https://orcid.org/0000-0002-8669-2030
Figures
Abstract
Background
Macadamia is a true dicotyledonous plant that thrives in a mild, humid, low wind environment. It is cultivated and traded internationally due to its high-quality nuts thus, has significant development prospects and scientific research value. However, information on the genetic resources of Macadamia spp. remains scanty.
Results
The mitochondria (mt) genomes of three economically important Macadamia species, Macadamia integrifolia, M. ternifolia and M. tetraphylla, were assembled through the Illumina sequencing platform. The results showed that each species has 71 genes, including 42 protein-coding genes, 26 tRNAs, and 3 rRNAs. Repeated sequence analysis, RNA editing site prediction, and analysis of genes migrating from chloroplast (cp) to mt were performed in the mt genomes of the three Macadamia species. Phylogenetic analysis based on the mt genome of the three Macadamia species and 35 other species was conducted to reveal the evolution and taxonomic status of Macadamia. Furthermore, the characteristics of the plant mt genome, including genome size and GC content, were studied through comparison with 36 other plant species. The final non-synonymous (Ka) and synonymous (Ks) substitution analysis showed that most of the protein-coding genes in the mt genome underwent negative selections, indicating their importance in the mt genome.
Citation: Niu Y, Lu Y, Song W, He X, Liu Z, Zheng C, et al. (2022) Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla). PLoS ONE 17(5): e0263545. https://doi.org/10.1371/journal.pone.0263545
Editor: Yanbin Yin, University of Nebraska-Lincoln, UNITED STATES
Received: January 18, 2022; Accepted: April 19, 2022; Published: May 3, 2022
Copyright: © 2022 Niu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: The assembled mitochondrial genome sequence and annotation have been deposited at GenBank (https://www.ncbi.nlm.nih.gov/genbank/) under the accession MW566570, MW566571 and MW566572.
Funding: This work was supported by the National Natural Science Foundation of China (No. 31760215 and No. 31801022) and the Technology Innovation Talents Project of Yunnan Province (2018HB086). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
1. Introduction
Macadamia spp belongs in the family Proteaceae, class Magnoliopsida, and order Proteales. The Proteaceae family has five subfamilies, 80 genera, and over 1600 species [1, 2]. Most of them are distributed in Oceania and South Africa, while a few are produced in East Asia and South America. Notably, more than 100 species in the Proteaceae family produce flowers that are traded internationally [3]. Besides, the species grown in the northeastern part of Oceania are also rich in nuts. The genus Macadamia comprises four species: Macadamia integrifolia, M. jansenii, M. ternifolia, and M. tetraphylla. These species are naturally distributed in the subtropical rain forests from southeastern Queensland in Australia to northeastern New South Wales [4, 5]. Among them, M. integrifolia and M. tetraphylla produce edible nuts; thus, most commercial cultivars are either these two species or their hybrids. The other two species, M. Jansenii and M. ternifolia produce non-edible nuts containing high levels of bitter cyanide glycosides, thus has not been used to guide the breeding [6, 7]. Macadamia seeds are sweet with high nutritional and medicinal value. Therefore, they have enjoyed the reputation of "King of Thousand Fruits". They are also used in international transactions due to their high economic value [8].
Mitochondria (mt) are organelles that primarily convert biomass energy in living cells into chemical energy to fuel biological activities [9]. Additionally, they participate in other biological processes, including cell differentiation, cell apoptosis, cell growth, and cell division [10–13]. Therefore, mt are central to life activities within individual cells and the entire living body [14]. Both plastids and mt harbor genetic information and are thought to have evolved through endosymbiosis of freely living bacteria [15–17]. In most seed plants, nuclear genetic information is inherited from both parents, while cp and mt are derived from maternal genes [18]. Thus, we can temporarily ignore the influence of paternal genes, thereby reducing the difficulty of genetic research and promoting the research of genetic mechanisms [19].
Studies have shown that the size of the mt genome varies significantly between different species. For example, plants have a larger mt genome than animals [20]. Furthermore, mt genome size in seed plants can vary by at least one order of magnitude ranging from ~ 222 bp in Brassica napus [21] and ~ 316 Kb in Allium cepa [22] to ~ 3.9 Mb in Amborella trichopoda [23] and a striking ~ 11.3 Mb in Silene conica [24]. This phenomenon may be caused by the abundance of non-coding regions and repeated elements in the plant mt genome [25]. DNA recombination between homologous sequences produces small circular sub-genomic DNA. The circular genomic DNA coexists with the complete "master" genome in the cell. These genomes typically have several kb repeats, leading to multiple heterogeneous forms of the genome [26–31]. The mutation rate of plant mt genomes is very low; however, their rearrangement rate is so high that there is almost no conservation of synteny [32–34].
The development of cost-effective and more efficient DNA sequencing methods like high-throughput sequencing has accelerated mt genome sequencing. So far (until June 2021), the mt genomes of 618 green plant species have been released in the NCBI (https://www.ncbi.nlm.nih.gov/) database. Long-term mutually beneficial symbiosis caused the mt to lose some of the original DNA, possibly by transfer, leaving only the DNA encoding it [35, 36]. Mt DNA integrates DNA from various sources by intracellular and horizontal transfer [37]. Therefore, regardless of the length, gene sequence and content, mt genome varies remarkably among different plant species [33]. The mt genome length of the smallest terrestrial plant is about 66 Kb, and that of the largest terrestrial plant is 11.3 Mb [24, 38, 39]; the number of genes is usually between 32 and 67 [40]. In this study, the mt genomes of three Macadamia species were sequenced, assembled, and annotated. Also, their genomic and structural features were analyzed and compared with other angiosperms (and gymnosperms). This study improves our understanding of Macadamia genetics and provides crucial data to inform future research on the evolution of mt genomes of land plants.
2. Materials and methods
2.1 Genome sequencing
The three Macadamia species examined in this study were collected from Yunnan Institute of Tropical Crops (Xishuangbanna, China; 101°28’ E, 21°92’ N). Total genomic DNA was extracted from fresh leaves using modified CTAB [41]. Meanwhile, the quantity and quality of extracted DNA was assessed by spectrophotometry and the integrity was evaluated using a 1% (w/v) agarose gel electrophoresis. The qualified DNA samples were used for Illumian DNA library construction, according to the standard procedure. Subsequently, a paired-end sequencing library with an insert size of 350 bp was constructed. The Illumina Hiseq 4000 high-throughput sequencing platform was used for sequencing. The sequencing strategy involved PE150 (Pair-End 150) and the sequencing data volume of not less than 1 Gb. Illumina high-throughput sequencing results initially existing as original image data files were converted into Raw Reads. CASAVA software was used for Base Calling.
2.2 Genome assembly and annotation
SPAdes v.3.5.0 [42] software was used to splice and assemble mt genome sequences. To correct the splicing results, the raw sequencing data were mapped to mitochondrial sequences using Geneious software [43]. DOGMA [44] and NCBI were used to annotate the mt genome. The Blastn and Blastp method was used to compare mt gene-encoding protein and rRNAs among related species. TRNA scan-SE2.0 [45] and ARWEN [46] were used to annotate tRNA. The tRNAs with unreasonable length and incomplete structure were eliminated. Subsequently, a tRNA secondary structure diagram was generated. The final mt genomes of M. integrifolia, M. ternifolia, and M. tetraphylla have been deposited in the GenBank (Accession number: MW566570/MW566571/MW566572).
2.3 Analysis of repeat structure and sequence
Microsatellites within the mt genomes of the three Macadamia species were identified using MISA [47, 48]. The minimum number of repeats for the motif length of 1, 2, 3, 4, 5, and 6 were 10, 6, 5, 4, 3, and 3, respectively, were identified in this analysis. The tandem repeats were detected using Tandem Repeats Finder v4.09 software [49] with default parameters.
2.4 DNA transformation from cp to mt and RNA editing analyses
The cp genome of M. integrifolia (NC_025288) was downloaded from the NCBI database. Chloroplast-like sequences were identified and the genome was mapped using TBtools [50]. The online program Predictive RNA Editor for Plants (PREP) suite [51] was adopted to identify the possible RNA editing sites in the protein-coding genes of the three Macadamia species. The cutoff value was set as 0.2 to ensure accurate prediction. The protein-coding genes from other plant mt genomes were used as references to reveal the RNA editing sites in the mt genomes of the three Macadamia species.
2.5 Phylogenetic tree construction and Ka/Ks analysis
The genome sequences of the three Macadamia species were compared with those of 35 (S1 Table) other plant species to further verify their phylogenetic position. Notably, the complete mt genome sequences of these species were available in the NCBI database. Phylogenetic analyses were performed on 23 conserved protein-coding genes (atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, matR, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7 and nad9) that were extracted from the mt genomes of the 35 plant species using TBtools [51]. These conserved genes were then aligned using Muscle [52] implemented in MEGA X [53]; the alignment was modified manually to eliminate gaps and missing data. The GTR + G + I model was determined to be the best model based on the Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) calculated by ModelFinder [54]. The Maximum Likelihood (ML) algorithm in MEGA X [53] was used to construct a phylogenetic tree. The bootstrap consensus tree was inferred from 1000 replications. Cycas taitungensis and Ginkgo biloba were designated as the outgroup in this analysis.
The Ka and Ks replacement rates of protein-coding genes in mitochondrial genomes of the three Macadamia species and other higher plants were analyzed. blastn in TBtools was used to extract the sequences of corresponding protein-coding genes in Macadamia and N. nucifera genomes. The Ka and Ks replacement rates of each protein-coding gene were estimated using N. nucifera genome as a reference.
3. Results and discussion
3.1 Genomic features of the mt genomes of the three Macadamia species
The mt genomes of M. integrifolia, M. ternifolia and M. tetraphylla have a typical terrestrial plant genome ring structure (Fig 1). A total of 71 unique genes were identified in the mt genomes of the three Macadamia species, including 42 protein-coding, 26 tRNA, and 3 rRNA genes (Table 1). In addition, two copies of rRNA26, ccmB, rps19, trnN-GTT, and trnH-GTG, and seven copies of trnM-CAT were identified. It has been established that the mt genomes of land plants contain a variable number of introns [55]. In the present study, the three mt genomes had ten genes with introns, length ranging from 13 bp (rps3) to 31,841 bp (cox2) where ccmFC, rpl2, rps3, and rps10 had two introns, cox2 had three, nad1, nad4, and nad5 had four and nad2 and nad7 had five introns. Besides, in all protein-coding genes, except atp6, cox1, nad1, nad4L, rps4, and rps10, which had ACG as the start codon, all the others had ATG as their start codon. In addition, the stop codons in all the protein-coding genes were: TAA 45.2%, TGA 28.6%, TAG 14.3%, CAA 9.5%, and CGA 2.4%.
Gene map showing 71 annotated genes of different functional groups.
The size and GC content of mt genome are the primary characteristics. Here, we compared the size and GC content of mt genomes between three Macadamia species and 36 other green plants, including four phorophytes, three bryophytes, two gymnosperms, four monocots, and 23 dicots (S1 Table). The size of the mt genomes ranged from 22,897 bp (Chlamydomonas moewusii) to 2,709,526 bp (Cucumis melo) (Fig 2). Compared to phorophytes and bryophytes, the mt genomes of the three Macadamia species are larger. The GC content in the mt genomes was also highly variable, ranging from 32.24% in Sphagnum palustric to 50.36% in Ginkgo biloba. Overall, the GC content of angiosperm mt genome (including monocots and dicots) is higher than that in bryophytes but less than in gymnosperms [56, 57], implying that the GC contents fluctuated following the angiosperms divergence from bryophytes and gymnosperms. Interestingly, the GC content significantly fluctuated in algae and was mostly conserved in angiosperms, although their genome sizes vary significantly.
The blue dots represent the genome size and the orange trend line shows the variation of GC content across the different taxa.
3.2 Repeat sequences analysis
Microsatellites or simple sequence repetitions (SSRs) are DNA fragments composed of short sequence repeating units of 1–6 base pairs [58]. Their unique value is created by their polymorphism, relative abundance, codominant inheritance, large-scale genome coverage, and PCR detection simplicity [59]. Based on the SSRs analysis, we identified 87 SSRs with SSRs monomers and dimers accounting for 70.11% of the total SSRs. Adenine (A) was the most repeated monomer with 19 (38%) out of the 50 identified monomer SSRs. The AT repeat was the most common dimer SSR, accounting for 66.67% of all the identified dimers. However, one hexamer [ATTAGG(X3)] was present in the mt genomes of three Macadamia species.
Among the reference mt genome, only Nelumbo nucifera has been published in the NCBI database. N. nucifera belongs to the family Nelumbonaceae and the same order (Proteales) with Macadamia. Therefore, the mt genome of N. nucifera was used as a reference for comparative analysis in the present study. The monomers in N. nucifera were lower than in the three Macadamia species, while pentamers and hexamers in N. nucifera were significantly higher than in the three Macadamia species (Fig 3A). Moreover, the SSRs in mt genomes of M. integrifolia, M. ternifolia, M. tetraphylla, and N. nucifera were mainly single-nucleotide A/T motifs, and dimer AT/TA motifs. Within the Macadamia genus, the mt SSRs among the different species are highly similar (Fig 3B). However, compared with N. nucifera, there were both differences and similarities. For example, the single nucleotide A/T in the three Macadamia species has 23-unit repeats, while N. nucifera has only nine. Nevertheless, their single-nucleotide C/G numbers were the same (two-unit repeats) (Fig 3B). In addition, the AG/CT and AT/AT motifs unit repetitions are the same, although N. nucifera also has an AC/GT motif, lacking in the three Macadamia species. Interestingly, the pentanucleotide AATGT/ACATT, ACTAG/AGTCT, and ACATT/AGTAT also had the same number of repetitions in the three Macadamia species and N. nucifera. Overall, the greater the nucleotide motif, the greater the difference between the three Macadamia species and N. nucifera.
Core repeating units ranging from 1 to 200 bases (tandem repeats) are widely present in eukaryotes and some prokaryotes genomes [60]. In the present study, 25, 21, and 20 tandem repeats (10–33 bp) were identified in the M. integrifolia, M. ternifolia, and M. tetraphylla with a match greater than 95% (S2–S4 Tables). The tandem repeats (11–20 bp and 21–30 bp) significantly varied among the three Macadamia species (Fig 3C), where M. ternifolia had the least number of repetitions, while M. integrifolia and M. tetraphylla had a very similar number of repetitions. However, N. nucifera had the least (11–20 bp and 21–30 bp) and had the highest (0–10 bp, 31–40 bp, 41–50 bp) tandem repeated compared to the three Macadamia species. Besides, no repetitions ranged from 51–60 bp among the four genomes, while the number of repetitions was the same for 60–70 bp and above.
3.3 The prediction of RNA editing
RNA editing is a post-transcriptional process entailing the addition, deletion, or conversion of bases in the coding region of a transcribed RNA. The conversion of cytosine to uridine is common in cp and mt genomes of plants [61–65], which improves protein preservation in plants. The accurate detection of ribonucleic acid editing is inseparable from the proteomics data. In the present study, we predicted 42 protein-coding genes (including two multi-copy genes: ccmB and rps19) in the mt genomes of the three Macadamia species using the PREP-mt program [51]. The findings revealed that the RNA editing sites were 688, 689, and 688 (Fig 4). Among the protein-coding genes, nad4 had the most RNA editing sites (59 sites), while atp8, rpl2, rpl10, rps1, rps2, rps7, rps10, rps11, rps13, rps14, rps19, sdh3, and sdh4 had less than 10 RNA editing sites. 236 RNA editing sites occurred in the first base position of the codon, 472 sites appeared in the second base position, and there was no RNA editing in the third base position. M. ternifolia had more than one RNA editing site, unlike the other two Macadamia species.
The bars of different colors represent the number of RNA-editing sites of each gene.
The RNA editing increases the diversity at the start and stop codons in protein-coding genes. However, even with RNA editing, 30.2% (208 positions) of amino acid hydrophobicity and 12.5% (86 positions) of amino acid hydrophilicity remained unchanged in the M. integrifolia and M. tetraphylla mt genomes. However, 6.7% (46 positions) of amino acids were converted from hydrophobic to hydrophilic, and 47.9% (330 positions) from hydrophilic to hydrophobic. In addition, five amino acids were converted from glutamine to stop codons and two from arginine to stop codons (Table 2). The findings in this study revealed that most amino acids were converted from serine to leucine (23.3%, 160 sites), proline to leucine (22.4%), and serine to phenylalanine (15.3%). The remaining 269 RNA editing sites included other RNA editing types, such as Ala-Val, His-Tyr, Leu-Phe, Pro-Phe, Pro-Ser, Arg-Cys, Arg-Trp, Thr-Ile, Thr- Met, Gln-X, and Arg-X (X = stop codon). Compared to M. integrifolia and M. tetraphylla, M. ternifolia only had one more RNA-edited site (Leu-Phe).
3.4 DNA migration from cp to mt
The cp-like sequences in the mt genome were detected by comparing against the complete cp genome sequence of M. integrifolia obtained from the NCBI database (Fig 5). We detected 28 fragments in the mt genome of M. integrifolia, ranging in size from 32 bp to 5,210 bp. The cp-like sequence had 36,902 bp, accounting for 5.4% of the mt genome. Five complete annotated tRNA genes were detected, namely trnH-GTG, trnM-CAT, trnW-CCA, trnD-GTC, and trnN-GTT, with some fragments of rrn18 genes. The findings also revealed that 28 insertion regions accounted for 23.2% of the cp genome, including seven complete protein-coding genes (petL, petG, ndhE, rps15, rpl23(X2), rpl2) and eight complete tRNA genes (trnH-GUG, trnD-GUC, trnM-CAU, trnW-CCA, trnP-UGG, trnP-GGG, trnI-CAU, trnN-GUU). Besides, several protein-coding genes were also identified, including psbA, rpoB, psbD, psbC, ndhC, rpl2, ycf2(X2), ndhB, rps7(X2), ndhD, ndhB and ycf1, and some tRNA genes (trnI-GAU, trnA-UGC, trnN-GUU), which migrated from the cp genome into the mt genome. But, most of these genes lost their integrity during the evolution process, and only their partial sequences were found in the mt genome. Furthermore, most cp-like sequences were located in the spacer region of the mt genome. These findings are consistent with previous research, where during evolution, tRNA genes were more conserved than the protein-coding genes and rRNA genes since they play an important role in mt genome [66].
Dots and heat maps inside the two chromosomes show where genes are located. The green lines in the circle show the regions of chloroplast-like sequences inserted from the chloroplast genome into the mt genome.
3.5 Phylogenetic analysis within higher plant mt genomes
Australia is the origin and center of diversity of the Proteaceae, and this is distributed across remnant landmasses of the southern supercontinent Gondwana [67]. The order Proteales inclusive of Proteaceae, Platanaceae and Nelumbonaceae was established relatively recently, on the basis of molecular data, and morphological synapomorphies for the order are yet to be identified [68, 69]. Phylogenetic analysis was performed to understand the evolution of the three Macadamia species compared to 29 dicots, four monocots, and two gymnosperms (out-groups). The phylogenetic tree was constructed based on the comparisons in the data matrix of 23 conserved protein-coding genes (Fig 6). The findings revealed that the phylogenetic tree strongly supports the separation of Proteales from rosids and asterids, the separation of eudicots from monocots and angiosperms from gymnosperms. The evolutionary relationships among all the taxa separated into 20 families (Leguminosae, Cucurbitaceae, Apiaceae, Apocynaceae, Solanaceae, Rosaceae, Caricaceae, Brassicaceae, Salicaceae, Bataceae, Malvaceae, Vitaceae, Lamiaceae, Nelumbonaceae, Proteaceae, Butomaceae, Arecaceae, Poaceae, Cycadaceae, and Ginkgoaceae) were efficiently deduced in the phylogenetic tree (Fig 6). The Macadamia chloroplast genome confirms the placement of this family with the morphologically divergent Plantanaceae (plane tree family) and Nelumbonaceae (sacred lotus family) in the basal eudicot order Proteales [70]. In addition, Phylogenetic analysis of chloroplast genomic variation revealed a latitudinal population structure of wild M. integrifolia germplasm, suggesting long-term regional isolation of maternal lineages [71]. Overall, evolutionary analyses of organelle genomes suggest that Proteaceae are most closely related to Nelumbonaceae.
The Maximum Likelihood tree was constructed based on the sequences of 23 conserved protein-coding genes. Colors indicate the families that the specific species belongs.
3.6 The substitution rates of protein-coding genes
In genetics, non-synonymous (Ka) and synonymous (Ks) substitution rates help understand the evolutionary dynamics of protein-coding genes among similar species since the Ka to Ks ratio indicates gene selection [72, 73]. In the present study, N. nucifera was used as a reference species to calculate the Ka/Ks ratio of 40 protein-coding genes present in the mt genome of three Macadamia species. The Ks of atp9 and rps14, and the Ka of rps12 was 0. Besides, in most protein-coding genes, the Ka/Ks ratio was significantly less than 1 (Fig 7). However, the Ka/Ks ratio of nad4, rpl2, rps3, rps4, and rps10 was greater than 1, with the rps3 ratio being 2.34, implying that these genes might have undergone mutation related positive selection following Macadamia and N. nucifera differentiation from their last common ancestor [74]. Besides, the ATP synthase, Cytochrome C biogenesis, Ubiquinol Cytochrome C reductase, and Maturases of Ka/Ks ratios were below 1, implying that the negative selection acted on these genes (Table 2). Therefore, these genes may be highly conserved during the evolution of higher plants [75].
4. Conclusions
The complete mt genomes of M. integrifolia, M. ternifolia and M. tetraphylla share many common features with angiosperm mt genomes. In this study, we found that the mt genomes of the three Macadamia species were circular like most mt genomes. Compared them with the GC content of the mt genome of 36 other green plants, the results supported the conclusion that the GC content in the Macadamia species and angiosperms are highly conserved. In addition, we conducted studies on SSRs and longer tandem repeats in the three sets of data. Besides, 688 RNA editing sites were identified in 42 protein-coding genes, providing important clues for predicting gene function with new codons. By detecting gene migration, we observed 28 fragments (with five complete tRNA genes) were transferred from the cp genome to mt genome. The subsequent phylogenetic analysis results also showed their accuracy in plant classification. Moreover, based on the Ka/Ks substitution of protein-coding genes, most coding genes have undergone negative selection, indicating that the protein-coding genes in the mt genome are conserved in Macadamia species. The findings of this study provide information on the mt genome of Macadamia species, which is key in understanding the evolutionary history of the family Proteaceae.
Supporting information
S1 Table. The abbreviations and NCBI accession numbers of mt genomes used in this study.
https://doi.org/10.1371/journal.pone.0263545.s001
(XLSX)
S2 Table. Perfect tandem repeats in the Macadamia integrifolia mitochondrial genome.
https://doi.org/10.1371/journal.pone.0263545.s002
(XLSX)
S3 Table. Perfect tandem repeats in the Macadamia ternifolia mitochondrial gemone.
https://doi.org/10.1371/journal.pone.0263545.s003
(XLSX)
S4 Table. Perfect tandem repeats in the Macadamia tetraphylla mitochondrial gemone.
https://doi.org/10.1371/journal.pone.0263545.s004
(XLSX)
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