Comparative chloroplast genomes of Paris Sect. Marmorata: Insights into repeat regions and evolutionary implications

- Comparative chloroplast genomes of Paris Sect.
- Thus, the availability of complete chloroplast genome sequences of Sect.
- Here, we determined chloroplast genomes of Sect.
- Marmorata, and conducted the whole chloroplast genome comparison..
- Results: This study presented detailed sequences and structural variations of chloroplast genomes of Sect.
- Inverted repeat contraction of this section was inferred via comparing the chloroplast genomes with the one of P.
- Therefore, this study enhances the understanding about evolution of Sect.
- Marmorata from the chloroplast genome, and provide genomic insights into genetic analyses of Sect.
- Li to explore the chloroplast genome analyses.
- What is more serious is that the wild plants are hard to find, but little is known about the sequence diversity and structure divergence of their chloroplast genomes..
- Chloroplast genomes of plants are known to be predominantly uniparentally inherited and highly conserved in both gene order and gene contents [8].
- Substitution rates of chloroplast genomes are much lower than those of nuclear DNA, which are even more substantially reduced in the IR regions [10]..
- Low levels of recombination and primarily uniparental inheritance make chloroplast genomes a valuable source of genetic markers for phylogenetic analyses and useful tools for DNA barcoding [11, 12].
- Therefore, genome-wide comparative analysis of SSRs distribu- tion in chloroplast genomes will lay the foundation for further monitoring gene flow, population differen- tiation and cytoplasmic diversity of Paris plants with intricate hybridization..
- The structural and nucleotide sequence varia- tions among chloroplast genomes of Sect.
- Marmorata can be exposed by combining the chloroplast genomes of this section aligned to different reference chloroplast genomes (e.g., P.
- Thus, chloroplast genomes of Sect.
- Marmorata chloroplast genomes.
- (2) to characterize global structural patterns of chloro- plast genomes of Sect.
- and (3) to explore codon usage patterns and substitution rates of protein coding genes from chloroplast genomes of Sect..
- Chloroplast genome assembly, organization, and features Illumina paired-end sequencing produced 692 Mb and 762 Mb of data from chloroplast genomes of P.
- As the other angiosperms, chloroplast genomes of Sect.
- The chloroplast genomes of Sect.
- However, differ- ent assembly strategies and different reference chloroplast genomes (i.e., P.
- In the light of sequence similarity, the chloroplast genome of P.
- contents revealed that two genes were unique to chloro- plast genomes sequenced in this study, and another four genes were unique to chloroplast genomes sequenced by Huang et al, respectively (Additional file 2: Figure S1)..
- A total of of Sect.
- 1 Gene map of chloroplast genomes of Paris Sect.
- Similar to the chloroplast genomes of P.
- yunnanensis , the chloroplast genomes of Sect..
- In general, the chloroplast genome features of Sect.
- Eleven sets of re- peats were identified in chloroplast genome sequences of P.
- Meanwhile, a total of 30 repeats were identified in chloroplast genome sequences of both P.
- In chloroplast genomes of Sect .
- Chloroplast genomes contain conserved genes, but the number of SSRs that they harbor varied.
- Compared to IR regions, the LSC and SSC regions contain more SSRs, and this finding is consistent with analyses of other angio- sperm chloroplast genomes [32–34].
- 0.5), which can be exploited for genetic diversity studies of Sect.
- Chloroplast genome comparison of sect.
- Marmorata The availability of complete chloroplast genomes from the genus Paris provides an opportunity to elucidate the chloroplast genome organization and sequence variation of Sect.
- Sequence divergence analyses of four chloroplast genomes of Sect.
- Marmor- ata revealed π values in the range from 0 to 0.01639 with an average of 0.0009, indicating there are a few differences among the four chloroplast genomes (Fig.
- This is in accordance with the previous study, as a lot of SNPs were detected in the above regions of other Paris chloroplast genomes [20].
- The overall sequence identities of four chloroplast genomes of Sect.
- Marmorata were plotted using mVISTA and the chloroplast genome of P.
- 2 Distribution of microsatellites in chloroplast genomes of Sect.
- a length distribution of SSRs in four chloroplast genomes of Sect.
- As ex- pected, non-coding regions exhibited higher sequence divergence than coding counterparts, and the most di- vergent non-coding regions in the chloroplast genomes located in the intergenic spacers.
- To evaluate the potential impact of the junction changes in the chloroplast genomes of Sect.
- Marmor- ata , we compared the IR boundaries of Sect.
- Additionally, the LSC/IR junction was detected a contraction event in subgenus Daiswa (expect for chloroplast genomes of P.
- More sequences are required to further analyze and confirm the IR boundaries of chloroplast genomes of the section.
- Codons of chloro- plast genes of Sect.
- As observed in chloroplast genomes of most land plants, codon usage patterns of this section are likely driven by the composition bias towards the high A/T content..
- The protein-coding genes from four chloroplast genomes of Sect.
- 3 Sliding window analysis of the whole chloroplast genome of Sect.
- Evolutionary rates of sect.
- To better understand the evolutionary forces shaping chloroplast genes of Sect.
- 4 Percent identity plot comparing the chloroplast genomes of Sect.
- Horizontal axis indicates the coordinates within the chloroplast genomes.
- 5 Comparison of boundaries among LSC, SSC and IR regions of chloroplast genomes of Sect.
- Complete chloroplast genome sequences of Sect..
- The chloroplast genomes exhibit a typical quadripartite structure of LSC and SSC regions separated by a pair of IRs, and they share similar features in the terms of gene organization and AT-rich content.
- Nevertheless, chloroplast genomes sequenced to- gether with the ones sequenced simultaneously can pro- vide insights into both the genetic relationships among Sect.
- The whole chloroplast genomes were amplified using long-range PCR and nine universal primer pairs according to the procedure outlined by Yang et al [53].
- yunnanensis chloroplast genome (Gen- bank accession No.
- The annotated chloroplast genomes were depos- ited in GenBank with accession numbers: P.
- Repeat elements in chloroplast genomes of P.
- Comparison of chloroplast genome sequences.
- Marmorata chloroplast genomes, several released chloroplast genomes were retrieved from NCBI: P..
- Four chloroplast genome sequences of Sect.
- A sliding window analysis was conducted to compare π among the chloroplast genomes of Sect.
- To reveal both inter- and intra-specific variations, the full alignments of chloroplast genome sequences of Sect.
- These substitution analyses of 77 conserved protein-coding genes from chloroplast genomes of Sect.
- Summary of chloroplast genome characteristics of Sect.
- List of gene function in the chloroplast genomes..
- Distribution of tandem repeats from the chloroplast genomes..
- Distribution of dispersed, forward and inverted/palindromic repeats from chloroplast genomes.
- Type and number of SSRs in the chloroplast genomes.
- Venn diagram analysis for gene composition from chloroplast genomes of Sect.
- Six kinds of SSR motifs in fifteen Paris chloroplast genomes.
- The K a /K s ratios of 71 protein-coding genes from chloroplast genome of Sect.
- Comparison of K a , K s , and K a /K s ratios of Sect.
- Number of SSRs in fifteen chloroplast genomes of Paris species.
- Polymorphism of SSRs in chloroplast genomes of Sect.
- The chloroplast genomes generated during the current study were deposited in NCBI with accession number MF495705 (P.
- Chloroplast genomes of plants.
- Methods for obtaining and analyzing whole chloroplast genome sequences.
- An update on chloroplast genomes..
- Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome.
- Establishing genomic tools and resources for Guizotia abyssinica (lf) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome.
- Analysis of complete chloroplast genome sequences improves phylogenetic resolution in Paris (Melanthiaceae).
- Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae.
- Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes..
- Insights from the complete chloroplast genome into the evolution of Sesamum indicum L.
- Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales.
- Insight into infrageneric circumscription through complete chloroplast genome sequences of two Trillium species.
- Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes.
- The complete chloroplast genome sequence of date palm (Phoenix dactylifera L).
- Dynamics of chloroplast genomes in green plants.
- Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs

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