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Structural variation and evolution of chloroplast tRNAs in green algae

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Bioinformatics and Genomics

Introduction

As autotrophic lineages with primary plastids, Viridiplantae, Rhodophyta and Cyanobacteria all originated from an endosymbiotic event, which also marked the origin of oxidative photosynthesis in eukaryotes (Keeling, 2010; Leliaert, Verbruggen & Zechman, 2011). Chlorophyta and Streptophyta are two major lineages that split early in the evolution of green plant (O’Kelly, 2007). The two taxa have subsequently produced the widespread and diverse groups. Among them, green algae in different environments have always maintained relatively independent evolution, not only shows obvious differences in biological characteristics, but also has great differences in genome genetic characteristics (Barsanti & Gualtieri, 2006). It is generally accepted that the Streptophyta branched out into the Land plants and Charophyta. The Chlorophyta gradually formed the extremely widespread core Chlorophyta and other green algae (Leliaert et al., 2012).

The core Chlorophyta including Ulvophyceae, Trebouxiophyceae, Chlorophyceae (UTC) and two small groups namely Chlorodendrophyceae and Pedinophyceae (Fučíková et al., 2014). In the core Chlorophyta, the evolutionary relationships between the various branches and between the UTC branches have been increasingly studied (Lemieux et al., 2015; Leliaert et al., 2016). Chlorodendrophyceae, as a small group of the core Chlorophyceae, is traditionally attributed to prasinophyceae and is considered to be an earlier branch of the core Chlorophyceae. Based on 18s rDNA data, a close relationship between Chlorodendrophyceae and UTC is confirmed (Cocquyt et al., 2010). As the main branch of the core Chlorophyta, UTC has abundant species, diverse living environments and the complicated evolutionary relationships. The monophyletic origin of the Chlorophyceae has been confirmed by analysis of a large number of genome sequences (Luo et al., 2010).

Because of the maternal genetic characteristics of chloroplasts, the chloroplast genome is not only structurally stable, but also relatively conservative in number, composition and arrangement (Palmer & Genetics, 1985; Raubeson & Jansen, 2005; Fučíková, Lewis & Lewis, 2016). Thus, studying the evolutionary relationships of species taxa from the perspective of the chloroplast genome can compensate for the deficiencies caused by the analysis of data such as 18S as well as 26S rDNA.

The chloroplast genome structure is usually circular, rarely linear, and consists of four parts, the large single copy region (LSC), the small single copy region (SSC) and the inverted repeat regions A and B (IRA, IRB) (Zhang et al., 2012). In most of angiosperm chloroplast genomes, there are generally about 120 coding genes, of which about 80 genes encode proteins involved in photosynthesis and gene expression, another 30 or so genes encode tRNAs (Greiner, Lehwark & Bock, 2019) and a few genes encode rRNAs (Masanori et al., 2003; Gao, Ying-Juan & Wang, 2010) (Fig. 1).

The chloroplast genome of C. reinhardtii.

Figure 1: The chloroplast genome of C. reinhardtii.

The 203828bp genome contains 109 unique genes, including 10 ribosomal RNA genes, 29 transfer RNA genes, and 69 protein-coding genes. The annotated genes are colored according to the functional categories shown in the legend at the lower left.

tRNA is essential for linking and matching mRNA and amino acids during protein synthesis and is functionally stable. The number of nucleotides of tRNA is also relatively conservative, usually 75–95 nt nucleotides (Goodenbour & Pan, 2006). Further, the clover-like secondary structure formed by nucleotide pairing and the inverted L-like tertiary structure formed by further folding have been relatively stable throughout evolution (Holley et al., 1965). So, it has been highly conserved in genetic evolution. Finally, based on the distribution of tRNAs in the eukaryotic chloroplast genome, little is known about the structure and its evolutionary mechanisms. We selected chloroplast tRNAs from green algae to investigate the structural variation and evolutionary features of chloroplast tRNAs.

In our study, we analyzed 14 species from five orders of the core Chlorophyceae to infer the possible evolutionary relationships of tRNAs in the chloroplast genome of Chlorophyceae. From the analysis results, we have not only obtained the sequence characteristics and structural features of tRNAs in the chloroplast genome of Chlorophyceae, but also discovered that chloroplast tRNAs of Chlorophyceae are consistent with those of monocotyledons and gymnosperms in terms of evolutionary patterns, sharing a common multi-phylogenetic pattern and rooted in a multiple common ancestor.

Materials & Methods

Sequence analysis of chloroplast tRNA genome

We selected 14 representative species from the NCBI genome database in five classes of the core green algae order. They are as following: Chlamydomonas reinhardtii (NC_005353.1), Hafniomonas laevis (NC_028583.1), Gonium pectoral (NC_020438.1), Characiochloris acuminata (NC_028584.1), Phacotus lenticularis (NC_028587.1) in the volvocales; Mychonastes homosphaera (NC_029671.1), Neochloris aquatica (NC_029670.1), Bracteacoccus giganteas (NC_028586.1), Tetradesmus obliquus (NC_008101.1), Ankyra judayi (NC_029735.1) in the sphaeropleales; Schizomeris leibleinii (NC_015645.1), Stigeoclonium helveticum (NC_008372.1) in the chaetophorales; Oedogonium cardiacum (NC_011031.1) in the oedogoniales and Floydiella terrestris (NC_014346.1) in the chaetopeltidales. We then used tRNAscan-SE software (http://lowelab.ucsc.edu/tRNAscan-SE/) to analyze the whole genome sequences of chloroplasts from different species (Chan et al., 2019). The specific parameters set by the tRNAscan-SE software are: sequence source: mixed (general tRNA model); Search mode: default; Query sequence: formatted (FASTA); Genetic Code for tRNA Isotype Prediction: universal. From the output of tRNAscan-SE, we can get the overall statistical information as well as the summary data of the whole search (Chan & Lowe, 2019). Through the analysis of the data, the total number of tRNAs in the chloroplast genome of each species, the distribution of anticodons of the chloroplast tRNA, the number of tRNAs with introns, and the gene sequence length of each subtype tRNA were recorded.

Multiple sequence alignment

We grouped the tRNA nucleotide sequences of 20 isoforms sequentially and performed tRNA isoform multiple sequence alignment using Multalin program to analyze the conserved tRNA isoform nucleotide sequences. Multalin’s parameter settings: Sequence input format: Auto, Result page format: a coloured image, Symbol comparison Table—Gap open def.—Gap ext def.: Blosum62-12-2, Gap penalty at opening: default, Gap penalty at extension: default, Gap penalty at extremities: none, One iteration only: no, Text size (image only): MediumBold, Text colour (image only): black, Background colour: white, High consensus colour: red, Low consensus colour: blue, Neutral colour: black, High consensus value: 90%, Low consensus value: 50%, Output style: Normal, Help Maximum line length: 130, Help Graduation step: 10 (Mohanta et al., 2017).

Phylogenetic tree construction

We constructed a phylogenetic tree based on the genomic sequences of tRNAs using MEGA X. Clustal format files of all tRNAs were then created by Clustal X 2.0 software. We used MEGA X software to convert the generated tRNA Clustal files to MEGA format. For the model selection for constructing a phylogenetic tree, the specific parameters are as follows: Models: Find Best DNA/Protein Models (ML); Select a Genetic Code: Standard; Analysis: Tree to Use: Automatic (Neighbor-joining tree), Statistical Method: Maximum likelihood: Substituton Model: Substitutions Type Nucleotide; Data Subset To USE: gaps/Missing Data Treatment: Partial deletion, Site Coverage Cutff (%): 95, Branch Swap Filter: very Strong; System Resource Usage: number of Threads: 3. Among the results of the resulting analysis, we selected the model with the lowest BIC index to construct the phylogenetic tree. Then we used the Phylogeny function to construct the developmental tree, the specific parameters are as follows: Analysis: Statistical Method: Maximum likelihood; Phylogeny test: Bootstrap method, No. of Bootstrap Replications: 1000; Model: Substitutions Type: Nucleotide; Model/Method: kimura-2-parameter model; Rates and patterns: rates among sites: gamma distributed with invariant sites (G+I), no of discrete gamma categories: 5 (Kimura, 1980).

tRNA transition /transversion analysis

We used the tRNA files in MEGA format in the MEGA software which further analyzed the transition /transversion rate of all tRNAs (Tamura, Nei & Kumar, 2004; Sudhir et al., 2018). The specific analysis process and parameters are as follows: Models: Compute MCL Transition/Transversion Bias, Scope: All Selected Taxa, Statistical Method: Maximum Composite Likelihood, Substitutions Type: Nucleotide, Model/Method: Tamura-Nei model, Gaps/Missing Data Treatment: Pairwise deletion.

Gene loss and duplication analysis

We analyzed chloroplast genomic tRNA gene duplication/loss events in chlorophyceae by Notung2.9 software (Chen, Durand & Farach-Colton, 2000; Vernot et al., 2008). We then used NCBI (https://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cg) to construct species trees for the analysis of duplication loss events of tRNA genes. Species used for construction include C. reinhardtii, H. laevis, G. pectorale, C. acuminata, and P. lenticularis in the volvocales; M. homosphaera, N. aquatica, B. giganteus, T. obliquus and A. judayi in the sphaeropleales; S. leibleinii and S. helveticum in the chaetophorales; O. cardiacum in the oedogoniales and F. terrestris in the chaetopeltidales. After constructing the species tree, import it into Notung2.9 software, and reconcile and analyze the 20 subtype tRNA gene trees and species tree one by one to obtain gene duplication and deletion nodes.

Results

Analysis of the number and sequence length of tRNA in chloroplast genome

For a more comprehensive analysis of the evolution of chloroplast tRNA genomes in Chlorophyceae (the core Chlorophyceae), fourteen species from the NCBI Genome Database were randomly selected from the main five orders of Chlorophyceae. Genome Database of 14 species. Subsequently, the tRNAscan-SE software was used to perform detailed sequence analysis of the chloroplast genomes of 14 species. Through preliminary analysis, the results show that the chloroplast genomes of all species contain 28-32 tRNAs. C. reinhardtii, C. acuminata, G. pectorale, N. aquatica, M. homosphaera and T. obliquus encode 29 tRNAs; A. judayi and O. cardiacum encode 32 tRNAs; and H. laevis, P. lenticularis, B. giganteus, S. leibleinii, S. helveticum and F. terrestris encode 31, 30, 27, 30, 28 and 25 tRNAs, respectively (Table 1). For the predicted 406 chloroplast tRNA gene sequences (except for 3 sequences containing introns), the length of the chloroplast tRNA gene sequence of all species ranges from 71 nt (NC_005353.1). tRNA 29-CysGCA) to 91 nt, and maintains an average of 75 nt, of which 73 nt and 74 nt length contain 32% and 28% respectively. Not only that, among the 20 subtypes of tRNAs, tRNAGlu, tRNALys and tRNAV al contain 73 nt, 72 nt and 73 nt nucleotides, respectively. The nucleotides contained in tRNAAsn, tRNAAsp, tRNACys, tRNAGln, tRNAGly, tRNAHis, tRNAPhe, tRNAPro, tRNAThr and tRNATrp were all below the mean value (75 nt), while the nucleotides contained in tRNALeu, tRNASer and tRNATyrare all above 80 nt nucleotides (Fig. 2) (Data S1).

Table 1:
Names of all species and the number of tRNAs in the chloroplast genome.
No. Name of the order Name of the family Name of the genus Name of the species No. of tRNAs
1 Chlamydomonadales Chlamydomonadaceae Chlamydomonas C. reinhardtii 29
2 Chlamydomonadales Dunaliellaceae Hafniomonas H. laevis 31
3 Chlamydomonadales Characiochloridaceae Characiochloris C. acuminata 29
4 Chlamydomonadales Phacotaceae Phacotus P. lenticularis 30
5 Chlamydomonadales Volvocaceae Gonium G. pectorale 29
6 Sphaeropleales Neochloridaceae Neochloris N. aquatica 29
7 Sphaeropleales Mychonastaceae Mychonastes M. homosphaera 29
8 Sphaeropleales Sphaeropleaceae Ankyra A. judayi 32
9 Sphaeropleales Bracteacoccaceae Bracteacoccus B. giganteus 27
10 Sphaeropleales Scenedesmaceae Tetradesmus T. obliquus 29
11 Chaetophorales Schizomeridaceae Schizomeris S. leibleinii 30
12 Chaetophorales Chaetophoraceae Stigeoclonium S. helveticum 28
13 Oedogoniales Oedogoniaceae Oedogonium O. cardiacum 32
14 Chaetopeltidales Chaetopeltidaceae Floydiella F. terrestris 25
DOI: 10.7717/peerj.11524/table-1
Distribution of the percentage of chloroplast tRNA gene sequence length in all species.

Figure 2: Distribution of the percentage of chloroplast tRNA gene sequence length in all species.

Anticodon distribution of chloroplast tRNA

To determine the distribution of anticodons in chloroplast tRNA, we further analyzed the chloroplast genome sequences of 14 species in detail using tRNAscan-SE software. The results show that chloroplast tRNAs of all species contain 23-27 antisense codon types, while each species encodes 25-32 antisense codons. The most common types of anti-codons are: ACG (tRNAArg), GAA (tRNAPhe), GTT (tRNAAsn), GTC (tRNAAsp), GTG (tRNAHis), GAT (tRNAIle), GTA (tRNATyr), GCA (tRNACys), CAT (tRNAMet), CCA (tRNATrp), TGC (tRNAAla), TCC (tRNAGly), TGG (tRNAPro), TGT (tRNAThr), TAC (tRNAV al), TGA (tRNASer), TAG (tRNALeu), TTT (tRNALys), TTG (tRNAGln), GCT (tRNASer) and TCT (tRNAArg). In addition, the results show that compared with the analyzed anticodons of other Chlorophyta chloroplast tRNAs, some anticodons are missing. Among them, GCC (tRNAGly) is missing only in N. aquatica; TTC (tRNAGlu) is only missing in F. terrestris; while TAA (tRNALeu) is missing in B. giganteus, T. obliquus, F. terrestris, S. leibleinii and O. cardiacum (Table 1).

Multiple sequence alignment analysis of chloroplast tRNA

After categorizing the 20 subtypes of tRNA, the corresponding nucleotide sequence of each was analyzed by sequence alignment (Table 2). The results show that the Ψ-loop contains a conserved sequence of U-U-C-x-A in the secondary structure of the 20 tRNA isoforms. And the first position of most tRNA nucleotide sequence has G nucleotide, while tRNAAsn and tRNAGln have U in the first position, tRNATrp and tRNAV al have A in the first position, and tRNAPro has C in the first position. Subsequently, no identical nucleotide sequence was found at positions 2 to 7 of the acceptor arm. In the D-arm, 7 subtypes of tRNA were found to have a conserved sequence of GCNN (N represents any nucleotide), and there is a conserved sequence of AGU- (- represents any nucleotide or no nucleotide) in the D-loop. This is consistent with the reported results of the conserved consensus sequence 7GUGGCNNAGU16- starting with the 7th nucleotide of the acceptor arm in a typical tRNA (Laslett & Canback, 2004). In addition, it was found that tRNAAla, tRNAArg, tRNAAsn, tRNAGly, tRNALle and tRNAphehave the same nucleotide sequence as G-C-U-C in the D-arm.

Table 2:
Sequence alignment of each secondary structure nucleotide of tRNA.
tRNA Isotypes Acceptor Arm D-arm D-loop AC- arm Anti-codon loop Variable loop Ψ-arm Ψ-loop
Ala G-G-G-G-G-U-A G-C-U-C A-G-U-U-G-G-U-A C-U-G-C-C U-U-U-G-C-A-A X-U-G-U-C A-G-G-G-G U-U-C-G-A-A-U
Arg G-G-G-C-U-X-G G-C-U-C A-G-U-G-G-A-X-U-X2-A X3-G-X C-U-U-C-U-A-A X-A-G-U-X X2-G-G-G U-U-C-G-A-A-U
Asn U-C-C-U-C-A-G G-C-U-C A-G-U-G-G-U-A G-U-C-G-G C-U-G-U-U-A-A U-G-G-U-C G-U-A-G-G U-U-C-A-A-G-U
Asp G-G-G-A-U-U-G G-U-U-C A-A-U-U-G-G-U-U-A C-C-G-C-C C-U-G-U-C-A-C A-A-G-U-U G-C-G-G-G U-U-C-G-A-G-U
Cys G-G-C-G-G-C-A G-C-C A-A-G-U-G-G-U-A-A G-A-G-G-A U-U-G-C-A-A-A U-A-U-U-C C-C-C-A-G U-U-C-G-A-A-U
Gln U-G-G-G-G-C-G G-C-C A-A-G-U-G-G-U-A-A G-U-G-G-U U-U-U-U-G-G-U C-A-U-U-C G-X-A-G-G U-U-C-G-A-A-U
Glu G-C-C-C-C-C-A G-U-C-U A-G-A-G-G-C-C-U-A C-C-U-C-C C-U-U-U-C-A-C G-A-A-A-C G-G-G-G-A U-U-C-G-A-A-U
Gly G-C-G-G-A-U-X G-C-U-C A-G-U-X-G-G-U-A C-X2-C-C U-U-G-C-C-A-A A-U-G-U-C G-C-G-C-G U-U-C-G-A-X-U
His G-C-G-G-G-C-G G-C-C A-A-G-U-G-G-U-A-A G-U-G-G-A U-U-G-U-G-A-C C-A-U-U-C G-C-G-G-G U-U-C-G-A-A-C
Leu G-C-C-U-U-U-G A-U-G G-A-A-U-X-G-G-U-A-G-A X2-G-G-X U-U-U-A-A-A-A U-G-C-U-X-U-X 3-A-X-G-X-G-C-G-U G-X-C-G-G U-U-C-A-A-G-U
Lle G-G-G-C-U-A-U G-C-U-C A-G-U-U-G-G-U-U-A C-A-C-C-C U-U-G-A-U-A-A A-G-G-U-X-C G-X-A-G-G U-U-C-A-A-G-U
Lys G-G-G-U-U-A-C A-C-U-C A-A-U-G-G-U-A U-C-G-G C-U-U-U-U-A-A U-A-A-G-U-U C-U-G-G-G U-U-C-G-A-G-U
Met X-G-C-A-G-X 2 G-X2-C A-G-U-C-G-G-X-U-A U-X-C-G-X C-U-C-A-U-A-A A-U-G-U-C G-C-A-G-G U-U-C-A-A-X-U
phe G-C-C-G-G-G-G G-C-U-C A-G-U-X-G-G-U-A G-A-G-G-A U-U-G-A-A-A-A G-U-G-U-C A-C-C-A-G U-U-C-A-A-U-C
Pro C-G-G-G-A-U-G G-C-G-C A-G-U-U-U-G-G-U-A U-X-U-G-C U-U-U-G-G-G-A G-G-G-U-C G-C-A-G-G U-U-C-G-A-A-U
Ser G-G-A-A-A-G-A G-C-X G-A-G-U-G-G-U-C-G-A-A X-C-G-G-X U-U-G-G-A-A-A U-G-U-A-G-C-X 6-G-X-U-X4-A-C-C G-A-G-G-G U-U-C-G-A-A-U
Thr G-C-C-U-G-C-U A-C-U-C A-A-U-C-G-G-U-A U-C-G-G-U U-U-U-G-U-A-A A-G-G-U-U A-U-C-G-G U-U-C-A-A-C-U
Trp A-C-G-C-C-C-U G-U-U-C A-G-U-X-G-G-U-A C-A-G-G-U U-U-C-C-A-A A-U-G-U-C G-U-G-G-G U-U-C-A-A-G-U
Tyr G-G-G-U-C-G-A C-C-C-G A-G-U-X-G-G-U-U-A-A G-C-G-G-A U-U-G-U-A-A-A U-G-G-C-U-X-A-X-G-C-C-U-A-C G-C-U-G-G U-U-C-G-A-A-U
Val A-G-G-C-C-C-A A-C-U-C A-G-U-U-G-G-U-A A-U-U-G-C C-U-U-A-C-A-A A-X-G-U-C A-U-C-G-G U-U-C-G-A-G-U
DOI: 10.7717/peerj.11524/table-2

No conserved sequences were found in the anticodon arms and variable loops, but in the anticodon loops, a conserved U nucleotide was found at the second nucleotide. In addition to tRNACys, tRNAGlu, tRNAGly and tRNAphe, it was found that there are conserved nucleotide sequences of GG at positions 52 and 53 (that is, positions 4 and 5 of the Ψ-arm); for positions 54, 55 and 56, the 58th and 60th nucleotides (that is, the 1, 2, 3, 5, and 7 positions of the Ψ-arm), except for tRNAHis and tRNAphe, all have the conserved nucleotide sequence of U-U-C-x-A-x-U. Among them, the nucleotide sequence of tRNAHis at positions 54-60 is U-U-C-G-A-A-C; the nucleotide sequence of tRNAphe at positions 54-60 is U-U-C-A-A-U-C.

Analysis of the number of each structure of chloroplast tRNA

After analyzing and sorting out the chloroplast tRNAs of 14 species, a total of 406 tRNA sequences (without 3 containing a group of introns) tRNA sequences were obtained. After statistical analysis of the number of nucleotides in each secondary structure of 406 tRNAs, we found that in the acceptor arm, the number of nucleotides is 6–7, of which 6-nucleotide tRNA accounts for 0.32%, 7-nucleotide tRNA accounted for 96.8%, which is consistent with the result that the number of acceptor arm nucleotides in the study is 7; In the D-arm, the number of nucleotides is 2–4, of which 3 nucleotides tRNA accounted for 28.3%, 4 nucleotides tRNA accounted for 71.4%, only NC_005353.1.tRNACys D-arm is 2 nucleotides; In the D-ring, the number of nucleotides is 7–12, accounting for 12.8%, 24.6%, 44.6%, 7.1%, 11.6% and 0.25% respectively. Only NC_008372.1.tRNATyr has 12 nucleotides. In the anticodon arm, the number of nucleotides is 4–5, of which tRNA containing 4 nucleotides accounted for 8.9%, and the proportion of tRNA containing 5 nucleotides was 91.1%. In the anticodon loop, the number of nucleotides is 7–9, 99.0% of the tRNA nucleotides are 7, and 0.73% of the tRNA nucleotides are 9. Similarly, only one tRNA has an anticodon ring structure with a nucleotide number of 8. For the variable loop, as the structure with the largest number of nucleotide changes in the tRNA secondary structure, among the 406 tRNAs tested, the number of nucleotides in the variable loop ranged from 3–22 nt, but 77.44% tRNA, the number of nucleotides in the variable loop is 5. In addition, we enumerate the secondary structures of three different tRNAs with variable loops/stems (Fig. S1). In the Ψ-arm, only one tRNA has 4 nucleotides, and the remaining 405 tRNAs have 5 nucleotides; in the Ψ-ring, the number of tRNA nucleotides is all 7, and there is no special structure of the variation. Therefore, it is speculated that the Ψ-loop in the tRNA secondary structure is the most conserved structural unit, which is consistent with the results of the previous multiple sequence alignments (Fig. 3).

Nucleotide proportion diagram of each element of tRNA secondary structure.

Figure 3: Nucleotide proportion diagram of each element of tRNA secondary structure.

Among the 406 tRNA measured, the tRNA with seven nucleotide length in the receptor arm, anticodon loop and Ψ-loop accounted for 96.8%, 99.01% and 99.75% of the measured tRNA, respectively. The tRNA with four nucleotide length in D-arm accounted for 71.43%, and the tRNA with five nucleotide length in inverse curvature arm, variable loop and Ψ-arm accounted for 91.13%, 70.44% and 100%, respectively. The tRNA of D-loop nucleotide length of eight accounted for 24.63% of the detected tRNA.

Analysis of introns in chloroplast tRNA

After analyzing the chloroplast tRNA genome sequence of all Chlorophyta, we found that the chloroplast tRNA of M. homosphaera (NC_029670.1) .tRNALeu (TAA)) in the sphaeropleales, S. leibleinii (NC_015645.1). tRNA Leu (TAA)) and S. helveticum (NC_008372.1). tRNALeu (TAA)) in the chaetophorales contain introns (Fig. 4). These three groups of introns are all located in the anticodon loop of tRNA, with nucleotide lengths of 174, 253, and 243, respectively. The starting points in the tRNA structure are 38, 39, 39, and from the analysis results, the scores (Internal scores) of these three tRNAs are 35.9 bits, 20.7 bits and 33.4 bits, respectively, indicating that they may not be functional. Subsequently, we selected the chloroplast genome sequences of five plants from the NCBI genome database, streptophytina Chaetosphaeridium globosum (NC_004115), Mesostigma viride (NC_002186), angiospermae Liriodendron tulipifera (NC_008326), monocotyledon Zea mays (NC_001666), and dicotyledons Vitis vinifera (NC_007957.1). The chloroplast tRNA gene sequences of these 5 plants were predicted by tRNAscan-SE software. It was found that tRNALeu (TAA), which also contains introns, was found in streptophytina, but this tRNA was not found in the chloroplast genome sequence of angiospermae L. tulipifera, monocotyledon Z. mays, and dicotyledons A. thaliana. Therefore, it is speculated that tRNALeu (TAA) containing introns in the chloroplast genome of green plants first appeared in Chlorophyta and Streptophytina. In addition, the chloroplast genome tRNALeu of angiosperms, monocots, and dicots was used as a peripheral group to construct a phylogenetic tree of tRNALeu (Fig. 5). It is clear from tree that the tRNALeu containing introns are close to each other on the evolutionary branch.

Diagram of tRNA secondary structure containing introns.

Figure 4: Diagram of tRNA secondary structure containing introns.

Among the chloroplast tRNA genomic sequences analysed from green algae, there are three sets of tRNA sequences with introns whose positions are all located in the anticodon loop. (A)–(C) show the secondary structure of these three tRNA sequences, with red and blue markers indicating the G–C and A–U bonds, respectively. (A) represents M. homosphaera, NC_029670.1.tRNALeu-TAA. (B) represents S. helveticum, NC_008372.1. tRNALeu-TAA. (C) represents S. leibleinii, NC_015645.1 tRNALeu- TAA.
The phylogenetic tree of tRNALeu.

Figure 5: The phylogenetic tree of tRNALeu.

The phylogenetic tree of tRNALeu is divided into three classes. From the tree, it can be seen that the tRNALeu containing introns is the closest in relation to each other. The classes represented by the species in the tree are colored in the lower left illustration.

Transition, transversion bias analysis

To better understand tRNA evolution, we performed MCL conversion and escape bias analyses on 20 tRNA isoforms measured in chloroplasts and compared the results with those of tRNA analysis in cyanobacteria and monocot chloroplasts (Mohanta et al., 2017; Mohanta et al., 2019). The results showed that although green algae and monocotyledon belong to eukaryotes, the transition and transversion results were consistent with the analysis results of cyanobacteria tRNA, and the chloroplast tRNA conversion rate of green algae was higher than the transversion rate. On the contrary, it is inconsistent with the chloroplast tRNA analysis results of monocotyledonous plants, because we found that in the chloroplast tRNA analysis results of monocotyledonous plants, the transformation rate and transversion rate of tRNAAla, tRNAAsn, tRNAAsp, tRNAHis, tRNAPhe and tRNAPro were almost equal, but did not appear in the chloroplast tRNA analysis results of green algae. In addition, from the data analysis, we found that the transition rate of tRNAAsp and tRNAV al is significantly higher than the transition rate. The transition rate between A ↔G in tRNAV al is as high as 30.95%, second only to the transition rate of C ↔U (33.32%) in tRNATrp. Not only that, the transition rate between A ↔C in tRNAV al is the lowest among all tRNAs analyzed, only 0.58% (Table 3).

Phylogenetic tree analysis of Chlorophyta chloroplast tRNA

After aligning and analyzing 406 tRNA sequences, a phylogenetic tree was constructed using all tRNA genome sequences. After sorting and analyzing, according to the evolutionary relationship of the phylogenetic tree, all tRNAs are divided into four clusters, the first cluster of tRNAs are: tRNAMet, tRNAArg, tRNATyr, tRNALeu, tRNASer; the second cluster of tRNAs are: tRNAHis, tRNAMet, tRNAGln, tRNACys , tRNAPhe, tRNAThr; the third cluster of tRNAs are: tRNAArg, tRNAHis, tRNAGln, tRNAGlu, tRNATrp, tRNAV al, tRNAlle, tRNAAsn, tRNALys; the fourth cluster of tRNAs are: tRNAAla, tRNAAsp, tRNAGly, tRNAPro, tRNAMet (Fig. 6). In addition, we can find several interesting phenomena from the evolutionary tree: firstly, there are multiple branches of tRNAArg and tRNAMet in the entire phylogenetic tree. It is speculated that this may be due to multiple mutations of these two tRNAs during the evolution process. Secondly, in the third cluster, tRNAArg (TCT) is the closest to tRNAAsn (GTT) and tRNATrp (CCA). From the sequence comparison results, the sequence similarity between tRNAArg (TCT) and tRNA Asn (GTT) was very high, reaching 80%. Similarly, the sequence similarity between tRNAArg (TCT) and tRNATrp (CCA) was also very high, reaching 77.36% (Figs. 7 and 8). The evolutionary relationship between tRNAArg(TCT) and tRNAArg(ACG) (TCG) is closer than that of other tRNAArg in the evolutionary tree, so we speculate that tRNAArg (TCT) is evolved from tRNAArg (ACG) (TCG); tRNAArg (CCT) has two points branches, one of which is similar to tRNAMet in genetic relationship, and the other branch is likely to be present in the branches of tRNASer due to mutations during evolution. In addition, in the evolutionary tree, the branches of tRNASer are obviously denser, which indicates that tRNASer seems to be susceptible to mutations. The secondary structure prediction results of tRNASer by tRNAscan-SE software also support it. There are three branches of tRNAMet (CAT), which are closely related to tRNAArg (CCT), tRNAThr (TGT) and tRNAPro (TGG).

Green algae chloroplast tRNA phylogeny tree.

Figure 6: Green algae chloroplast tRNA phylogeny tree.

In the constructed phylogenetic tree, all tRNAs are divided into four clusters according to the evolutionary relationship of the phylogenetic tree. It is speculated from the branching display of the phylogenetic tree that the fourth cluster of tRNA is relatively advanced in the evolutionary relationship. There are mutations in the evolution of green algae chloroplast tRNA, with tRNAMet, tRNAArg and tRNASer being the most obvious.
Table 3:
Transition rate/transversion rate of tRNA.
Ala A U C G Leu A U C G
A ___ 5.04 4.52 21.42 A ___ 3.93 3.65 18.60
U 3.77 ___ 12.51 6.08 U 3.88 ___ 16.34 4.88
C 3.70 13.95 ___ 6.08 C 3.88 17.60 ___ 4.88
G 13.29 5.04 4.52 ___ G 14.79 3.93 3.65 ___
Arg Lys
A ___ 4.98 4.96 17.89 A ___ 4.10 3.19 19.54
U 4.50 ___ 13.85 5.78 U 3.67 ___ 13.68 3.54
C 4.50 13.91 ___ 5.78 C 3.67 17.56 ___ 3.54
G 13.93 4.98 4.96 ___ G 20.25 4.10 3.19 ___
Asn Met
A ___ 2.96 2.44 20.14 A ___ 7.42 7.39 10.19
U 2.25 ___ 20.19 3.57 U 6.89 ___ 10.70 8.17
C 2.25 24.50 ___ 3.57 C 6.89 10.74 ___ 8.17
G 12.70 2.96 2.44 ___ G 8.60 7.42 7.39 ___
Asp Phe
A ___ 1.32 1.39 28.74 A ___ 3.88 3.61 17.25
U 0.96 ___ 22.97 1.76 U 3.64 ___ 18.26 4.87
C 0.96 21.68 ___ 1.76 C 3.64 19.62 ___ 4.87
G 15.74 1.32 1.39 ___ G 12.89 3.88 3.61 ___
Cys Pro
A ___ 2.60 2.71 13.68 A ___ 5.18 4.39 21.70
U 2.50 ___ 27.16 2.97 U 3.53 ___ 12.50 6.73
C 2.50 26.08 ___ 2.97 C 3.53 14.74 ___ 6.73
G 11.51 2.60 2.71 ___ G 11.38 5.18 4.39 ___
Gln Ser
A ___ 5.12 5.62 16.35 A ___ 6.81 5.59 12,38
U 3.09 ___ 18.44 6.49 U 5.11 ___ 13.16 7.48
C 3.09 16.78 ___ 6.49 C 5.11 16.03 ___ 7.48
G 7.80 5.12 5.62 ___ G 8.47 6.81 5.59 ___
Glu Thr
A ___ 2.98 4.64 20.10 A ___ 4.96 3.39 15.37
U 3.17 ___ 21.18 4.21 U 4.22 ___ 14.38 4.09
C 3.17 13.59 ___ 4.21 C 4.22 21.06 ___ 4.09
G 15.11 2.98 4.64 ___ G 15.87 4.96 3.39 ___
Gly Trp
A ___ 3.85 3.97 21.20 A ___ 2.95 2.43 9.83
U 2.81 ___ 17.96 4.57 U 2.40 ___ 27.45 3.03
C 2.81 17.40 ___ 4.57 C 2.40 33.32 ___ 3.03
G 13.04 3.85 3.97 ___ G 7.78 2.95 2.43 ___
His Tyr
A ___ 2.66 3.36 25.29 A ___ 2.95 2.86 23.69
U 2.05 ___ 20.89 3.92 U 2.27 ___ 18.95 3.84
C 2.05 16.57 ___ 3.92 C 2.27 19.50 ___ 3.84
G 13.25 2.66 3.36 ___ G 14.00 2.95 2.86 ___
lle Val
A ___ 4.46 3.77 15.65 A ___ 0.67 0.58 30.95
U 4.26 ___ 16.49 4.93 U 0.61 ___ 17.80 0.73
C 4.26 19.49 ___ 4.93 C 0.61 20.36 ___ 0.73
G 13.51 4.46 3.77 ___ G 25.70 0.67 0.58 ___
DOI: 10.7717/peerj.11524/table-3

Analysis of duplication and loss of chloroplast tRNA

In the evolution of tRNA, there are not only transformation and transversion events, but also duplication and loss events. Therefore, studying the duplication and loss of chloroplast tRNA is very important for its evolution. After analysis, we’ve got the loss and duplication tree (Fig. S2). And the results showed that among all the tRNAs tested, duplications events occurred a total of 151 times, conditional duplications events occurred a total of 101 times, and losses events occurred a total of 311 times (Table 4) (Data S2). Therefore, we speculate that a large number of genes may be lost during the evolution of the chloroplast tRNA. In addition, we found that tRNAMet had a higher D/L (duplication/loss) score than other tRNAs, while tRNAPro and tRNATry had a lower D/L score, which may be due to the fact that tRNAPro and tRNATry are more conserved during evolution.

Sequence alignment of tRNAArg (TCT) and tRNAAsn (GTT).

Figure 7: Sequence alignment of tRNAArg (TCT) and tRNAAsn (GTT).

The homologous sequence of tRNAArg (TCT) and tRNAAsn (GTT) is up to 80%. The species were H. laevis (NC_028583.1), O. cardiacum (NC_011031.1), F. terrestris (NC_014342.1).
Sequence alignment of tRNAArg (TCT) and tRNATrp (CCA).

Figure 8: Sequence alignment of tRNAArg (TCT) and tRNATrp (CCA).

The homologous sequence of tRNAArg (TCT) and tRNATrp (CCA) was 77.36%. The species were: H. laevis (NC_028583.1), G. pectoralis (NC_020438.1), C. reinhardtii (NC_005353.1), S. helveticum (NC_008372.1).
Table 4:
Duplication and loss events of each subtype tRNA.
tRNA D/L score Duplications Conditional duplications Losses
Ala 39.0 16 3 15
Arg 31.5 9 10 18
Asn 19.0 4 4 13
Asp 20.0 4 3 14
Cys 18.0 4 2 12
Glu 43.0 14 3 22
Gln 26.5 7 3 16
Gly 50.5 13 7 31
His 27.0 6 3 18
Ile 22.0 12 6 4
Leu 29.0 8 9 17
Lys 13.5 3 3 9
Met 55.5 15 12 33
Phe 17.0 4 2 11
Pro 9.0 2 7 6
Ser 43.5 13 9 24
Thr 19.0 4 3 13
Trp 10.0 2 5 7
Tyr 24.0 6 2 15
Val 20.5 5 5 13
DOI: 10.7717/peerj.11524/table-4

Discussion

No tRNAs of the two subtypes selenocysteine and possible suppressor were found to be present in the analyzed chloroplast genomes of the Chlorophyceae. There are 11 subtypes of tRNAs that encoded only one tRNA in 14 species, and 9 subtypes of tRNAs encoded different numbers of tRNAs. Among these 9 subtypes of tRNAs, the tRNAGlu was not found in F. terrestris. It is speculated that in F. terrestris, the codon recognition of glutamate may rely on the introduction of tRNA from the cytoplasm. To prove that the chloroplast is the evidence that tRNA can be introduced from the cytoplasm (Wolfe, Morden & Palmer, 1992; Smith, 2009). tRNAArg appeared 5 times in O. cardiacum, tRNASer appeared 4 times in S. leibleinii, and tRNAMet appeared 4 times in P. lenticularis. Therefore, based on the fact that tRNAArg, tRNASer and tRNAMet occur frequently in the species, we speculate that it may be because these three groups of tRNA are more prone to mutation during evolution, which is consistent with the results of the constructed phylogenetic tree. The characteristic of tRNA is a clover secondary structure composed of three hairpin loops and a terminal spiral stem, and the length of tRNA is generally between 75–95 nt (Goodenbour & Pan, 2006). In our study, it was found that 73.4% of the sequence lengths of tRNA of the 14 chloroplast species were less than 75 nt, which may have a great relationship with the tRNA has been in a conserved evolutionary stage.

Anticodons are of great significance in the process of protein synthesis. Anticodons and codons can introduce specific amino acids into the ribosome through base pairing (Sciarrino & Sorba, 2012). At the same time, anticodons and codons also differ greatly in number and evolutionary conservation. Anticodons also have variability in different organisms and organelles (Tong & Wong, 2004). In the 14 species analyzed, the anticodons were missing to varying degrees. At the same time, it was discovered that the missing tRNAGly (GCC) anticodon in N. aquatica was compensated by the tRNAGly (TCC) anticodon. The missing anticodon tRNALeu (TAA) in B. giganteus, T. obliquus, F. terrestris, S. leibleinii and O. cardiacum is compensated by the anticodon tRNALeu (TAG). But only in F. terrestris neither the anticodon tRNAGlu (TTC) nor the anticodon tRNAGlu (CTC) was found. In the chloroplast genome of Chlorophyceae, the gene sequences of tRNAAsn, tRNAAsp, tRNACys, tRNAGlu, tRNAHis, tRNALys and tRNAThr of the 20 subtypes of tRNAs of 14 species maintain relative conservation. In addition, it was also found that the variable loops of the three tRNAs were significantly longer than those of other tRNAs, which may be due to the fact that the variable loops have a certain influence on the orientation of the L-shaped tertiary structure of tRNAs (Bessho et al., 2007). Among them, the variable loop of tRNASer is the longest and is not conserved, which results in that tRNASer is susceptible to mutation in the phylogenetic tree.

As an important feature to distinguish prokaryotic genes, introns are widely present in eukaryotic genes, and a small amount are present in prokaryotes (Dai et al., 2003). The existence of introns in genes and their conservation information are closely related to the evolutionary origin and evolutionary relationship of species genes. For a long time, the main functions and research directions of introns have focused on the direction of gene expression regulation and selective splicing mechanism (Toor et al., 2008; Li et al., 2015; Swagata et al., 2018), but studies on introns as indicators of species evolution are relatively rare. The size and number of introns are not fixed in eukaryotic genes (Wu et al., 2013). The different ways in which repetitive sequences accumulate in plants and animals give rise to the fact that the length and number of introns in plants is much smaller than in higher animals (Wendel et al., 2002). Intron-containing tRNA genes are found in all kingdoms of life (Schmidt & Matera, 2020), and are rare in higher plants, but in Chlorophyta, more than half of tRNA genes contain an intron (Michaud et al., 2011). The distribution of introns in tRNA genes is also diverse, and can be located in different positions of tRNA genes, while the tRNAscan-SE server is difficult to accurately predict tRNA genes whose introns are not 37/38 and split tRNA genes (Sugahara et al., 2006). Therefore, in the process of analyzing the tRNA of the chloroplast genome of Chlorophyta, we only found that part of the tRNA genome contains a set of introns in the anti-codon ring. At the same time, based on the analysis scores of the tRNAscan-SE server, it is found that the scores of these three groups of tRNA are relatively low. It is speculated that these three groups of introns are not functional.

In the constructed tRNA phylogenetic tree, we found that the chloroplast tRNA of Chlorophyta was consistent with the tRNA of monocotyledonous and gymnospermatic chloroplasts in evolutionary pattern, with a common multi-phylogenetic pattern, and was rooted in a multiple common ancestor (Fig. 6). However, in the phylogenetic map of chloroplast genome constructed by us (Fig. S3), it was found that the branches of other species were not consistent with the branches of species tree except S. Leibleinii and S. helveticum in Chaetophorales, which indicated that the chloroplast evolution of chlorophyta was not inconsistent with the evolution pattern and direction of species evolution.

The conversion between nucleotides (U ↔C, A ↔G) and transversion (U ↔A, U ↔G, C ↔A, C ↔G) are important indicators for analyzing the evolution of tRNA genes. Research usually uses MAGE X software analysis and statistics. The MAGE X analysis in the data shows that the frequency of the nuclear genome of drosophilid is twice as high as the frequency of transversion (Begun et al., 2007). In the DNA sequences of many genomes, cyanobacteria tRNA and some monocot chloroplast tRNA genes, transition occurs more frequently than transversion occurs (Gojobori, Li & Dan, 1982; Wakeley, 1994; Mohanta et al., 2017; Mohanta et al., 2019). In this study, the MAGE X software measured the rate of transition/transversion greater than k1 (Purines) and K2 (Pyrimidines), indicating a higher frequency of transition than transversion in the chloroplast tRNA gene of Chlorophyta, which is similar to the results of the above analysis (Table 5). In the process of species evolution, gene duplication and loss affect the change of species genes. Gene duplication is an effective way to generate new gene functions in the genome, and gene loss can effectively shape gene families (Rasmussen & Kellis, 2012; Teufel, Liu & Liberles, 2016). In the event of gene sequence duplication loss in Chlorophyta chloroplast tRNA, tRNAMet, tRNAArg and tRNASer all occurred at a high level, which may lead to multiple appearances of these three tRNAs in the chloroplast genome and active evolution in the phylogenetic trees constructed.

Table 5:
The rate ratio of transition/transversion k1 (purines) and k2 (pyrimidines).
tRNA k1 (Purines) k2 (Pyrimidines)
Ala 3.526 2.766
Arg 3.098 2.794
Asn 5.635 8.266
Asp 16.319 16.478
Cys 4.611 10.021
Gln 2.521 3.279
Glu 4.769 4.56
Gly 4.638 4.522
His 6.45 6.219
Leu 3.815 4.48
Lle 3.174 4.368
Lys 5.526 4.286
Met 1.248 1.447
phe 3.541 5.06
Pro 3.223 2.845
Ser 1.656 2.355
Thr 3.76 4.243
Trp 3.242 11.299
Tyr 6.167 6.616
Val 42.19 30.49
DOI: 10.7717/peerj.11524/table-5

Conclusions

Through the sequence variation and evolutionary analysis of the chloroplast genome tRNA of chlorophyceae, we found that the chloroplast genome contains 28-32 tRNAs, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anticodon loop of the tRNA, but scored poorly when analyzed by the tRNAscan-SE software. Therefore, we speculate that these introns are not functional. After multiple sequence alignment, the Ψ-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the gene duplication and gene loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. According to the constructed phylogenetic tree, it was found that there were mutations in the evolution of chlorophyta chloroplast tRNA, with tRNAMet, tRNAArg and tRNASer being the most obvious.

Supplemental Information

tRNA secondary structures of different variable loops/arms

In the 409 groups of tRNA secondary structures we analyzed, in addition to the tRNA sequences with introns, we also surprisingly found that there were some tRNA secondary structures with abnormal structures. Fig. A–C is the secondary structure diagram of the three tRNA sequences of C. cuminata (tRNA Leu-TAG, tRNA Arg-ACG, tRNA Ser-GCT), and their variable loops/arms are different. The red and blue markers indicate the G–C and A–U bonds, respectively.

DOI: 10.7717/peerj.11524/supp-1

The loss and duplication tree

252 duplication events (duplication and conditional duplication) are detected in all of the gymnosperm chloroplast tRNA genes, and gene loss events are detected with 311. Blue, Duplication events; Gray, Loss events; D, Duplication node; cD, Conditional Duplication node.

DOI: 10.7717/peerj.11524/supp-2

The phylogenetic map of chloroplast genome

In the phylogenetic map of chloroplast genome, it was found that the branches of other species were not consistent with the branches of species tree except S. Leibleinii and S. helveticum in Chaetophorales, which indicated that the chloroplast evolution of chlorophyta was not inconsistent with the evolution pattern and direction of species evolution.

DOI: 10.7717/peerj.11524/supp-3

Raw data for Fig. 2

The tRNA type of the species as well as the length of the tRNA sequence.

DOI: 10.7717/peerj.11524/supp-4

Raw data for Table 4

The specific occurrence of replication events, conditional replication events and loss events for subtypes of tRNA for all species

DOI: 10.7717/peerj.11524/supp-5

Anticodon distribution of chloroplast tRNA

DOI: 10.7717/peerj.11524/supp-6