The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

- The complete chloroplast genome of.
- Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily..
- Results: A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives..
- Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions.
- Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model.
- Conclusions: This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives.
- 1 School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China Full list of author information is available at the end of the article.
- In this study, we reported and characterized the complete chloroplast genome sequence of Stauntonia chinensis and compared it with another 38 chloroplast genomes of Ranunculales taxa previously published (in- cluding species from Berberidaceae, Circaeasteraceae, Eupteleaceae, Lardizabalaceae, Menispermaceae, Papa- veraceae, and Ranunculaceae).
- Our results will be useful as a resource for marker development, species discrimin- ation, and the inference of phylogenetic relationships for family Lardizabalaceae based on these comprehensive analyses of chloroplast genomes..
- The chloroplast genome of Stauntonia chinensis.
- Of 113 genes, six protein-coding genes (rpl2, rpl23, ycf2, ndhB, rps7, and rps12), seven tRNA genes ((trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-ACG, trnN-GUU) and 4 rRNA genes (rrn16, rrn23, rrn4.5, rrn5) were duplicated in the IR regions.
- In total, 85 protein- coding genes in the Stauntonia chinensis chloroplast genome were encoded by 26,246 codons.
- Similar to other angiosperm chloroplast gen- ome, codon usage in the Stauntonia chinensis chloro- plast genome was biased towards A and U at the third codon position, according to RSCU values (with a threshold of RSCU >.
- Further, the pattern of codon usage bias in the subfamily Lardizabaloideae and other species in Ranunculales were investigated (Fig.
- Five type of repeat structures, including tandem, for- ward, palindromic, complement, and reverse repeats were identified using REPuter software in eight se- quenced chloroplast genomes of Lardizabaloideae spe- cies.
- 1 Gene map of the chloroplast genome of Stauntonia chinensis.
- The darker gray columns in the inner circle correspond to the GC content, and small single copy (SSC), large single copy (LSC), and inverted repeats (IRA, IRB) are indicated respectively.
- 3b), and majority of the repeats were distributed in non-coding regions, including the intergenic regions and introns..
- type of the SSRs were mononucleotides SSRs (especially for A/T, Fig.
- Furthermore, Stauntonia chinensis chloroplast genome contained four tri-nucleotides and four tetra- nucleotides, while other seven chloroplast genomes were found to have 34 tri-nucleotides and 31 tetra-nucleotides..
- Additionally, none of penta- and hexa-nucleotides were found in Stauntonia chinensis chloroplast genome..
- Table 3 Genes with introns in the chloroplast genome of Stauntonia chinensis.
- a rps12 gene is trans-spliced gene with the two duplicated 3′ end exons in IR regions and 5′ end exon in the LSC region.
- Table 2 Group of genes within the Stauntonia chinensis chloroplast genome.
- To evaluate the potential impact of the junc- tion changes, we compared the IR boundaries of the.
- Although the majority of genomic structure, such as gene order and gene num- ber were conserved, the eight chloroplast genomes of Lardizabaloideae species showed visible divergences at the IRA/LSC and IRB/SSC borders.
- Some differences in the IR expansions and contractions still existed.
- Thus, we found that the IR regions of the eight chloroplast genomes were con- served, except the chloroplast genomes of Decaisnea Table 4 Relative synonymous codon usage (RSCU) in the Stauntonia chinensis chloroplast genome.
- 3 The repeat elements in the chloroplast genome of eight Lardizabaloideae species.
- 4 The comparison of the LSC, IR, and SSC boundary regions among the eight Lardizabaloideae species chloroplast genomes.
- insignis and Sinofranchetia chinensis, which were slightly expanded compared with that of the other species..
- To further investigate the divergence of chloroplast ge- nomes among Lardizabaloideae species, a global se- quence alignment of eight chloroplast genomes were compared using the annotated chloroplast genome of A..
- Although sequence similarities were very high in IR regions, the chloroplast genomes exhibited less conserved in LSC and SSC regions (Fig.
- A sliding window analyses of the whole chloroplast ge- nomes of eight Lardizabaloideae species indicated that most of the variation occurred in the LSC and SSC re- gions, which exhibited higher nucleotide variability (Pi) in comparison to IR regions (Fig.
- The most divergent non-coding regions among the eight Lardizabaloideae chloroplast genomes were trnH-psbA, trnK-rps16, rps16-trnQ, trnC-petN, trnT-psbD, ycf3-trnS-.
- Although coding regions were conserved, minor sequence variation was observed among the eight chloroplast genomes in the trnK, matK, psaJ, rpl16, ndhF, ccsA, ndhA, and ycf1 gene as shown in Fig.
- Similarly, mauve alignment results re- vealed that no large structural changes such as gene order rearrangements was detected across these eight chloroplast genomes of Lardizabaloideae species (Add- itional file 2), although some inversions were present in LSC and SSC regions in other Ranunculales species, such as Pulsatilla chinensis, Anemone trullifolia, and Anemoclema glaucifolium..
- 5 Sequence alignment of eight Lardizabaloideae chloroplast genomes using the mVISTA program with A.
- Bayesian and ML trees reconstructed based on the CCG dataset were highly congruent in identifying the phylo- genetic position of these seven families in the order Ranunculales (Fig.
- 6 Nucleotide diversity (Pi) in the complete chloroplast genomes of eight Lardizabaloideae species.
- Architecture of chloroplast genomes in subfamily Lardizabaloideae.
- Recently, chloroplast genomes have become to be useful tools to evaluate the genetic divergence among related species [30, 31].
- Here we present the complete chloroplast genome of Stauntonia chinensis.
- The organization of the chloroplast genomes among eight Lardizabaloideae spe- cies exhibited a high degree of synteny, implying that these genomes were evolutionary conserved at the genome-scale level (Table 1, Figs.
- Heatmap shows pairwise Ka/Ks ratios between every concatenated single-copy CDs sequence in the multigene nucleotide alignment.
- our study, both genome-scale level alignments and nucleotide diversity analyses of the eight Lardizabaloi- deae chloroplast genomes revealed common variable sites, including eleven intergenic regions and eight coding genes (Figs.
- *Indicate that the posterior probabilities of the site is >.
- a-f Partial aligned amino acids sequences of the ndhD, ndhF, ndhH, ndhI, ndhJ and ndhK gene, respectively.
- Generally, Lardizabaloideae species exhibited a sig- nificant difference in number and length of repeats within their chloroplast genomes.
- Most of the repeats were distributed in non-coding regions, including the intergenic regions and introns, reflecting the fact that the evolution of non-coding regions was higher than that of coding regions (Fig.
- However, several repeats occurred in the same gene (ycf2) or paralogs (pasA/psaB and trnS-GCU/trnS-UGA/trnS-GGA), which might be caused by replication slippage, generating improper se- quence recombination [45, 46].
- In summary, repetitive sequences present in chloroplast genomes could facili- tate the species discrimination and act as tools for inves- tigating levels of genetic diversity in subfamily Lardizabaloideae..
- Although pairwise Ka/Ks ratios showed most of the chloroplast genes of Ranunculales species experi- enced purifying or no selection pressures, at least 25 chloroplast protein coding genes were identified with significant posterior probabilities suggesting sites with positive selection in Lardizabaloideae species, which in- dicated these genes might have evolved to adapt to en- vironmental conditions (Table 5).
- Tree constructed by Maximum likelihood (ML) and Bayesian inference (BI) methods with the posterior probabilities of BI and the bootstrap values of ML above the branches based on: a protein-coding genes CDs sequences, b the complete chloroplast genome sequences.
- Among all positively selected genes, we found that the accD gene possessed the maximum number of sites under positive selection in Lardizabaloideae species, sug- gesting that the accD gene may play a pivotal role in the adaptive evolution of these species [57].
- As an important modulator of photosynthetic electron trans- port, recent study has revealed that positive selection of the rbcL gene was fairly common in all the main lineages of land plants [58, 59].
- This is the first report of the complete chloroplast gen- ome sequence of Stauntonia chinensis.
- The architectural and the phylogenomic analysis of complete chloroplast genomes of eight Lardizabaloideae plants and relevant species could provide valuable genomic resource of this subfamily and its relatives.
- Our genomics ana- lysis of these complete chloroplast genomes will lead to potential applications in the understanding of evolution and adaptation of species in the subfamily Lardizabaloideae..
- Chloroplast genome sequencing, assembly and annotation.
- The filtered reads were aligned with the Akebia trifoliata chloroplast genome (GenBank accession KU204898), and mapped to the reference chloroplast genomes [67, 68].
- Repeat structures (forward, palindromic, complement, and reverse) within the chloroplast genomes were ana- lyzed using REPuter (https://bibiserv.cebitec.uni-bielefeld..
- Comparative chloroplast genomes of eight Lardizabaloi- deae species were carried out and visualized by using mVISTA online software (http://genome.lbl.gov/vista/.
- The complete chloroplast genome (CCG) sequences and concatenated single-copy protein coding genes CDs of all 39 taxa were aligned using ClustalW.
- of the trees were discarded as burn-in, and the remaining trees were used to build a 50% majority-rule consensus tree..
- Gene arrangement map was carried out with only one copy of the IR using Mauve v2.4.0 software.
- Local collinear blocks are represented by blocks of the same color connected by lines..
- Partial alignment of amino acids sequences in the other 19 positively selected genes..
- Summary of complete chloroplast genomes of all 39 taxa in this study..
- We especially appreciate the conversation with the members of our group in developing some of the ideas presented in this study..
- All raw reads are available in the short sequence archive under accession no.
- All of the complete genome sequences used in this study were downloaded from NCBI (https://www.ncbi.nlm.nih.gov), and the accession numbers can be found in Additional file 5..
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