- Analysis of six chloroplast genomes provides insight into the evolution of Chrysosplenium (Saxifragaceae). - Although some progress has been made in the systematics and biogeography of Chrysosplenium , its chloroplast genome evolution remains to be investigated.. - they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. - The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection.. - estimation suggested that the genes related to photosynthesis (such as ycf2 ) were under positive selection at sites in the coding region.. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - 1 Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, Hubei, China Full list of author information is available at the end of the article Wu et al. - The chloroplast genome is typically quadripartite in struc- ture, containing a large single copy (LSC) and a small sin- gle copy (SSC) separated by a pair of inverted repeats (IR).. - Strong purifying selection detected rather than expected positive selection in chloro- plast genome of the green alga (Ostreobium quekettii) fa- cilitated its extremely low light adaptation [5]. - The genus plays an important role in the phylogeny of Saxifragaceae, comprises about 79 peren- nial herbs [7], and mainly occurs in the northern hemi- sphere, with the highest species diversity in East Asia;. - only two species, Chrysosplenium valdivicum Hook and Chrysosplenium macranthum Hook, are found in the Southern Hemisphere [8, 9]. - Therefore, examination of the chloroplast ge- nomes of Chrysosplenium species may provide insight into the impacts of low light in angiosperms.. - In this study, we aimed to provide a comprehensive insight into the evolution of the chloroplast genomes of. - several Chrysosplenium species. - First, we sequenced the chloroplast genomes of six Chrysosplenium species in addition to a previous study [21]. - Organization of the Chloroplast Genomes of Chrysosplenium species. - The chloroplast genomes of the Chrysosplenium species contain the typical quadripartite structures (Fig. - The rps12 gene in Chrysosplenium was recog- nized as a trans-spliced gene, with the first exon located in the LSC region and the other one or two exons dis- tributed in the IR regions. - GC content, nucleotide diversity, and repeat analysis When we compared the total GC content of the chloro- plast genomes of Chrysosplenium species with that of the chloroplast genomes of the three non-Chrysosple- nium Saxifragaceae species (S. - 1 Gene map of the Chrysosplenium macrophyllum chloroplast genomes. - The dark gray area in the inner circle corresponds to GC content while the light gray corresponds to the adenine-thymine (AT) content of the genome. - The small (SSC) and large (LSC) single copy regions and inverted repeat (IRa and IRb) regions are noted in the inner circle. - Table 1 General information and comparison of chloroplast genomes of Saxifragaceae species. - Within the Chrysosple- nium species, the GC contents in subgenus Oppositifolia were slightly lower than those in subgenus Alternifolia, regardless of the total GC contents or those in GC3.. - The IR regions were more conserved than the LSC and SSC regions, with average Pi values of 0.00586 in IR regions, 0.01760 in the LSC region, and 0.01900 in the SSC region (Additional file 2: Supplementary Table S6 and Additional file 3: Supplementary Figure S2). - In the LSC region, psbT has the highest Pi value of 0.22159, followed by trnG-GCC with Pi value of 0.10369.. - Among the mono-, di-, tri-, tetra-, penta-, and hexa- nucleotide categories of SSRs in the chloroplast genomes of the Chrysosplenium species, mono-nucleotide repeats were the most common (Additional File 4: Supplemen- tary Table S7 and Additional File 5: Supplementary Fig- ure S3A) ranging from 42.42% (C. - Moreover, the overlap of ycf1 pseudogenes and ndhF ap- peared in different locations among the Chrysosplenium species: in the region of the SSC for C. - The trnH genes of the seven Chrysosplenium species were located in the LSC region, 2–19 bp away from the IRa–LSC border.. - When comparing the genome boundaries of the Chry- sosplenium species to the other three non-Chrysosple- nium species of Saxifragaceae, ndhF was at the IRb/SSC boundary in most species of Chrysosplenium, except for C. - ramosum, which showed contraction of the SSC and expansion of IRb. - stolonifera, the contraction of the LSC region resulted in the rpl22 gene being at the Table 2 Genes encoded in the C. - macrophyllum chloroplast genome. - Genes in the IR regions are followed by the. - IRb/LSC junction, which placed the whole rps19 gene in the IRb region. - The rps19 pseudogenes were also found in the IRa region in S. - When these data were combined with the phylogenetic tree of the three clades (S. - 3), we found that the chloroplast genome structure within Chrysosplenium species is not strongly conserved, although the gene content is conserved.. - LAGAN and Shuffle-LAGAN gave very similar results in the genetic divergence among the chloroplast genomes of Sax- ifragaceae species (Fig. - The chloroplast genomes of the Chrysosplenium species were more conserved when compared with the three non-Chrysosplenium species of Saxifragaceae, and the inter- genic spacer (IGS) regions had the highest levels of divergence:. - We calculated the Ka/Ks ratios, the ratios of the rate of non-synonymous substitutions (Ka) to the rate of syn- onymous substitutions (Ks), at the species level by concat- enating all of the 79 genes into a super-matrix. - The Ka/Ks ratios were also calculated for all of the 79 protein-coding genes of the ten chloroplast genomes of Chrysosplenium separately (Fig. - Most of the other genes had a Ka/Ks ratio range from 0.1–. - Phylogenetic analyses yielded a well-supported phyl- ogeny of Saxifrageles with most of the nodes having maximum likelihood (ML) bootstrap support values >. - 3 Comparison of the borders of the LSC, SSC, and IR regions among ten chloroplast genomes. - Gene numbers were slightly different due to the loss of rpl32 or transfer of the gene to the nucleus [22–26]. - DNA se- quences of closely related species from different environ- ments show marked differences in GC content, which has a direct impact on the amino acid sequences of the proteins in the respective environments [29]. - Therefore, the se- lective pressure of the unique habitat of Chrysosplenium species (insufficient light energy) resulted in the lower overall GC contents and GC3 contents in their chloro- plast genomes.. - 4 The comparative analysis with LAGAN program of the whole-chloroplast genome of seven different species from the family of Saxifragaceae. - The percentage of identity is shown in the vertical axis, ranging from 50 to 100%, while the horizontal axis shows the position within the chloroplast genome. - Each arrow displays the annotated genes and direction of their transcription in the reference genome ( C.. - This heatmap shows pairwise Ka/Ks ratios between every sequence in the multigene nucleotide alignment. - The scale factors associated with each value are shown on the top right side of the figure. - This heatmap shows pairwise Ka/Ks ratios among each individual gene in the Chrysosplenium species. - most genes were subjected to purifying selection to retain conserved functions in the Chrysosplenium. - In the opposite environment, sunlight, including UV ra- diation, induces DNA damage, mutations and rear- rangements [33, 34], which may contribute to an increase in mutation rates. - As one of the most prevalent form in natural selection, puri- fying selection constantly sweeps away deleterious mutations in population. - Therefore, the purifying se- lection on most chloroplast genes within Chrysosple- nium would be evolutionary result of the preservation of the adaptive characteristics of Chrysosplenium species.. - 7 The partial alignment of 19 genes suggesting sites with positive selection in the BEB test. - However, due to the extremely high Ka/Ks value. - unknown function, ycf2 is a valuable resource for future research of the adaptive evolution of Chrysosplenium.. - In this study, we sequenced the chloroplast genomes of six Chrysosplenium species and revealed the chloroplast genomic features between the Oppositifolia (C. - We discussed the com- prehensive features of the chloroplast genomes, such as gene content and GC content, in these seven species of Chrysosplenium. - At the chloroplast genome level, the Ka/Ks ratios of the in- dividual sequences showed that Chrysosplenium species were subjected to purifying selection compared to the non-Chrysosplenium species. - Also, our results supported the classifica- tion of the genus into two subgenera based on the morphology of opposite leaves or alternate leaves. - These findings will be valuable for further study of the chloro- plast genomes of Chrysosplenium species and provide valuable resources for studies of plant adaptation to low light conditions.. - sinicum belonging to the Oppositifolia subgenus. - To get a complete chloroplast genome, which can be used as a reference in assembling chloroplast genome of the other five species, C. - Chloroplast genome assembly and annotation. - The sequencing of the chloroplast DNA of C. - The clean reads were aligned to the complete chloroplast genome of C.. - The GC content of the whole chloroplast genome and the third position GC content of codons for all ten species were calculated using an in-house Python script. - The contraction or expansion between boundary regions of the chloroplast genome in each species was drawn by IRscope [56]. - All protein-coding sequences (CDSs) from each of the 31 species were concatenated into a super matrix for in- ferring phylogenetic tree. - In addition, the Ka/Ks ratio was es- timated for each of the 79 genes within Chrysosplenium separately. - The branch-site model in the pro- gram codeml of the PAML v4.9 package [60] was used to assess potential positive selection in Chrysosplenium that was set as the foreground branch. - The best-fitting nucleotide substi- tution model was determined using the Akaike Informa- tion Criterion in the model-finder IQ-TREE [63]. - Additional File 3 Comparison of nucleotide diversity (Pi) between the chloroplast genomes of Chrysosplenium. - Analyses of repeat sequences in the ten species of Saxifragaceae. - (A) The analysis of simple sequence repeats (SSRs) in chloroplast genomes of Saxifragaceae. - The comparative analysis with Shuffle-LAGAN pro- gram of the whole chloroplast genome of seven different species from the family of Saxifragaceae.. - The whole protein sequences of the nuclear genome of C. - Evolutionary dynamics of chloroplast genomes in low light: a case study of the endolithic green alga Ostreobium quekettii. - An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV.. - Plants of the world online. - Synopsis of the genus Chrysosplenium L. - An update on chloroplast genomes.. - The complete chloroplast genome of a Korean endemic plant Chrysosplenium aureobracteatum Y.I. - Direct measurement of the transfer rate of chloroplast DNA into the nucleus. - High-frequency gene transfer from the chloroplast genome to the nucleus. - Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and transfer of the rpl32 gene to the nucleus in the ancestor of the subfamily Thalictroideae. - loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus . - Genetic recombination: patterns in the genome. - the evolution of the plastid chromosome in land plants: gene content, gene order, gene function. - RNA-binding activity of the matK protein encodecd by the chloroplast trnk intron from mustard ( Sinapis alba L. - Molecular evolution and phylogeny of the angiosperm ycf2 gene. - The complete chloroplast genome of the Jerusalem artichoke ( Helianthus tuberosus L.) and an adaptive. - evolutionary analysis of the ycf2 gene. - Statistical properties of the branch-site test of positive selection
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