important insights into the charac- teristics of plastid genomes of the members of this genus.
- The chloroplast genomes of the 21 Bupleurum species displayed the typical quadripartite structure, comprising a pair of IR regions which were separated by a LSC and a SSC region.
- The chloroplast genomes size of Bupleurum, ranging from 154,925 to 156,108 bp, is lar- ger than those of the other genera in the Apiaceae family (e.
- The chloroplast genomes of the Bupleurum species.
- Previous studies suggested that the size variations of the chloro- plast genomes resulted from expansion and contraction of the IR regions .
- The gene/intron content and relative gene positions were highly conserved in Bupleurum species and almost identical to those in other members of the Apiaceae family .
- respectively, were identified as pseudogenes on account of an incomplete duplication of the normal functional copy..
- However, the morphological similarities of the Bupleurum species make their authentication ex- tremely difficult.
- With the development of the molecular technology, many of the chloroplast genome regions, es- pecially the mutational hotspots (e.g.
- In a comparative analysis of the complete plastid gen- ome of 5 Bupleurum species, only 8 highly variable regions (Pi >.
- The matK gene is one of the fastest evolutionary genes, which functions in light-regulated activities and plant development [64, 65].
- However, our analyses also showed strong purifying selection on most of the genes..
- Purifying selection, one of the most prevalent mechanisms in natural selection, constantly eliminates deleterious mutations [73].
- Most of the genes in these chloroplast genomes were thus subjected to ex- tensive purifying selection to retain conserved functions in Bupleurum.
- The distribution of Ka/Ks indicated that most of the genes in the SSC region have experienced higher selection pressures than those in other chloro- plast genome regions, whereas the IR region is more conserved.
- Phylogenetic inference from plastid genomes of the genus Bupleurum in East Asia.
- East Asian, es- pecially China, is one of the diversity center for the genus Bupleurum.
- However, the sub- genus subdivision of the genus Bupleurum remains un- resolved in this present study because of the lack of chloroplast genome data from subg.
- To access a complete reassessment of the interspe- cific relationship of Bupleurum, more complete plastid genomes information is required, especially the data of subg.
- Comparative analysis of chloroplast genomes of the 4 species against the published data of 17 Bupleurum species revealed that the chloroplast ge- nomes of Bupleurum species were extremely conserved with similarities in terms of chloroplast genome organization, tendency of SDRs and SSRs, and gene con- tent.
- In spite of the highly conservation of the chloro- plast genomes of the Bupleurum species, some mutational hotspots have been detected, which can be potentially used as high-resolution DNA barcodes in dis- crimination of Bupleurum taxa.
- The chloroplast genomes information reported herein and the comparative analysis of Bupleurum chloroplast genomes provide important insights into the evolution of the chloroplast genomes and phylogeny of Bupleurum..
- Leaf from a total of 7 individuals of the 4 Bupleurum species (two individuals for each of B.
- Details information of the samples and voucher numbers of the specimens were shown in Additional file 2: Table S3..
- The quality and concentration of the ex- tracted DNA were detected by 1.0% agarose gel electro- phoresis and by a NanoDrop 2000C spectrophotometry (Thermo Fisher, US).
- The details of the quantity and quality of raw reads, and coverage depth of the assembled genomes were provided in Additional file 2: Table S4..
- The visual presentations of the physical circular maps of the ge- nomes were generated using OGDRAW [89].
- Finally, the annotated chloroplast genomes of the 4 Bupleurum species were submitted to the National Center for Biotechnology Information database (NCBI) under the accession numbers MW135450- MW135456, which were listed in Additional file 2:.
- First, the chloroplast genome characteristics of the 4 Bupleurum species were described.
- In order to examine the divergence hotspots among the Bupleurum species, the whole chloroplast sequences of the 4 Bupleurum species, together with 17 published chloroplast genomes of Bupleurum species downloaded from NCBI database (Additional file 2: Table S5), were aligned using Geneious software.
- Selective pressure estimation for the 21 Bupleurum species was carried out by calculating the ratio of the non-synonymous substitution (Ka) to the synonymous substitution rate (Ks) for all protein-coding genes se- quences in DnaSP v6..
- ZC conceived the study and provided the funding, reviewed and revised the drafts of the paper.
- The funders had no role in study design, data collection, analysis and interpretation, or preparation of the manuscript..
- Sequence information of the 7 chloroplast genomes of the four Bupleurum species (B.
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