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Brief Report

Plastome Evolution of Asyneuma japonicum: Insights into Structural Variation, Genomic Divergence, and Phylogenetic Tree

by
Byeong-Seon Park
1,
Won-Sub Yoon
2,
Chang-Kug Kim
3 and
Yong-Kab Kim
1,*
1
Department of Information Communication Engineering, Wonkwang University, Iksan 54538, Republic of Korea
2
Department of Mechanical Design Engineering, Wonkwang University, Iksan 54538, Republic of Korea
3
Genomics Division, National Institute of Agricultural Sciences, Jeonju 54874, Republic of Korea
*
Author to whom correspondence should be addressed.
Appl. Sci. 2024, 14(15), 6572; https://doi.org/10.3390/app14156572
Submission received: 3 July 2024 / Revised: 21 July 2024 / Accepted: 25 July 2024 / Published: 27 July 2024
(This article belongs to the Section Applied Biosciences and Bioengineering)
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Abstract

:
Asyneuma japonicum is an ornamental flowering plant in East Asia. The genus Asyneuma is difficult to distinguish taxonomically because of its morphological similarities with the genus Campanula. We constructed the first complete plastome of A. japonicum (NCBI accession number: OR805474) using the Illumina platform. This plastome is a circular ring structure with a length of 185,875 base pairs. It is organized into four parts: a pair of inverted repeats (33,084 bp each) as well as large (83,795 bp) and small (35,912 bp) single-copy regions. One hundred nine unique genes were encoded in the assembled plastome. Using structural variations, junction boundaries, rearrangements, divergent hotspots, and phylogenetic analysis, we revealed that A. japonicum was in the closest evolutionary position to Hanabusaya asiatica and it had a large evolutionary divergence from the Campanulaceae family due to gene rearrangements.

1. Introduction

Asyneuma japonicum is an ornamental flowering plant that grows mainly in East Asia [1]. The genus Asyneuma contains about 150 species including subspecies [2], and they are characterized by herbaceous, violet/blue flowers and capsule fruits [3]. Recently, the demand for molecular information to classify Asyneuma species has increased because traditional morphological methods cannot accurately distinguish between Asyneuma and the taxonomically close genus Campanula [4].
Plant chloroplasts are important cell organelles which play a major role in survival activities [5], influencing photosynthetic activity, compound production, evolution, and diverse signaling pathways [6]. A chloroplast genome (plastome) can be changed to facilitate the adaptation of a plant species toward specific survival strategies [7], and its sequences are effective for observing the changing events in the conserved genes of coding regions [8]. Therefore, plastome sequences are widely utilized in evolutionary studies owing to their advantageous properties, such as their small size, low-frequency mutations, and haploid inheritance [9]. Generally, a plastome has a circularized double-stranded loop structure with four regions: a pair of inverted repeat (IR) parts that are identical fragments of equal lengths (IRa/IRb) and two single-copy (LSC and SSC) parts that are distinguished by IRa and IRb [10]. Plastomes have highly conserved sequences in functional gene contents [11], and their variations provide phylogenetic insights for effective evolutionary studies [12].
In Campanulaceae species, although the plastome is well conserved in most plants, several rearrangement events have been found in a few lineage plastomes [13], and large-scale sequence variations have also been discovered [14]. These mutations mainly occur due to structural variations such as gene rearrangements, gene duplications, and repeat sequences [15]. Although many plastome sequences have been revealed in various plant species, plastomes have not been reported for any Asyneuma species, and their molecular positions and phylogenetic relationships are unclear because previous studies have only focused on comparing taxonomic characteristics. In this study, we registered a complete plastome of A. japonicum (NCBI accession number: OR805474) belonging to the Campanulaceae (Bellflower) family. Our molecular data provide a basic resource for clarifying the evolutionary history of Campanulaceae species.

2. Materials and Methods

2.1. Sequencing, Assembly, and Annotation

Whole plants were collected from Iksan city (geographic coordinate: 35°58′05″ N, 126°57′31″ E), Jeonbuk province, Korea. For DNA extraction, 3 g of young leaves was used, and DNA quality was tested using a NanoDropTM Lite Spectro-photometer (Thermo Inc., Waltham, MA, USA). Passed DNA samples were quantified for Illumina paired-end (PE) library construction. The PE library was sequenced by a HiSeq X platform (Illumina Inc., San Diego, CA, USA) with 125 nucleotides in PE mode. To remove poor-quality sequences and used adapters, trimming was performed with a Phred quality score < 20. Constructed contigs were assembled and verified using a CLC Assembler (CLC Bio, Aarhus, Denmark) with an assembly accuracy test. The genome used as a reference for assembly was from Adenophora remotiflora (NCBI, accession number: OP920648). Online GeSeq [16] and Artemis tool (version 17) [17] were used for gene annotation, and multi-layer ring diagrams were created using CPGView (version 1.4.6) [18].

2.2. Codon Usage and Repetitive DNA Sequences

Codon usage indicates the actual ratio of synonymous codons for evolutionary studies. The relative synonymous codon usage (RSCU) index is used mainly to evaluate mutational bias between synonymous codons [19]. According to variations in RSCU values, RSCU > 1 codon has a positive bias compared to other synonymous codons, RSCU = 1 codon indicates no bias between the two codons, and RSCU < 1 codon has a negative bias compared to other codons [20]. The RSCU values were calculated using MEGA 11 (version 11) [21].
Repetitive DNA sequences (repeats) have short- and long-type patterns with multi-copy sequences. Simple sequence repeats (SSRs) have repeat units of less than 7 bp, while long tandem repeats have repeat units of 7 bp or more. SSRs (repeat units <7 bp) were detected by online MISA [22] set at unit size–minimum number of repeats of nucleotides: 10-mononucleotides, 6-dinucleotides, 5-trinucleotides, and 4-multitrinucleotides. Long tandem repeats (repeat unit ≥7 bp) were identified by Tandem Repeats Finder (version 4.04) set at a maximum size of 500, an alignment score of 50, match numbers of 2, mismatch numbers of 7, and a matching ratio of 80% [23].

2.3. Comparison of Plastome Structure and Genomic Divergence

To discover the structural variations at the four boundary junction positions, boundary shifts were analyzed using an online IRscope [24] with A. japonicum as a reference. To identify genomic divergence, gene rearrangement possibility was calculated using a Mauve progressive algorithm [25]. Locally collinear blocks (LCBs) were visualized in six genus species (selecting one plastome per genus). To investigate genes in hypervariable regions predicted by the Mauve algorithm, multi-layer alignments were performed using online mVISTA [26].

2.4. Phylogenetic Diversity

To elucidate the phylogenetic diversity, representative species were selected using online NCBI/BLASTN (megablast, expect threshold 0.05, accessed on 24 January 2024) with A. japonicum sequences as query data (Table S1). This included 24 complete plastomes of the Campanulaceae family and one outgroup (Helianthus annuus, NC_007977). To construct a phylogenetic tree, 33 commonly shared genes were multi-aligned using MAFFT (version 5.3) [27]. To create a maximum-likelihood (ML) tree, genetic distances were calculated with 1000 bootstrap replications using MEGA11 (version 11), and gaps/missing data were resolved with the complete deletion method.

3. Results and Discussion

3.1. Plastome Features of A. japonicum

The A. japonicum plastome was constructed using the 3.15 Gb trimmed sequences from 21,588,275 PE reads. The whole plastome is a circular ring structure measuring 185,875 bp in length with a guanine–cytosine (GC) content of 37.9% (Figure 1). Its structure comprises four parts; each region has a different nucleotide length: LSC (83,795 bp), SSC (35,912 bp), and IRb/IRa (33,084 bp).
A total of 109 genes were obtained through the removal of 23 duplicate genes, of which the psbB gene had three copies, the trnL-CAA gene had four copies, and 20 genes had two copies. From 109 unique genes, we annotated 75 protein-coding genes and 34 RNA-related genes. Twenty-three genes have introns as non-coding sequences, including the ycf3, clpP (×2), and rps12 (×2) genes with two separate introns, and seventeen genes (atpF, petD, petB, rpl2, rpl16, rpoC1, ndhA (×2), ndhB, trnA-UGC (×2), trnG-UCC, trnI-GAU (×2), trnL-UAA, trnK-UUU, and trnV-UAC) have one intron.
Additionally, RNA splicing events, a major cause of protein diversity [28], were observed, such as 12 cis-spliced genes (atpF, clpP (×2), petD, petB, ndhA (×2), ndhB, rpl2, rpl16, rpoC1, and ycf3) and an rps12 trans-spliced gene (Figure S1). In the cis-splicing structures, two clpP copies and ycf3 have two introns. Previous studies indicate that ClpP encodes a protease enzyme crucial for protein processing [29], and ycf3 plays a role in regulating the photosystem of the plant membrane [30].
The functional genes were categorized into three categories: forty-six genes of photosynthesis metabolism, fifty-seven genes of self-replication, and six genes in the “other genes” category (Table 1). In the photosynthesis category, photosystems are crucial multi-subunit complexes for photosynthesis [31]. Photosystem I group contains five psa family genes and two additional genes (ycf3 and ycf4). Although ycf3 and ycf4 genes are not essential for photosynthesis, they are often included in photosystem I [32]. Photosystem II group contains 15 psb family genes that encode protein subunits in photosystem II [33]. In the other categories, ribosome groups contained twelve rps and seven rpl family genes. The unknown group contains two hypothetical genes (ycf1 and ycf2) which have been presumed to be non-functional pseudogenes in plants [34]. However, these pseudogenes were recently found to have potential use as molecular markers [35].

3.2. Plastome Structure with Codon Usage and Repeat Sequences

Plastome structure is influenced by multiple factors, such as the loss/inversion of genes, abundant repetitive elements, gene boundary shifts in IR regions, and gene rearrangements [36]. We analyzed the structural composition using codon usage bias and repeat sequences. Codon usage bias is influenced by nucleotide replication, sequence mutation, and the intensity of gene expression [37]. The RSCU index is an actual frequency ratio of each synonymous codon, and this index directly reflects codon usage bias [38]. To analyze codon usage bias, sixty-one synonymous codons and three stop codons (UGA, UAG, and UAA) were detected based on 75 newly annotated protein-coding genes. Twenty amino acids were encoded by the 64 detected codons. Only two amino acids (methionine and tryptophan) contained one codon, and eighteen amino acids contained two or more codons (Figure 2). Notably, three amino acids (leucine, arginine, and serine) showed complex compositions encoded by six codon types. The RSCU values ranged from 0.37 to 1.83 for all codons, and synonymous codons were classified into three categories for measuring codon preference. Twenty-six high-frequency codons exhibited a preference region (RSCU > 1), thirty-two low-frequency codons had a frequency bias (RSCU < 1), and three codons (AGU, UGG, and CCU) displayed no frequency bias (RSCU  =  1).
High-frequency codons (RSCU > 1) play an important role in plastome mutations because they have a more positive bias, whereas low-frequency codons (RSCU < 1) have a negative bias on codon usage [39]. Of these high-frequency codons, 22 codons possess A or U nucleotides at the end point (third position of codons), and these high A/U preference (22/26, 85%) trends have been reported in other Campanulaceae species [40].
Plastome repeats play a major role in structural variations through insertion–deletion (InDel), duplication, and rearrangement [41]. To investigate structural variations, we identified the 145 repeat sequences consisting of 50 SSRs and 95 long tandem repeats. Generally, SSRs are mainly used in evolutionary studies because of their high variability in genetic polymorphism [42]. All SSRs ranged from 10 to 18 bp in length and were classified into three nucleotides types (thirty-eight mono-, four di-, and eight tri-). The ratio of adenine (A)/thymine (T) repeat units was 100% in the mono- and di-nucleotide types (Table S2). In the long tandem repeats, all repeats showed a period size ranging from 9 to 150 bp, while copy numbers appeared in the range from 1.8 to 11.4 copies (Table S3). Interestingly, both SSRs and long tandem repeats contained more A/T nucleotides than other nucleotide types. These results are similar to previous reports, indicating that repeats in many plant species mainly contain short A or T repeats [43].

3.3. Structural Variation Analysis through Boundaries between IR and SC Regions

Although plastome sequences are generally well conserved, structural variations such as boundary shifts have been reported to be a major cause of evolution [44]. Using six plastome sequences, we investigated boundary shifting such as contraction and expansion events in the IR boundaries. In all boundary regions, gene variations exhibited highly variable trends at the boundary junction parts (Figure 3). At the LSC/IRb (JLB) boundary junction, six genes (ycf2, rpl22, rps19, trnL, rpl2, and rrn16) were found. The ycf2 hypothetical gene was located 51 base pairs to the left of the JLB boundary, while structural variations were observed in other species. Recently, ycf2 has been implicated as a potential molecular marker [45], and its phylogenetic classification shows high polymorphism across family species [46]. At the SSC/IRa (JSA) boundary, four genes (ndhE, ndhF, ndhG, and psaC) were discovered. Generally, a plastome contains many ndh family genes, but only three ndh genes were found in the JSA boundary. These ndh genes cause variations in SSC size through gene loss and retention [47]. Notably, two copies of ndhE genes were located separately at the two boundaries. A complete ndhE gene (305 bp) was situated at the IRb/SSC (JSB) boundary, while a pseudogene (165 bp) shifted by four base pairs from the IRa to the SSC region. The results of boundary shifting analysis indicate that many evolutionary events have occurred between A. japonicum and Campanulaceae species.

3.4. Genomic Divergence Comparison through Rearrangements and Divergent Hotspots

To investigate gene rearrangements within Campanulaceae species, LCB patterns were visualized. Connected color lines illustrate a highly rearranged structure across six species, and IR regions had more stable LCBs than LSC and SSC regions (Figure 4). To better characterize LCBs at the sequence level, the whole sequence of A. japonicum was compared to that of H. asiatica, A. remotiflora, and C. carpatica species. The results indicate that sequence orders had largely moved between A. japonicum and the other species (Figure S2). Both LCB rearrangements and sequence orders showed that considerable variation occurred intensively in the SSC region at positions of 116,880–152,791 bp (Figure 4 and Figure S2).
To clarify the divergent hotspots in hypervariable regions predicted by the LCBs, multi-layer alignment was performed using mVISTA with four genus species. Alignment for homology comparison showed that many non-conserved genes were found in whole positions (Figure 5). These genes were mainly discovered in single-copy regions, which were analyzed to have a high level of rearrangement of LCBs (Figure 4 and Figure 5). The presence of these genes indicates that A. japonicum experienced high structural variability in the plastome.
Generally, conserved genes in IR regions are used as evolutionary stability indicators because these genes maintain plastome stability in most plants [48]. We found ten protein-coding genes and nine RNA-related genes in IR regions (Table S4). Of the detected IR genes, the clpP gene has three exons, three genes (ndhA, trnA-UGC, and trnI-GAU) have two exons, and the remaining genes have one exon. Interestingly, the clpP gene has two introns and three exons consisting of 146 bp for exon-1, 284 bp for exon-2, and 242 bp for exon-3. Previous studies have suggested that the clpP gene may have affected plastome structures with structural variations in mutation hotspots [49].
The LCB and divergent hotspot results differ from previous studies [50] in that coding regions have mostly conserved genes in most plant species. However, large-scale rearrangement events have been reported in coding regions of Campanulaceae species [13,14]. Considering that rearrangement variations occur very rarely [51], many non-conserved genes of coding regions suggest that Asyneuma species have undergone a large evolutionary divergence.

3.5. Plastome Diversity Analysis through Phylogenetic Tree

To better explore the phylogeny of the newly assembled A. japonicum, a phylogenetic ML tree was constructed using 25 plastomes with 33 shared genes. These plastomes used to build the ML tree contained multiple genera, including seven Adenophora species and six Campanula species in the Campanulaceae family. A phylogenetic tree is useful for inferring evolution in different taxonomic species [52], and increased plastome resources enable more precise phylogenetic analysis in Campanulaceae species [53].
The ML trees were divided into three clades, except for H. annuus as an outgroup (Figure 6). In all clades, different genus species were mostly separated with high bootstrap values. In clade I, A. japonicum was classified into a single cluster with strong supports (bootstrap value = 99%), and it was closely related to H. asiatica and the Adenophora group (bootstrap value = 100%). Clades I and II showed that most species were classified into the Adenophora and Campanula groups, respectively. Clade III was split into two major subclades corresponding to the Codonopsis and Cyclocodon groups. These findings show that A. japonicum is in the closest evolutionary position to H. asiatica and that the genus Asyneuma is more distantly related to other genera of Campanulaceae species.

4. Conclusions

In the genus Asyneuma of the Campanulaceae family, although many taxonomic studies have been conducted, a complete plastome has not been previously reported. We first constructed a complete plastome of A. japonicum. The newly assembled plastome was evaluated for structural variations through codon usage, repeat sequences, and junction boundaries. Evolutionary relationships were revealed using rearrangements, divergent hotspots, and phylogenetic tree analysis. Although annotated gene contents are largely conserved, A. japonicum has a large evolutionary divergence due to gene rearrangements. Therefore, our findings suggest that A. japonicum has undergone a markedly different evolutionary history compared to other Campanulaceae family members.

Supplementary Materials

The following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/app14156572/s1, Figure S1: Features of 12 cis-splicing genes in Asyneuma japonicum; Figure S2: Comparison of sequence orders between Asyneuma japonicum and the other three plastome sequences; Table S1: List of 24 plastome sequences from NCBI/GenBank; Table S2: Simple sequence repeats (SSRs) of Asyneuma japonicum using MISA; Table S3: Long tandem repeats of Asyneuma japonicum using Tandem Repeats Finder; Table S4: Features of contained genes on pair of inverted repeat (IR) regions.

Author Contributions

Investigation, data collection, and curation: B.-S.P. and C.-K.K.; conceptualization and methodology: B.-S.P., W.-S.Y. and C.-K.K.; bioinformatics, visualization, and writing: B.-S.P., C.-K.K. and W.-S.Y.; editing and review: Y.-K.K. All authors have read and agreed to the published version of the manuscript.

Funding

This study was funded by Wonkwang University in 2024 (Wonkwang 2024).

Data Availability Statement

Whole sequences of Asyneuma japonicum were submitted to NCBI under accession number OR805474. All relevant data were registered in NCBI database under PRJNA1037590 BioProject, SAMN38190506 BioSample, and SRR26772222 SRA data archive sequences.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Borsch, T.; Berendsohn, W.; Dalcin, E.; Delmas, M.; Demissew, S.; Elliott, A.; Fritsch, P.; Fuchs, A.; Geltman, D.; Güner, A.; et al. World Flora Online: Placing taxonomists at the heart of a definitive and comprehensive global resource on the world’s plants. Taxon 2020, 69, 1311–1341. [Google Scholar] [CrossRef]
  2. Hassler, M. World Plants. Synonymic Checklist and Distribution of the World Flora. Version 19.2. Last Update 17 April 2024. Available online: https://www.worldplants.de (accessed on 25 April 2024).
  3. Lakušić, D.; Eddie, W.M.; Shuka, L.; Lazarević, M.; Barina, Z. The evolving “fate” of Asyneuma comosiforme: Validation of Hayekia, a new monotypic genus of Campanulaceae from Albania. Willdenowia 2019, 49, 81–93. [Google Scholar] [CrossRef]
  4. Andreychuk, R.R.; Kolomiychuk, V.P.; Odintsova, A.V. Morpho-anatomical structure and development of fruit in Asyneuma canescens (Саmpanulaceae). Regul. Mech. Biosyst. 2020, 11, 513–519. [Google Scholar] [CrossRef]
  5. Zoschke, R.; Bock, R. Chloroplast translation: Structural and functional organization, operational control, and regulation. Plant Cell 2018, 30, 745–770. [Google Scholar] [CrossRef]
  6. Roston, R.L.; Jouhet, J.; Yu, F.; Gao, H. Editorial: Structure and Function of Chloroplasts. Front. Plant Sci. 2018, 9, 1656. [Google Scholar] [CrossRef] [PubMed]
  7. Wang, Y.; Wang, S.; Liu, Y.; Yuan, Q.; Sun, J.; Guo, L. Chloroplast genome variation and phylogenetic relationships of Atractylodes species. BMC Genom. 2021, 22, 103. [Google Scholar] [CrossRef]
  8. Yang, Q.; Fu, G.F.; Wu, Z.Q.; Li, L.; Zhao, J.L.; Li, Q.J. Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China. Front. Plant Sci. 2021, 12, 774482. [Google Scholar] [CrossRef] [PubMed]
  9. Daniell, H.; Lin, C.S.; Yu, M.; Chang, W.J. Chloroplast Genomes: Diversity, Evolution, and Applications in Genetic Engineering. Genome Biol. 2016, 17, 134. [Google Scholar] [CrossRef] [PubMed]
  10. Mower, J.P.; Vickrey, T.L. Structural diversity among plastid genomes of land plants. In Advances in Botanical Research; Chaw, S.M., Jansen, R.K., Eds.; Academic Press: Cambridge, MA, USA, 2018; Volume 58, pp. 263–292. [Google Scholar]
  11. Dobrogojski, J.; Adamiec, M.; Lucinski, R. The chloroplast genome: A review. Acta Physiol. Plant 2020, 42, 98. [Google Scholar] [CrossRef]
  12. Yoon, W.S.; Kim, C.K.; Kim, Y.K. The First Complete Chloroplast Genome of Campanula carpatica: Genome Characterization and Phylogenetic Diversity. Genes 2023, 14, 1597. [Google Scholar] [CrossRef]
  13. Cosner, M.E.; Raubeson, L.A.; Jansen, R.K. Chloroplast DNA rearrangements in Campanulaceae: Phylogenetic utility of highly rearranged genomes. BMC Evol. Biol. 2004, 4, 27. [Google Scholar] [CrossRef] [PubMed]
  14. Knox, E.B. The dynamic history of plastid genomes in the Campanulaceae sensu lato is unique among angiosperms. Proc. Natl. Acad. Sci. USA 2014, 111, 11097–11102. [Google Scholar] [CrossRef] [PubMed]
  15. Li, C.J.; Wang, R.N.; Li, D.Z. Comparative analysis of plastid genomes within the Campanulaceae and phylogenetic implications. PLoS ONE 2020, 15, e0233167. [Google Scholar] [CrossRef] [PubMed]
  16. Tillich, M.; Lehwark, P.; Pellizzer, T.; Ulbricht-Jones, E.S.; Fischer, A.; Bock, R.; Greiner, S. GeSeq-versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017, 45, W6–W11. [Google Scholar] [CrossRef] [PubMed]
  17. Carver, T.; Harris, S.R.; Berriman, M.; Parkhill, J.; McQuillan, J.A. Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012, 28, 464–469. [Google Scholar] [CrossRef] [PubMed]
  18. Liu, S.; Ni, Y.; Li, J.; Zhang, X.; Yang, H.; Chen, H.; Liu, C. CPGView: A package for visualizing detailed chloroplast genome structures. Mol. Ecol. Resour. 2023, 23, 694–704. [Google Scholar] [CrossRef] [PubMed]
  19. Zhang, P.; Xu, W.; Lu, X.; Wang, L. Analysis of codon usage bias of chloroplast genomes in Gynostemma species. Physiol. Mol. Biol. Plants 2021, 27, 2727–2737. [Google Scholar] [CrossRef] [PubMed]
  20. Yang, L.; Abduraimov, O.; Tojibaev, K.; Shomurodov, K.; Zhang, Y.-M.; Li, W.-J. Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L. BMC Genom. 2022, 23, 643. [Google Scholar] [CrossRef]
  21. Tamura, K.; Stecher, G.; Kumar, S. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 2021, 38, 3022–3027. [Google Scholar] [CrossRef]
  22. Beier, S.; Thiel, T.; Münch, T.; Scholz, U.; Mascher, M. MISA-web: A web server for microsatellite prediction. Bioinformatics 2017, 33, 2583–2585. [Google Scholar] [CrossRef]
  23. Benson, G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 1999, 27, 573–580. [Google Scholar] [CrossRef]
  24. Amiryousefi, A.; Hyvönen, J.; Poczai, P. IRscope: An online program to visualize the junction sites of chloroplast genomes. Bioinformatics 2018, 34, 3030–3031. [Google Scholar] [CrossRef]
  25. Darling, A.C.E.; Mau, B.; Blattner, F.R.; Perna, N.T. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004, 14, 1394–1403. [Google Scholar] [CrossRef]
  26. Frazer, K.A.; Pachter, L.; Poliakov, A.; Rubin, E.M.; Dubchak, I. VISTA: Computational tools for comparative genomics. Nucleic Acids Res. 2004, 32, W273–W279. [Google Scholar] [CrossRef]
  27. Katoh, K.; Rozewicki, J.; Yamada, K.D. MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinform. 2018, 20, 1160–1166. [Google Scholar] [CrossRef] [PubMed]
  28. Kitamura, K.; Nimura, K. Regulation of RNA Splicing: Aberrant Splicing Regulation and Therapeutic Targets in Cancer. Cells 2021, 10, 923. [Google Scholar] [CrossRef] [PubMed]
  29. Gao, L.L.; Hong, Z.H.; Wang, Y.; Wu, G.Z. Chloroplast proteostasis: A story of birth, life, and death. Plant Commun. 2023, 4, 100424. [Google Scholar] [CrossRef]
  30. Xiang, Y.L.; Jin, X.J.; Shen, C.; Cheng, X.F.; Shu, L.; Zhu, R.L. New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes. Cladistics 2022, 38, 649–662. [Google Scholar] [CrossRef]
  31. Scobeyeva, V.A.; Artyushin, I.V.; Krinitsina, A.A.; Nikitin, P.A.; Antipin, M.I.; Kuptsov, S.V.; Belenikin, M.S.; Omelchenko, D.O.; Logacheva, M.D.; Konorov, E.A.; et al. Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions. Front. Genet. 2021, 12, 674783. [Google Scholar] [CrossRef] [PubMed]
  32. Khan, M.S.; Riaz, R.; Majid, M.; Mehmood, K.; Mustafa, G.; Joyia, F.A. The tobacco chloroplast YCF4 gene is essential for transcriptional gene regulation and plants photoautotrophic growth. Front. Plant Sci. 2022, 13, 1014236. [Google Scholar] [CrossRef]
  33. Yang, T.; Sahu, S.K.; Yang, L.; Liu, Y.; Mu, W.; Liu, X.; Strube, M.L.; Liu, H.; Zhong, B. Comparative analyses of 3,654 plastid genomes unravel insights into evolutionary dynamics and phylogenetic discordance of green plants. Front Plant Sci. 2022, 13, 808156. [Google Scholar] [CrossRef]
  34. Dong, W.; Xu, C.; Li, C.; Sun, J.; Zuo, Y.; Shi, S.; Cheng, T.; Guo, J.; Zhou, S. Ycf1, the most promising plastid DNA barcode of land plants. Sci. Rep. 2015, 5, 8348. [Google Scholar] [CrossRef] [PubMed]
  35. Zhu, B.; Qian, F.; Hou, Y.; Yang, W.; Cai, M.; Wu, X. Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae). PLoS ONE 2021, 16, e0248556. [Google Scholar] [CrossRef] [PubMed]
  36. Li, Z.Z.; Lehtonen, S.; Chen, J.M. The dynamic history of plastome structure across aquatic subclass Alismatidae. BMC Plant Biol. 2023, 23, 125. [Google Scholar] [CrossRef]
  37. Parvathy, S.T.; Udayasuriyan, V.; Bhadana, V. Codon usage bias. Mol. Biol. Rep. 2021, 49, 539–565. [Google Scholar] [CrossRef]
  38. Zeng, Y.-J.; Shen, L.-W.; Chen, S.-Q.; Qu, S.; Hou, N. Codon usage profiling of chloroplast genome in Juglandaceae. Forests 2023, 14, 378. [Google Scholar] [CrossRef]
  39. Yang, L.; Deng, S.; Zhu, Y.; Da, Q. Comparative chloroplast genomics of 34 species in subtribe Swertiinae (Gentianaceae) with implications for its phylogeny. BMC Plant Biol. 2023, 23, 164. [Google Scholar] [CrossRef]
  40. Du, X.; Zeng, T.; Feng, Q.; Hu, L.; Luo, X.; Weng, Q.; Zhu, B. The Complete Chloroplast Genome Sequence of Yellow Mustard (Sinapis alba L.) and Its Phylogenetic Relationship to Other Brassicaceae Species. Gene 2020, 731, 144340. [Google Scholar] [CrossRef] [PubMed]
  41. Charboneau, J.L.M.; Cronn, R.C.; Liston, A.; Wojciechowski, M.F.; Sanderson, M.J. Plastome structural evolution and homoplastic inversions in Neo-Astragalus (Fabaceae). Genome Biol. Evol. 2021, 13, evab215. [Google Scholar] [CrossRef]
  42. Bhattarai, G.; Shi, A.; Kandel, D.R.; Solis-Gracia, N.; da Silva, J.A.; Avila, C.A. Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions. Sci. Rep. 2021, 11, 9999. [Google Scholar] [CrossRef]
  43. Monzon, A.M.; Arrías, P.N.; Elofsson, A.; Mier, P.; Andrade-Navarro, M.A.; Bevilacqua, M.; Clementel, D.; Bateman, A.; Hirsh, L.; Fornasari, M.S.; et al. A STRP-ed definition of Structured Tandem Repeats in Proteins. J. Struct. Biol. 2023, 215, 108023. [Google Scholar] [CrossRef] [PubMed]
  44. Yang, H.; Wang, L.; Chen, H.; Jiang, M.; Wu, W.; Liu, S.; Wang, J.; Liu, C. Phylogenetic Analysis and Development of Molecular Markers for Five Medicinal Alpinia Species Based on Complete Plastome Sequences. BMC Plant Biol. 2021, 21, 431. [Google Scholar] [CrossRef] [PubMed]
  45. Feng, Z.; Zheng, Y.; Jiang, Y.; Pei, J.; Huang, L. Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes. Sci. Rep. 2024, 14, 9783. [Google Scholar] [CrossRef] [PubMed]
  46. Machado, L.O.; Vieira, L.N.; Stefenon, V.M.; Faoro, H.; Pedrosa, F.O.; Guerra, M.P.; Nodari, R.O. Molecular relationships of Campomanesia xanthocarpa within Myrtaceae based on the complete plastome sequence and on the plastid ycf2 gene. Genet. Mol. Biol. 2020, 43, e20180377. [Google Scholar] [CrossRef] [PubMed]
  47. Jiang, H.; Tian, J.; Yang, J.; Dong, X.; Zhong, Z.; Mwachala, G.; Zhang, C.; Hu, G.; Wang, Q. Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences. BMC Plant Biol. 2022, 22, 177. [Google Scholar] [CrossRef]
  48. Gu, X.; Zhu, M.; Su, Y.; Wang, T. A Large Intergenic Spacer Leads to the Increase in Genome Size and Sequential Gene Movement around IR/SC Boundaries in the Chloroplast Genome of Adiantum malesianum (Pteridaceae). Int. J. Mol. Sci. 2022, 23, 15616. [Google Scholar] [CrossRef] [PubMed]
  49. Wu, S.; Chen, J.; Li, Y.; Liu, A.; Li, A.; Yin, M.; Shrestha, N.; Liu, J.; Ren, G. Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives. BMC Plant Biol. 2021, 21, 421. [Google Scholar] [CrossRef] [PubMed]
  50. Zhang, X.; Rong, C.; Qin, L.; Mo, C.; Fan, L.; Yan, J.; Zhang, M. Complete chloroplast genome sequence of Malus hupehensis: Genome structure, comparative analysis, and phylogenetic relationships. Molecules 2018, 23, 2917. [Google Scholar] [CrossRef] [PubMed]
  51. Luo, C.; Li, Y.; Budhathoki, R.; Shi, J.; Yer, H.; Li, X.; Yan, B.; Wang, Q.; Wen, Y.; Huang, M.; et al. Complete chloroplast genomes of Impatiens cyanantha and Impatiens monticola: Insights into genome structures, mutational hotspots, comparative and phylogenetic analysis with its congeneric species. PLoS ONE 2021, 16, e0248182. [Google Scholar] [CrossRef]
  52. Lian, C.; Yang, H.; Lan, J.; Zhang, X.; Zhang, F.; Yang, J.; Chen, S. Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens. PLoS ONE 2022, 17, e0266546. [Google Scholar] [CrossRef]
  53. Kagame, S.P.; Gichira, A.W.; Chen, L.Y.; Wang, Q.F. Systematics of Lobelioideae (Campanulaceae): Review, phylogenetic and biogeographic analyses. PhytoKeys 2021, 174, 13. [Google Scholar] [CrossRef] [PubMed]
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Figure 1. The plastome multi-layer circular map of A. japonicum. The ring map has six circular tracks showing repeat sequences, conserved regions, GC base content, and annotated gene names. The colored boxes represent the gene names in clockwise and counter-clockwise directions.
Figure 1. The plastome multi-layer circular map of A. japonicum. The ring map has six circular tracks showing repeat sequences, conserved regions, GC base content, and annotated gene names. The colored boxes represent the gene names in clockwise and counter-clockwise directions.
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Figure 2. The codon distribution of synonymous codons and stop codons. The histograms show each encoded amino acid with colored boxes indicating individual codons. Amino acids are shown on the x-axis, and RSCU values are presented on the y-axis.
Figure 2. The codon distribution of synonymous codons and stop codons. The histograms show each encoded amino acid with colored boxes indicating individual codons. Amino acids are shown on the x-axis, and RSCU values are presented on the y-axis.
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Figure 3. Visualization of the junction characteristics in four boundaries using IRscope with A. japonicum as a reference. The colored boxes show the four identified regions, and JLB, JSB, JSA, and JLA indicate a junction boundary between the two regions.
Figure 3. Visualization of the junction characteristics in four boundaries using IRscope with A. japonicum as a reference. The colored boxes show the four identified regions, and JLB, JSB, JSA, and JLA indicate a junction boundary between the two regions.
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Figure 4. Features of multiple alignment with local collinear blocks (LCBs) using Mauve progressive algorithm. Color-coded LCBs present conserved sequences of collinear blocks, and color lines represent connecting relationships of each LCB.
Figure 4. Features of multiple alignment with local collinear blocks (LCBs) using Mauve progressive algorithm. Color-coded LCBs present conserved sequences of collinear blocks, and color lines represent connecting relationships of each LCB.
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Figure 5. Visualization of plastome alignments for homology comparison using mVISTA with A. japonicum as a reference. Arrows show location/direction of gene. X- and y-axes indicate genome sequence length and pairwise percent of identity, respectively. Blue-coded box shows conserved genes (exon), and red-coded box shows conserved non-coding sequences (CNSs).
Figure 5. Visualization of plastome alignments for homology comparison using mVISTA with A. japonicum as a reference. Arrows show location/direction of gene. X- and y-axes indicate genome sequence length and pairwise percent of identity, respectively. Blue-coded box shows conserved genes (exon), and red-coded box shows conserved non-coding sequences (CNSs).
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Figure 6. A phylogenetic maximum-likelihood (ML) tree using 25 plastomes with 33 commonly shared genes. The ML bootstrap values and NCBI accession numbers are presented on each node. Excluding the outgroup, 24 plastomes belong to the Campanulaceae family. Clades I, II, and III contain 9, 6, and 9 species, respectively.
Figure 6. A phylogenetic maximum-likelihood (ML) tree using 25 plastomes with 33 commonly shared genes. The ML bootstrap values and NCBI accession numbers are presented on each node. Excluding the outgroup, 24 plastomes belong to the Campanulaceae family. Clades I, II, and III contain 9, 6, and 9 species, respectively.
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Table 1. Plastome gene composition in classified categories.
Table 1. Plastome gene composition in classified categories.
CategoryGroupGene Name
PhotosynthesisPhotosystem IpsaA, psaB, psaC, psaI, psaJ, ycf3 **, ycf4
Photosystem IIpsbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z
NADH 1ndhA *, B *, C, D, E, F, G, H, I, J, K
ATP synthaseatpA, B, E, F *, H, I
Cytochrome 2petA, B *, D *, G, L, N
Rubisco unitrbcL
Self-replicationSmall ribosomerps2, 3, 4, 7, 8, 11, 12 **, 14, 15, 16, 18, 19
Large ribosomerpl2 *, 14, 16 *, 20, 22, 33, 36
RNA polymeraserpoA, B, C1 *, C2
Ribosomal RNArrn4.5, 5, 16, 23
Transfer RNAtrnA-UGC *, trnC-GCA, trnD-GUC, trnE-UUC, trnfM-CAU, trnF-GAA, trnG-GCC, trnG-UCC *, trnH-GUG, trnI-CAU, trnI-GAU *, trnK-UUU *, trnL-CAA, trnL-UAA *, trnL-UAG, trnM-CAU, trnN-GUU, trnP-UGG, trnQ-UUG, trnR-AGC, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA,
trnT-GGU, trnT-UGU, trnV-GAC, trnV-UAC *, trnW-CCA, trnY-GUA
Other genesC-types cytochromes (ccsA), envelope membrane proteins (cemA), protease (clpP **), maturase (matK), unknown (ycf1, ycf2)
1 NADH dehydrogenase; 2 chloroplast cytochrome b6f complex. Common names of family genes are omitted. * and ** indicate that the gene contains one and two introns, respectively.
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Park, B.-S.; Yoon, W.-S.; Kim, C.-K.; Kim, Y.-K. Plastome Evolution of Asyneuma japonicum: Insights into Structural Variation, Genomic Divergence, and Phylogenetic Tree. Appl. Sci. 2024, 14, 6572. https://doi.org/10.3390/app14156572

AMA Style

Park B-S, Yoon W-S, Kim C-K, Kim Y-K. Plastome Evolution of Asyneuma japonicum: Insights into Structural Variation, Genomic Divergence, and Phylogenetic Tree. Applied Sciences. 2024; 14(15):6572. https://doi.org/10.3390/app14156572

Chicago/Turabian Style

Park, Byeong-Seon, Won-Sub Yoon, Chang-Kug Kim, and Yong-Kab Kim. 2024. "Plastome Evolution of Asyneuma japonicum: Insights into Structural Variation, Genomic Divergence, and Phylogenetic Tree" Applied Sciences 14, no. 15: 6572. https://doi.org/10.3390/app14156572

APA Style

Park, B. -S., Yoon, W. -S., Kim, C. -K., & Kim, Y. -K. (2024). Plastome Evolution of Asyneuma japonicum: Insights into Structural Variation, Genomic Divergence, and Phylogenetic Tree. Applied Sciences, 14(15), 6572. https://doi.org/10.3390/app14156572

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