- Comparative chloroplast genomics of the genus Taxodium. - The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. - Comparative analysis of the 3 cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat (TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. - All these characteristics highlight the important role of repeats in the evolution of cp genomes.. - Conclusions: This study added new evidence for the role of repeats in the dynamics mechanism of cp genome mutation and rearrangement. - They have been popularized and applied in 18 provinces and municipalities of China, bringing better ecological and social benefits in the urban landscaping, ecological civilization construction, sponge city construc- tion, and ecological restoration of the Yangtze River eco- nomic zone [4]. - 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article. - The typical feature of the cp genomes of conifers were the loss of IR region [6]. - analyzed the plas- tomes of 24 representative genera in all of the five cupressophyte families, and found that every cupresso- phyte family has evolved its own specific and novel sIR systems, for example the rpoC2-IR in Sciadopitysis [7], the trnN-IR in Podocarpaceae [8], and the rrn5-IR in Araucariaceae [8]. - For example, a 335 bp trnN-GUU containing sIR and a 211 bp sIR in the IGS of Torreya fargesii [10]. - Changes in the gene and structure of cp genomes in the genus has not been referred. - taxonomy of the genus Taxodium, it is impossible to de- termine which taxa the published chloroplast genome belongs to. - The results would advance our current under- standing of the complexity, dynamics, and evolution of cp in conifers.. - The nucleo- tide sequences of the four plastid genomes range from 131,947 bp in T. - The gene map of the T. - A total of 639 TRs were detected in the T. - the total length of repeats was 8462 bp, and TRs were widely distributed in the coding and non-coding regions of the cp genome (Fig. - Mononucleotide repeats were the most abundant SSRs, accounting for of the total, of which 238 repeat units were A/T and only five were G/C (Additional file 4). - Of the dinucleo- tide repeats, 34 were AT/TA type, 17 were AG/TC type, four were AC/TG type, and none were GC/CG type. - Because of the high A/T content of repeat mo- tifs, an increase in repeats will lead to a low GC con- tent of chloroplast genes. - In the Taxodium, TRs were only de- tected in T. - For Cupressaceae, there are two major insertion positions, one located in the middle of the CDS, the other one is near the C-terminal region.. - Fifty dispersed repeats were detected in the T. - In the T. - In the T.. - For sIR2, one copy was located in the intergenic region (IGS) region of petA-ccsA and the other in the psbJ-clpP IGS.. - Semi-quantitative PCR with a vari- able number of cycles was conducted to verify the pres- ence of the two isomers. - Total Length (bp): The total length of the sample assembly result. - GC content of the sample assembly sequence. - the content of unknown base N in the sample assembly sequence. - Accession No.: Accession number of the complete chloroplast genome in genebank database. - To quantify the relative frequency of the two iso- meric genomic forms, Illumina paired-end reads were mapped to the genome and isomer frequencies were calculated using the method of Guo [9]. - 1 Circular gene map of the chloroplast genome of T. - 2 Distribution of conserved gene blocks, TRs, indels, and SNPs in the plastomes of T. - The relative height of the dot position in the figure represents the relative number of polymorphic loci within non-overlapping bins of 200 bp. - Repeats in the three different colors were treated separately in statistical analysis. - Dots with a high relative position, represent more polymorphic loci in the 200 bp window. - The red rectangle (HR01-HR11) showed the locations of the 11 selected hypervariable regions. - Therefore, there were at least 13 rearrangements in the process of transformation from cycad chloroplast genome structure to T. - The size of the conversed gene blocks ranged from 1236 bp to 40489 bp. - Five of the 13 inversion end- points occurred near tRNAs, including trnI, trnT, trnQ, trnF, and trnM. - endpoint (116761) between conserved gene blocks S10 and S11 was in the 95-nucleotide repeat TP located on clpP-accD.The accD gene or its adjacent region is a hot rearrangement area of cupressophyte cp genomes, Li et al. - We also analysis the sequence variability of the genes adjacent to the ycf1 gene in Taxodium.. - The gene order around ycf1 of the 44 analyzed spe- cies could be classified into twelve types (Fig. - The right side of the phylogenetic tree showed the position of tandem repeats on the ycf1 gene. - The length of the horizontal line was drawn according to the length of multiple sequence alignment, which included the length of gaps. - the diversity of gene organization around ycf1 gene, it is speculated that ycf1 gene may be frequently in- volved in the rearrangement events of cupressophytes cp genomes.. - Twelve indel sequences were non-integer multi- ples of repeat motifs, i.e., the indel sequences contained partial incomplete repeat motif sequences. - Of the 51. - Table 4 SIRs in the cpDNA of Taxodium ascendens. - No mutations appeared on start/stop codon or caused the triplet codon of the site mutates into a ter- mination codon. - Of the 69 SNPs were located within the TR se- quences were located within 100 bp win- dows adjacent to the repeats, and only were located outside the 100 bp windows adjacent to repeats (Fig. - Regions enriched with indels and SNPs can be consid- ered as hypervariable regions in the complete cp gen- ome. - Since most indels show periodic variation of repeat motifs, the number of polymorphic sites contained in an indel is affected not only by the degree of periodic vari- ation but also by the size of the repeat motif. - Based on this principle, the most variable regions of the Taxodium cp genome are clpP-accD, trnV-rps12, ndhF- trnN, trnV-ndhC, trnI-trnL, ycf1-rpl20, atpI-atpH, rpl36- rps11, ycf1, psbJ-clpP, and trnI-rrn16(Fig. - Table 5 Information of the 13 conserved gene blocks of Taxodium cp genomes compared with Cycas taitungensis. - The direction of the arrow of genes was from the N-terminal to the C-terminal.. - However, there is a distinct difference between Pinaceae and cupressophyte species, in that the former has more of these sIRs than the latter, and species of the subclade Cupressaceae all have relatively shorter sIRs compared to other two subclades within the cupresso- phyte clade [11]. - Unanimously, cp genome rearrange- ments are much more frequent in cupressophytes, especially in the subclade Cupressaceae, than in Pinaceae [11]. - ascendens, and we iden- tified at least 13 rearrangements in the process of trans- formation from Cycad to T. - thus, the rearrangement breakpoints may selectively constrain some regions of the cp genome [20, 21]. - Note: Synonymous: Synonymous mutation in the gene region. - Nonsynonymous: Nonsynonymous mutation in the gene region. - Intergenic: SNP in the intergenic region. - The cause of the different con- tents between the two isomers in individuals is unclear, and the length of sIR may be one factor [10].. - that is, TR mutation is the result of the interaction of DNA slippage and DNA replication repair systems. - The hypothesis holds that the repeat se- quence is formed by the increase in length of the ori- ginal repeat motif by copy slip, while the original microsatellite sequence may come from a random point mutation. - When the new strand and template strand are mismatched occasionally, DNA polymerase synthesis on the mismatched DNA strand will cause the length of the new strand to change. - Repeat sequence is one of the main cause of DNA replication fork arrest [25], as a result, DNA poly- merases, including high-fidelity DNA polymerase and error-prone repair polymerases, are widely recruited to restart replication [26–28]. - Eleven hypervariable regions of the Taxodium cp gen- ome were identified in this study. - The length of the ycf1 genes showed an extraordinary expansion, and there were universal in- sertion of TRs. - Thus, similar to accD gene and its sur- rounding regions, ycf1 gene may play an important role in the cp genome structural evolution of cupressophytes.. - The cp gnomes of Taxodium were characterized by sev- eral unusual features, such as the loss of the typical IRA copy, the wide spread of TRs, extensive genomic inver- sions, the presence of isomeric plastomes, and the big variation of ycf1 genes among genus. - All these character- istics highlight the potentially important role of repeats in the dynamics of cp genome mutation and rearrange- ment. - The comparative chloroplast genomics of the genus Taxodium advances our understanding of the dynamics, complexity, and evolution of cp genomes in Cupressophytes.. - Three coding gene se- quence with the highest coverage was used as a seed se- quence for de novo assembly of the chloroplast genome by NOVOPlasty v with the reference genome as a template. - Phobos-v3.3.12 software [42] was used to detect TRs in the cp genomes. - Fifty-one single copy coding genes of the 44 species were used for multiple sequence alignment. - To quantify the relative fre- quency of the two isomeric genomic forms, Illumina paired-end reads were mapped to the genome using Bowtie 2 [36] with default parameters. - [9] was used to count repeat- spanning read pairs, enabling us to quantify the fre- quency of the repeat in each possible genomic arrangement.. - InDel refers to the insertion and deletion of sequences in the genome. - InDel loci were then compared with the sequencing Reads of the samples 150 bp upstream and downstream of the reference se- quence using BWA [(http://bio-bwa.sourceforge.net/) software and SAMtools [45] (http://samtools.source- forge.net. - The se- quence of 100 bp on each side of the reference sequence SNP locus was extracted, and then the extracted se- quence was compared with the assembly result using BLAST [40] to verify the SNP locus. - Additional file 1 Basic information of the 120 genes in Taxodium distichum, Taxodium mucronatum, and Taxodium ascenden chloroplast genomes.. - Additional file 3 Tandem repeats detected in the Taxodium ascendens chloroplast genome using Phobos software.. - Additional file 5 Dispersed repeats detected in the Taxodium distichum, Taxodium mucronatum, and Taxodium ascenden chloroplast genomes.. - Additional file 8 List of the 8 highly variable regions in Taxodium chloroplast genomes.. - HD performed the experiments, analyzed the data, prepared figures and/or tables,authored drafts of the paper. - YY conceived and designed the experiments, reviewed and revised the drafts of the paper. - Sequence information of the 3 cp genomes is available in the NCBI database under the accession number MN535011- MN535013. - Comparative analysis of the complete chloroplast genome among Prunus mume, P. - Predominant and substoichiometric isomers of the plastid genome coexist within juniperus plants and have shifted multiple times during cupressophyte evolution. - Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. - A catalogue of the plants native or naturalized in the vicinity of New Bern, North Carolina. - Extensive rearrangements in the chloroplast genome of trachelium caeruleum are associated with repeats and tRNA genes. - The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. - Ancient nuclear plastid DNA in the yew family (taxaceae). - Microsatellite mutations in the germline. - dependence on the length of the microsatellite
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