- Chloroplast genome variation and. - Background: Atractylodes DC is the basic original plant of the widely used herbal medicines “ Baizhu ” and. - Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus.. - Results: The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. - Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae. - Conclusions: Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.. - There are multiple configurations of the chloroplast genome in the cell. - Compared with the mitochondrial or nuclear genome, the plant chloroplast genome has a higher conservation in terms of structure, gene number and gene composition. - The results showed that the chloroplast genome contains additional. - Full list of author information is available at the end of the article. - Comparative chloroplast genome sequences provide an opportunity to discover the sequence variation and iden- tify mutation hotspot regions, while also detecting the gene loss and duplication events. - Atractylodes is a small East Asian endemic genus of the Asteraceae family with 6 species and is distributed in China, Japan, and the Korean Peninsula. - All species of the genus have been used as an herbal medi- cine except A. - The “Pharmacopoeia of the People’s Republic of China” states that “Cangzhu” is the dried rhizome of A. - Similar medicinal effects and mixed use reflect the complexity of the systematic relationship of the original plant. - Several studies have used several chloroplast markers, such as atpB-rbcL trnK , trnL-F, and/or nuclear ITS, to determine the relationship of the genus [15–17]. - How- ever, the phylogenetic relationships within Atractylodes have been poorly defined because of limited number of DNA sequences and low number of the variation markers. - In this study, we sequenced the chloroplast genome of all six Atractylodes species. - Chloroplast genome sequencing and features of Atractylodes species. - Six complete chloroplast genome se- quences were deposited in GenBank with accession numbers MT834519 to MT834524. - The total chloroplast genome size ranged from 152,294 bp ( A. - The chloroplast genome of Atractylodes has 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes (Fig. - The majority of the SSR-related indels are related to the A/T type SSRs (28 times). - All SSR-related indels are located in the non-coding regions.. - The size of the non-SSR-related indels ranges from 1 to 971 bp, with one bp indels being the most common (Fig. - The majority of the NR-indels are located in the non- coding regions (91.67. - A total of 265 SSRs were detected in the chloroplast ge- nomes of six Atractylodes species by the GMATA analysis.. - Table 1 The basic chloroplast genome information of six Atractylodes species. - Percent of chloroplast genome reads. - Chloroplast genome coverage(X . - SSR events are distributed randomly in the chloroplast genome. - A comparative analysis based on mVISTA was per- formed in the six chloroplast genomes of Atractylodes to determine the level of divergence (Fig. - 2 Gene maps of the chloroplast genomes of Atractylodes. - Genes on the inside of the large circle are transcribed clockwise and those on the outside are transcribed counter clockwise. - The dashed area represents the GC composition of the chloroplast genome. - The coding regions of the clpP , ycf1 and rps19 genes are more variable than the coding regions of other genes.. - Additionally, we compared single nucleotide substi- tutions and nucleotide diversity in the total, LSC, SSC and IR regions of the chloroplast genomes (Table 3).. - The Table 2 The basic chloroplast genome information of six Atractylodes species. - 3 Analyses of indels in the Atractylodes chloroplast genomes. - (B) Number and size of non-SSR- related indels in the six Atractylodes chloroplast genomes. - The nucleotide diversity was measured by DNAsp to identify the mutation hotspot regions in the whole Atractylodes chloroplast genomes (Fig. - trnL in the group A dataset. - all these features are located in the LSC region. - The universal DNA barcodes had lower variability than that of the newly identified markers.. - Using the whole plastome sequences, we preformed phylogenetic analysis of the 37 tribe Cynareae species.. - The topologies of the ML and BI trees are essentially consistent (Fig. - The chloroplast genome of Atractylodes. - The chloroplast genome size ranges from 152,294 bp ( A. - All species have 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, in the chloroplast genome. - The chloroplast genome is conserved similar to the majority of plants. - The mVISTA results and nucleotide diversity tests indicate high similarities between the chloroplast genomes implying that the divergence of the Atractylodes. - 4 The type and distribution of SSRs in the six Atractylodes chloroplast genomes. - (A) Frequency of SSR occurrence in the LSC, SSC, and IR regions. - chloroplast genome is lower than that of other species . - In SSR- related indels, polymerase slippage results in addition or deletion of short spans of sequences that repeat at one side of the region flanking the indels [24]. - The majority of the SSR-related indels are primarily detected in the. - Intramolecular recombination and hairpins or the stem-loop secondary structure are caus- ing the majority of the non-SSR-related mutations [26].. - Nucleotide divergence is significantly correlated with size and abundance of the nearby indels [27–29], which indicate that indels are associated mutation hotspots.. - 5 Visualization of genome alignment of the chloroplast genomes of six Atractylodes species using A. - The x-axis represents the coordinate in the chloroplast genome. - The sequence similarity of the aligned regions is shown as horizontal bars indicating the average percent identity within 50 – 100%. - Complete chloroplast genome . - Large-scale applica- tion of high-throughput technology enhanced availability of the sequencing of the whole chloroplast genomes resulting in resolution of closely related species using plastome sequences . - The results indicate the presence of the deep phylogen- etic relationships in Atractylodes . - carlinoides is lo- cated at the base of the genus and A. - The taxonomic controversy of Atractylodes is predominantly concentrated in the A.. - According to the chloroplast genome data, A. - of the A. - In this study, the chloroplast genome data provide effective markers to infer the phylogeny of Atractylodes. - However, sampling of additional individuals of the species of the A. - 6 Sliding-window analysis of the whole chloroplast genomes. - X-axis: position of the midpoint of a window. - The mutation events in the chloroplast genome are not universally randomly distrib- uted within the sequence and are concentrated in certain regions forming the “hotspot” regions [12]. - Comparison of the chloroplast genome sequences is an effective strat- egy to identify the mutation hotspots and these highly variable regions can be used as the specific DNA barcodes. - The psbM-trnD region is a part of the trnC-trnD inter- genic marker which is divided into three intergenic re- gions, trnC-petN , petN-psbM , and psbM-trnD . - Then, the chloroplast genome contigs were selected by the Blast program using the chloroplast genome of A. - Geneious 8.1 [40] was used to map all reads to the assembled chloroplast genome sequence to verify the assembling accuracy. - The complete chloroplast genome sequences were annotated with Plann [41] using A. - information sites in the chloroplast genome were assigned using MEGA 7.0 [45].. - chinensis was used as a reference to determine the size and position of the indels events.. - Comparison of the chloroplast genomes and divergent hotspot identification. - Comparison of the whole chloroplast genomes of Atracty- lodes was performed by the mVISTA program (http://. - The nucleotide diversity of the chloroplast genome was calculated based on the sliding window ana- lysis using the DnaSP v5.10 software [47]. - Thirty-seven chloroplast genome sequences were used for phylogenetic analysis, including six Atractylodes samples and 31 samples of other species of Cynareae and Lactuceae from the GenBank (Table S2). - All chloroplast genome sequences were aligned using MAFFT and ambiguous alignment regions were trimmed by Gblocks 0.91b [48].. - Table 4 The variability of the hypervariable markers and universal chloroplast DNA barcodes. - Finally, average standard deviation of the split frequencies <0.01 was verified. - Information on the chloroplast genome downloaded from Genbank for phylogenetic analysis.. - YL and YW participated in the experiments. - The funding agencies had no role in the design of the experiment, analysis, and interpretation of data and in writing the manuscript.. - The complete chloroplast genome sequence of strawberry (Fragaria X ananassa Duch.) and comparison with related species of Rosaceae. - Resolving the systematic positions of enigmatic taxa: manipulating the chloroplast genome data of Saxifragales. - Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros.. - Genome comparison reveals mutation hotspots in the chloroplast genome and phylogenetic relationships of Ormosia species. - Comparative Analysis of the Complete Chloroplast Genomes of Four Aconitum Medicinal Species.. - Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses. - Comparative genomics and phylogenetic analysis revealed the chloroplast genome variation and interspecific relationships of Corylus (Betulaceae) species. - The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. - Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. - Cai C-N, Ma H, Ci X-Q, Conran JG, Li J: Comparative phylogenetic analyses of Chinese Horsfieldia (Myristicaceae) using complete chloroplast genome sequences
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