Next Article in Journal
Study on the Preparation and Effect of Tomato Seedling Disease Biocontrol Compound Seed-Coating Agent
Previous Article in Journal
Cytotoxicity and Genotoxicity of Epoxy Resin-Based Root Canal Sealers before and after Setting Procedures
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Life
Volume 12
Issue 6
10.3390/life12060848
life-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus

by
Xi Xia
1,†,
Jingyu Peng
2,†,
Lin Yang
1,
Xueli Zhao
1,
Anan Duan
1 and
Dawei Wang
1,*
1
Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China
2
Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100089, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Life 2022, 12(6), 848; https://doi.org/10.3390/life12060848
Submission received: 16 May 2022 / Revised: 1 June 2022 / Accepted: 2 June 2022 / Published: 7 June 2022
(This article belongs to the Section Evolutionary Biology)
Browse Figures
Versions Notes

Abstract

:
The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89–104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.

1. Introduction

The genus Ficus is the most numerous species of evergreen plants in the family Moraceae and is mainly found in subtropical and tropical areas [1]. For a long time, numerous Ficus species have been utilized as sources for food and pharmacy because of their rich nutritional content [2]. The genus Ficus is one of the largest woody genera of angiosperms, and the subdivision of the genus has been a concern of taxonomists [3]. The present relatively complete taxonomic system for the genus Ficus was proposed by Berg [4], which divided the genus Ficus into six subgenera (subgenus Urostigma, subgenus Pharmacosycea, subgenus Sycomorus, subgenus Ficus, subgenus Sycidium, and subgenus Synoecia) based on previous molecular phylogenetic analyses and morphological characters. However, the use of morphological and molecular markers for the identification of the Ficus genus are controversial or limited due to overlapping phenotypic characteristics or morphological similarities among the Ficus genus [3,5,6,7]. Therefore, the provision of additionalgenomic information is imperative for the understanding of the Ficus genus, and for the safe and effective utilization of Ficus.
The chloroplast (cp) is a unique organelle in the plant cell that not only plays a vital part in photosynthesis, but also participates in the synthesis of other organisms [8,9,10]. The cp genomes in plants are uniparentally inherited and consists of a highly conserved genomic structure a small single-copy (SSC), a couple of inverse-repeat (IR) regions, and a large single-copy (LSC), which also has a large number of variable loci [11,12]. Therefore, cp genomes have often been used to research the evolution, interspecific divergence, adaptive population history and phylogeny of related species [12,13,14]. With the emergence of the whole-genome sequencing era, the whole cp genomes have been extensively used in phylogenetic differentiation studies, species taxonomic identification and genetic breeding [15,16,17,18,19]. Although the cp genomes of some genus of Ficus have been reported previously [20,21,22,23,24,25,26,27], the eight Ficus species studied here have not been reported. As such, we compared the cp genome structures of eight Ficus species to provide a useful genomic resource for Ficus species.
In our study, the complete cp genomes of eight Ficus species were sequenced, which possess economically significant values (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens). The structural features and sequence differences of the eight Ficus species were then compared and analyzed, while the phylogeny of the eight Ficus species was inferred from the reported cp genomes of the Ficus genus. The results of this study can provide guidance for the subsequent conservation and utilization of Ficus species.

2. Materials and Methods

2.1. Plant Materials and DNA Extraction

Eight taxa, F. altissima, F. auriculata, F. benjamina, F. curtipes, F. heteromorpha, F. lyrata, F. microcarpa, and F. virens, represented the genus Ficus of the family Moraceae. We collected young, fresh, and non-diseased leaves from the adult plants of the target species, which were then frozen into liquid nitrogen. In addition, the voucher specimens were preserved in the herbarium of Southwest Forestry University, Kunming, Yunnan, China (Table S1). DNA extraction was performed using a modified CTAB method [28].

2.2. Genome Sequencing, Assembly and Annotation

Sequencing was performed by Annoroad Gene Technology (Beijing, China) to generate libraries with an average insert size of 400 bp from total DNA on an Illumina-based platform (Illumina Novaseq 6000). Then, the raw data obtained by sequencing were assembled using GetOrganelle v1.6.0 software with Ficus religiosa as the reference [29]. The assembled sequences were annotated with Geneious prime using F. religiosa as a reference and manually adjusted for start and stop codons. The genome mapping of the annotated Ficus cp genomes was conducted using OGdraw online [30]. The GenBank accession numbers of the eight Ficus species are shown in Table S1.

2.3. Simple Sequence Repeats (SSR) and Repetitive Sequence Analysis

Identification of SSRs was performed using MISA [31], and the specific parameter settings were as in Zhao et al. [32]. The forward (F), reverse (R), complementary (C), and palindromic (P) oligonucleotide repeats were determined by the REPuter program [33], and then the tandem repeats were subdivided using the network-based Tandem Repeat Finding [34], and the REPuter and Tandem Repeat specific parameters were set as in Yang et al. [35].

2.4. Genome Comparison and Divergent Hotspots Identification

Expansion or contraction of the IR region was investigated and visualized by IR scope [36]. The alignment of the eight Ficus cp genome sequences of species was performed using MAFFT v7 [37], and the completed sequences were subsequently compared using the Shuffle-LAGAN mode in mVISTA [38]. The nucleotide variability (Pi) of the cp genome was analyzed using DnaSp v5.10 [39], with the following settings: a step size of 200 bp and a window length of 800 bp.

2.5. Non-Synonymous (Ka) and Synonymous (Ks) Substitution Rate Analysis

First, the selected protein-coding genes (length > 300 bp) were paired in MAFFT. Then, the Ka/Ks value of the screened genes was calculated using the KaKs_calculator [40] with reference to Ivanova et al. [41].

2.6. Phylogenetic Analysis

To estimate phylogenetic relationships of eight Ficus species in the genus Ficus, cp genomes of 34 taxa were compared (Table S2), including 31 Ficus species, and 3 Flacourtiaceae species (Flacourtia indica, Homalium ceylanicum and Poliothyrsis sinensis) were set as outgroups. The sequence alignment of 34 cp genomic matrices was made using MAFFT v7 software. In order to obtain robust phylogenetic relationships, we constructed phylogenetic trees for the genus Ficus using the maximum likelihood (ML) method. The optimal nucleotide substitution model (K3Pu + F + R5) was selected using ModelFinder [42]. ML analyses was performed using IQ-tree 1.5.5 [43] under ultrafast bootstrap (1000) and the partition model (partitioned analysis with mixed data) [44]. The ML tree was visualized by using FigTree v1.4.0.

3. Results

3.1. Genomic Characteristics of Chloroplast

The cp genomes of F. altissima, F. auriculata, F. benjamina, F. curtipes, F. heteromorpha, F. lyrata, F. microcarpa, and F. virens were sequenced, generating approximately 2.61, 2.89, 2.52, 2.35, 2.60, 2.62, 2.52 and 2.56 Gb of paired-end reads, respectively. The average depth of coverage for the eight Ficus cp genomes was approximately 3244×.The eight newly sequenced chloroplast genomes of the genus Ficus (F. altissima, F. auriculata, F. benjamina, F. curtipes, F. heteromorpha, F. lyrata, F. microcarpa, and F. virens) were typical quadripartite structure with a length range of 160,333 bp (F. heteromorpha) ~ 160,772 bp (F. curtipes) (Figure 1). The LSC region of the eight Ficus species cp genomes ranged from 88,426(F. auriculata) to 89,149 (F. curtipes) bp, the SSC region from 19,183 (F. virens) to 20,158 (F. microcarpa) bp, and the IRb region from 25,743 (F. curtipes) to 26,249 (F. virens) bp (IRa: 25,743 to 26,249 bp). The cp genomes of all eight Ficus were uploaded to NCBI and GenBank accession numbers were obtained (Table S1).
We annotated a total of 127 unique genes, containing 83 protein-coding genes, 8 rRNAs and 36 tRNAs, in eight Ficus species showing similar genomic structures. Nineteen of the genes contained one intron and three genes contained two introns (Table 1). In all eight Ficus species, their cp genomes were AT-rich, with 64.1% of the genomes made up of A/T nucleotides. The GC content of the IR regions, LSC and SSC regions, protein-coding sequences, tRNA, and rRNA among the eight Ficus cp genomes was similar, with 42.4–42.7%, 32.7%, 37.1–37.2%, 52.9% and 55.4% GC content, respectively (Table S3).

3.2. SSR and Repetitive Sequence Analysis

We detected 94, 91, 100, 89, 92, 101, 93 and 104 SSR loci in F. altissima, F. auriculata, F. benjamina, F. curtipes, F. heteromorpha, F. lyrata, F. microcarpa and F. virens cp genomes, respectively. Among them, the richest repeat type was mono-nucleotides (53–68), followed by di-nucleotides (17–20), tetra-nucleotides (8–10), tri-nucleotides (4–5), penta-nucleotides (2–4), and hexa-nucleotides (0–2), respectively. The A/T repeat motif accounted for a large proportion (52–67) among all of the repeat types, followed by AT/AT (17–19), but the other repeat motifs were very rare. Mono-nucleotide repeat motifs (A/T), di-nucleotide repeat motifs (AT/TA), tri-nucleotide repeat motifs (AAG/CTT, AAT/ATT), tetra-nucleotide repeat motifs (AAAG/CTTT, AAAT/ATTT, AATT/AATT, AGAT/ATCT) and penta-nucleotides repeat motifs (AAAGG/CCTTT, AATTC/AATTG) were present in each cp genome (Figure 2a,b; Table S4).
The analysis of the eight cp genomes using REPuter showed that a total of 512 repeats were identified. The number of repeats in each species ranged from 57 (F. altissima) to 71 (F. auriculata), with palindromic repeats being the most abundant types (39–51), followed by forward repeats (13–19) and reverse (2–4) repeats. The complement repeats are rare in these 8 cp genomes (Figure 2c; Table S5). The results of the tandem repeats showed a total number of 341 tandem repeats for the eight cp genomes, ranging from 33 (F. auriculata) to 47 (F. altissima and F. benjamina) (Figure 2d).

3.3. IR Constriction and Expansion

We performed a comparative analysis of the contraction and expansion of the IR/SC region boundary in eight Ficus species (Figure 3). The genes at the junctions of the eight Ficus species included rps19, ndhF, rpl22, rpl2, psbA, trnH, and ycf1. The ndhF gene of F. curtipes, F. heteromorpha, and F. lyrata was located exclusively in the SSC region, ranging from 3 to 657 bp away from the boundary of JSB. The ndhF gene of F. altissima, F. auriculata, F. benjamina, F. microcarpa, and F. virens was mainly located in the SSC region, but a small proportion of the ndhF gene spanned the junction 15 to 521 bp into the IRb region. The rps19 gene of F. curtipes, F. lyrata, and F. virens was located in the LSC region, which for F. auriculata was located in the IRb region, while the gene in F. altissima, F. benjamina, F. heteromorpha and F. microcarpa spans the LSC and IRb boundary. We also observed that the ycf1 gene in all eight Ficus cp genomes spanned the SSC and IRa junctions, but the majority were located in the SSC region, and the length of the ycf1 gene in the IRa was within the range of 1008–1493 bp. In the eight Ficus cp genomes, the trnH, psbA, and rpl22 genes were located exclusively in the LSC region, and the distance between the trnH gene and JLA ranged from 46 to 169 bp.

3.4. Sequence Divergence Analysis

To determine the sequence differences among the eight Ficus cp genomes, we used Ficus religiosa as a reference genome and compared them using mVISTA (Figure 4). It is apparent from Figure 4 that the eight Ficus cp genomes were highly conserved, but regions of divergence among intergenic regions were also found, such as trnT-UGU_trnL-UAA, rps16_trnQ-UUG, trnT-GGU_psbD, petA_psbJ rpoB_trnC-GCA, petN_psbM, atpB_rbcL, and rpl32_trnL-UAG. Subsequently, we calculated the nucleotide variability (Pi), as the Pi value allows for a better assessment of the degree of sequence divergence (Figure 5). From the results, the degree of divergence in the LSC and SSC regions exceeded that of the IR region, and the average value of Pi in the eight Ficus species was approximately 0.0033. Then, Pi > 0.0128 was identified as the hotspot region, and a total of eight high variance regions were found: trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1, where the ndhF_trnL-UAG region has the highest Pi value (0.0202). The identification of these highly variable regions offers invaluable information for the evolution of markers in Ficus.

3.5. Non-Synonymous (Ka) and Synonymous (Ks) Substitution Rate Analysis

We calculated the Ka/Ks ratios of the eight Ficus chloroplast genomes using F. religiosa as the reference with a total of 53 protein genes reselected based on 300 bp length (Figure 6; Table S6). The Ka/Ks ratio results indicate that gene-specificity is the majority, and the remaining small portion is region-specific (the IR, SSC, and LSC regions showed comparable values). The Ka range of eight Ficus chloroplast genomes was from 0 to 2.6149, and the Ks values ranged from 0 to 5.0893. The highest Ka and Ks was for the ycf1 gene between F. altissima and F. religiosa (ka = 2.6149, ks = 5.0893), while the values of Ka and Ks for a large number of genes were equal to 0. The average Ka/Ks ratio for the 53 protein genes was 0.1211 and the average Ka/Ks value for ycf1 was 1.0476, with only the ycf1 gene having a Ka/Ks value greater than 1 among the genes tested.

3.6. Phylogenomic Analysis

The phylogenetic relationships of the genus Ficus were inferred by maximum likelihood, and the support obtained by this method was high and it strongly supported the monophyly of the genus Ficus. The phylogenetic tree shows that the genus Ficus is divided into five main branches (Figure 7). Cluster I contained eight species of the subgenus Urostigma. Seven species of the subgenus Sycomorus formed a monophyletic cluster with high support. Cluster III contained two species of the subgenus Pharmacosycea and Ficus lyrata. Cluster Ⅳ contained three species of the subgenus Synoecia and four species of the subgenus Ficus. Six species of the subgenus Ficus formed Cluster Ⅴ.

4. Discussion

4.1. Chloroplast Genomic DNA Structures

In the present study, we sequenced the eight Ficus species cp genomes, which laid the foundation for a comprehensive comparison of the cp genome sequences of Moraceae. The eight Ficus species reported in this study differ somewhat in chloroplast size, but in general they are roughly similar in chloroplast genome length to those reported so far for Ficus species, with all being around 160,000 bp in length [8,27]. The structure of the eight Ficus cp genomes, like most angiosperms, also has a typical quadripartite structure [8,45,46,47]. Moreover, we found that the content of the eight Ficus cp genomes was dominated by A/T, up to 64.1%, and this result was similar to that in other plants [48,49,50]. The lower G/C content of the Ficus genomes may be related to its own spontaneous mutations [51]. We also found that the GC content of LSC and SSC were lower than the IR regions, which were common in Ficus species [27,52,53], and this may be so due to the existence of rRNA and tRNA genes in the IR region [54].

4.2. Identification of SSRs and Repeat Sequences

Repeated sequences have been shown to be associated with the rearrangement, evolution and divergence of cp genome sequences, as well as having an important function in the phylogeny [12,55,56]. The number and distribution of the four repeats in the eight Ficus cp genomes, and the distribution of the repeats were similar in the cp genomes of Ficus, which was strongly related to the high conservation within the Ficus species. The cpSSR markers have been frequently used for intraspecific identification and genetic evolutionary analysis because of their high mutation rate [57,58,59]. The results of this study indicated that the mono-nucleotide repeats were the richer repeat type in the eight Ficus species, with the A/T being the enriched repeat motif, similar to other higher plant studies [13,60], indicating that the higher plants were dominated by low-level repeat motif [61]. The SSRs and repeats detected in this study were important for the subsequent phylogenetic studies and taxonomy of the genus Ficus, and even the family Moraceae.

4.3. IR Constriction and Expansion

Scientists have noticed that the expansion and contraction of the IR regions affects the size of the chloroplasts [56,62]. Moreover, it may cause border genes to enter the IR or SC [63]. In our study, most of the genes (rpl22, rpl2, ycf1, trnH, and psbA) in the eight Ficus species were identical at the IR/SC boundary positions, and differed only in length, further suggesting that the Ficus species are closely related and have highly conserved cp genomes. The cp genomes of monocots and dicots have distinct differences in gene arrangement; for example, the trnH gene is located in the LSC region in dicots, whereas it is located in the IR region in monocots [64]. Interestingly, we found that the rps19 gene of F. auriculata was located exclusively in the IRb region, which would be very rare in dicotyledons [65,66,67], and this may be the case because of expansion from the IR region to the LSC region.

4.4. Sequence Divergence Analysis

A comparative analysis of hypervariable regions in plant cp genomes can better identify mutation hotspots and provide a basis for genetic diversity analysis [68,69]. In this study, to identify variable regions, we calculated the percentage of variable characters (coding and non-coding regions) in eight Ficus species cp genomes. The results of the study were similar to those of angiosperms, where the non-coding regions were much more variable than the coding regions [70,71,72]. At the same time, we also found that the SC region of the eight Ficus species in this study were more variable than the IR region, which was consistent with previous results [73,74]. In previous studies, a large number of hypervariable regions were used as DNA barcodes for other plants [75,76,77]. We identified eight hypervariable regions in the Ficus cp genomes (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). The discovery of these hypervariable regions could provide vast amounts of information for the development of molecular markers for phylogenetic analyses.

4.5. Non-Synonymous (Ka) and Synonymous (Ks) Substitution Rate Analysis

The Ka/Ks reveal selection pressure on protein-coding genes and they have a key role in evolutionary studies [78]. Non-synonymous nucleotide substitutions occurred with a lower frequency than synonymous substitutions in most genes, subject to purifying selection [65]. Thus, the ratio of Ka/Ks > 1 indicates probable positive selection; Ka/Ks < 1 indicates purifying selection, while Ka/Ks values of nearly 1 indicate neutral evolution [79]. The results of this study showed that a great many genes had Ka and Ks values that are equal to 0, indicating that these eight Ficus chloroplast genomes are relatively conservative. However, the highest Ka and Ks values were for the gene between F. altissima and F. religiosa (ka = 2.6149, ks = 5.0893), suggesting that it is more variable in F. altissima. The ycf1 gene was under positive selection in the Ficus cp genome, and so the ycf1 gene may have an important role in the adaptation of Ficus species to different environments [80]. However, it cannot be excluded that it may be a pseudogene, as the gene often becomes pseudogenic in angiosperm cp genomes [81]. Therefore, further studies are needed to determine whether the ycf1 gene is in a positive selection state in the Ficus cp genome. The Ka/Ks values were less than 1 for all genes except ycf1, which indicated that these cp genomes underwent extensive purifying selection.

4.6. Phylogenomic Analysis

The cp genome was the most vital genetic resource for inferring plant evolutionary relationships and was well suited for analyzing comparative plant relatedness [82,83]. In this study, in order to determine the phylogenetic relationships of eight Ficus genus, phylogenetic trees were structured using ML methods. The findings indicated that all Ficus species clustered in the one clade with high values, a finding that is consistent with the phylogeny inferred by previous work using cpDNA fragments [8].
According to the results of the phylogenetic analysis, species of the three subgenera (subgenus Sycomorus, subgenus Synoecia, and subgenus Pharmacosycea) were all monophyletic taxa and had strong support values, suggesting that the cp genome was suited for resolving the phylogeny of the Ficus. Berg [4] has pointed out the existence of some morphological similarities between the subgenus Ficus and the subgenus Synoecia. The results of the present study showed that the subgenus Ficus and the subgenus Synoecia are clustered into one branch, indicating a close relationship between the two subgenera. Therefore, the taxonomic treatment of the subgenus Synoecia and subgenus Ficus requires further study.
The results of Rønsted [84] suggest that the subgenus Urostigma belongs to a non-monophyletic origin, and we obtained similar results. Interestingly, in the present study, Ficus lyrata showed a close relationship with the subgenus Pharmacosycea, and so further research is needed on the subgenus classification of F. lyrata.
Based on morphological traits [85] as well as molecular data [6], it was previously suggested that Ficus tikoua should be classified as subgenus Sycomorus and our phylogenetic analysis provides strong evidence for this classification. Subgenus Urostigma and subgenus Sycomorus formed a clade, indicating that the two subgenera are closely related. Zhang [86] points out that F. auriculata and F. beipeiensis should be classified as the same species, but our study results clearly do not support this classification. In our result, F. auriculata and F. beipeiensis were still somewhat different, despite being more closely related. Our results show that the F. formosana, F. heteromorpha, F. erecta and F. pandurate of the Ficus gasparriniana-F. heteromorpha complex of sect. Ficus cluster together, a result that is consistent with those obtained in previous phylogenetic studies based on SSR markers [87].

5. Conclusions

In our study, we assembled and analyzed the cp genomes of eight Ficus species. By comparing these cp genomes, the results show that the structures of these cp genomes are similar to those of most angiosperm genomes, which exhibit a typical tetragonal structure. Additionally, we obtained valuable genetic resources, including SSRs, highly variable loci, and repetitive sequences. Phylogenetic analysis shows that all Ficus species were clustered in the same clade. The present study provides a clearer phylogenetic framework for the taxonomy of the genus Ficus, and it will help in the species identification of these species, and in genetic diversity studies.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/life12060848/s1. Table S1: List of samples voucher collection information and GenBank accessions; Table S2: The 34 chloroplast genomes used for phylogenetic analysis; Table S3: Base composition in the chloroplast genomes of Ficus species; Table S4: Types and numbers of SSRs motifs in eight Ficus cp genomes; Table S5: Repeats in the chloroplast genome of eight Ficus species; Table S6 The rates of Ka, Ks and Ka/Ks of 53 protein coding genes in 8 Ficus species by pairwise comparison computed by KaKs_Calculator with default parameters.

Author Contributions

Data curation, wrote the manuscript, methodology, software, X.X. and J.P.; resources, L.Y. and A.D.; conceptualization, software, X.Z.; supervision, funding acquisition, D.W. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Forestry Science and Technology Development Project of National Forestry and Grassland Administration of China (No. KJZXSA2019036), and the Fund of Ten-Thousand Talents Program of Yunnan Province (YNWR–QNBJ–2020-230).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The chloroplast genomes sequences of eight Ficus species (F. altissima, F. auriculata, F. benjamina, F. curtipes, F. heteromorpha, F. lyrata, F. microcarpa, F. virens) have been uploaded to NCBI and the GenBank accession numbers are MW043478.1, MW039147.1, MW039146.1, MW039143.1, MW039145.1, MW039148.1, MW039144.1, MW039142.1.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Badgujar, S.B.; Patel, V.V.; Bandivdekar, A.H.; Mahajan, R.T. Traditional uses, phytochemistry and pharmacology of Ficus carica: A review. Pharm. Biol. 2014, 52, 1487–1503. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Tkachenko, G.; Buyun, L.; Osadovskyy, Z.; Truhan, M.; Goncharenko, V. In vitro screening of antimicrobial activity of ethanolic extract obtained from Ficus lyrata warb. (moraceae) leaves. Agroecol. J. 2016, 2, 155–160. [Google Scholar]
  3. Zhang, Z.; Wang, X.M.; Liao, S.; Zhang, J.H.; Li, H.Q. Phylogenetic reconstruction of Ficus subg. Synoecia and its allies (Moraceae), with implications on the origin of the climbing habit. Taxon 2020, 69, 927–945. [Google Scholar] [CrossRef]
  4. Berg, C.C. Flora Malesiana precursor for the treatment of Moraceae 1: The main subdivision of Ficus: The subgenera. Blumea 2003, 48, 166–177. [Google Scholar] [CrossRef] [Green Version]
  5. Xu, L.; Harrison, R.D.; Yang, P.; Yang, D.R. New insight into the phylogenetic and biogeographic history of genus Ficus: Vicariance played a relatively minor role compared with ecological opportunity and dispersal. J. Syst. Evol. 2011, 49, 546–557. [Google Scholar] [CrossRef]
  6. Li, H.M.; Wang, S.; Chen, J.Y.; Gui, P.J. Molecular phylogeny of Ficus section Ficus in China based on four DNA regions. J. Syst. Evolution. 2012, 50, 422–432. [Google Scholar] [CrossRef]
  7. Fatihah, H.N.; Mat, N.; Zaimah, A.R.; Zuhailah, M.N.; Norhaslinda, H.; Khairil, M.; Ghani, A.Y.; Ali, A.M. Morphological phylogenetic analysis of seven varieties of Ficus deltoidea Jack from the Malay Peninsula of Malaysia. PLoS ONE 2012, 7, e52441. [Google Scholar] [CrossRef]
  8. Bruun-Lund, S.; Clement, W.L.; Kjellberg, F.; Rønsted, N. First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae). Mol. Phylogenetics Evol. 2017, 109, 93–104. [Google Scholar] [CrossRef] [PubMed]
  9. Neuhaus, H.E.; Emes, M.J. Nonphotosynthetic metabolism in plastids. Annu. Rev. Plant Biol. 2000, 51, 111–140. [Google Scholar] [CrossRef] [PubMed]
  10. Qian, J.; Song, J.; Gao, H.; Zhu, Y.; Xu, J.; Pang, X.; Yao, H.; Sun, C.; Li, X.; Li, C.; et al. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS ONE 2013, 8, e57607. [Google Scholar] [CrossRef]
  11. Hu, S.; Sablok, G.; Wang, B.; Qu, D.; Barbaro, E.; Viola, R.; Li, M.; Varotto, C. Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats. BMC Genom. 2015, 16, 306. [Google Scholar] [CrossRef] [Green Version]
  12. Wicke, S.; Schneeweiss, G.M.; dePamphilis, C.W.; Müller, K.F.; Quandt, D. The evolution of the plastid chromosome in land plants: Gene content, gene order, gene function. Plant Mol. Biol. 2011, 76, 273–297. [Google Scholar] [CrossRef] [Green Version]
  13. Hong, Z.; Wu, Z.; Zhao, K.; Yang, Z.; Zhang, N.; Guo, J.; Tembrock, L.R.; Xu, D. Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae). Int. J. Mol. Sci. 2020, 21, 3758. [Google Scholar] [CrossRef]
  14. Zhong, B.; Xi, Z.; Goremykin, V.V.; Fong, R.; McLenachan, P.A.; Novis, P.M.; Davis, C.C.; Penny, D. Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes. Mol. Biol. Evol. 2014, 31, 177–183. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  15. Alves-Pereira, A.; Clement, C.R.; Picanço-Rodrigues, D.; Veasey, E.A.; Dequigiovanni, G.; Ramos, S.L.F.; Pinheiro, J.B.; Zucchi, M.I. Patterns of nuclear and chloroplast genetic diversity and structure of manioc along major Brazilian Amazonian rivers. Ann. Botany. 2018, 121, 625–639. [Google Scholar] [CrossRef] [PubMed]
  16. Deng, Y.W.; Luo, Y.Y.; He, Y.; Qin, X.S.; Li, C.G.; Deng, X.M. Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species. Forests 2020, 11, 267. [Google Scholar] [CrossRef] [Green Version]
  17. Jiang, L.; Li, M.; Zhao, F.; Chu, S.; Zha, L.; Xu, T.; Peng, H.; Zhang, W. Molecular Identification and Taxonomic Implication of Herbal Species in Genus Corydalis (Papaveraceae). Molecules 2018, 23, 1393. [Google Scholar] [CrossRef] [Green Version]
  18. Sun, J.; Wang, Y.; Liu, Y.; Xu, C.; Yuan, Q.; Guo, L.; Huang, L. Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species. Sci. Rep. 2020, 10, 11466. [Google Scholar] [CrossRef] [PubMed]
  19. Yang, C.; Ma, Y.; Cheng, B.; Zhou, L.; Yu, C.; Luo, L.; Pan, H.; Zhang, Q. Molecular Evidence for Hybrid Origin and Phenotypic Variation of Rosa Section Chinenses. Genes 2020, 11, 996. [Google Scholar] [CrossRef]
  20. Chen, H.; Liu, Q.; Tang, L. The plastid genome of winter cropping plants Ficus tinctoria (Moraceae). Mitochondrial DNA B-Resour. 2020, 5, 2703–2704. [Google Scholar] [CrossRef]
  21. Chi, W.; Chi, L.J.; Pan, H.W.; Xia, X.L.; Huang, Z.H. Characteristic Analysis of the Complete Chloroplast Genome of Ficus concinna Miq. var. subsessilis Corner -An Ancient Tree from Zhejiang Province, China. J. Hainan Normal Univ. 2020, 33, 50–57. [Google Scholar]
  22. Han, F.; Li, J.; Yuan, J.; Yu, J. The complete chloroplast genome sequence of Ficus beipeiensis (Moraceae), an endemic and endangered plant in China. Mitochondrial DNA B-Resour. 2021, 6, 604–605. [Google Scholar] [CrossRef]
  23. Liu, Y.; Chen, W.; Li, F.; Li, C.; Xie, X.; Chao, Z.; Tian, E. The complete chloroplast genome sequence of Ficus hirta (Moraceae). Mitochondrial DNA Part B Resour. 2019, 4, 4041–4042. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  24. Mao, Q.; Bi, G. Complete chloroplast genome of Ficus racemosa (Moraceae). Mitochondrial DNA 2016, 27, 4655–4656. [Google Scholar] [CrossRef]
  25. Wang, J.; Wang, T.Y.; Wang, L.Y.; Zhang, J.G.; Zeng, Y.F. Assembling and Analysis of the Whole Chloroplast Genome Sequence of Elaeagnus angustifolia and Its Codon Usage Bias. Acta Botanica Boreali-Occidentalia Sinica 2019, 39, 1559–1572. [Google Scholar]
  26. Xu, S.; Guo, S.; Fan, D.; Wang, J. The complete chloroplast genome sequence of Ficus formosana Maxim (Moraceae) from Guangzhou, China. Mitochondrial DNA B-Resour. 2021, 6, 1895–1896. [Google Scholar] [CrossRef]
  27. Yu, H.; Nason, J.D. Nuclear and chloroplast DNA phylogeography of Ficus hirta: Obligate pollination mutualism and constraints on range expansion in response to climate change. New Phytol. 2013, 197, 276–289. [Google Scholar] [CrossRef]
  28. Yang, J.B.; Li, D.Z.; Li, H.T. Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol. Ecol. Resour. 2014, 14, 1024–1031. [Google Scholar] [CrossRef]
  29. Jin, J.J.; Yu, W.B.; Yang, J.B.; Song, Y.; dePamphilis, C.W.; Yi, T.S.; Li, D.Z. GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020, 21, 241. [Google Scholar] [CrossRef]
  30. Lohse, M.; Drechsel, O.; Bock, R. OrganellarGenomeDRAW (OGDRAW): A tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 2007, 52, 267–274. [Google Scholar] [CrossRef] [PubMed]
  31. 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] [Green Version]
  32. Zhao, X.L.; Zhu, Z.M. Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes. Plants 2020, 9, 1116. [Google Scholar] [CrossRef] [PubMed]
  33. Kurtz, S.; Choudhuri, J.V.; Ohlebusch, E.; Schleiermacher, C.; Stoye, J.; Giegerich, R. REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001, 29, 4633–4642. [Google Scholar] [CrossRef] [Green Version]
  34. Benson, G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 1999, 27, 573–580. [Google Scholar] [CrossRef] [Green Version]
  35. Yang, Z.; Wang, G.; Ma, Q.; Ma, W.; Liang, L.; Zhao, T. The complete chloroplast genomes of three Betulaceae species: Implications for molecular phylogeny and historical biogeography. PeerJ 2019, 7, e6320. [Google Scholar] [CrossRef]
  36. 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] [PubMed]
  37. Katoh, K.; Standley, D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  38. Dubchak, I.; Ryaboy, D.V. VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes. Methods Mol. Biol. 2006, 338, 69–89. [Google Scholar] [PubMed]
  39. Librado, P.; Rozas, J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25, 1451–14522. [Google Scholar] [CrossRef] [Green Version]
  40. Wang, D.; Zhang, Y.; Zhang, Z.; Zhu, J.; Yu, J. KaKs_Calculator 2.0: A toolkit incorporating gamma-series methods and sliding window strategies. Genom. Proteom. Bioinform. 2010, 8, 77–80. [Google Scholar] [CrossRef] [Green Version]
  41. Ivanova, Z.; Sablok, G.; Daskalova, E.; Zahmanova, G.; Apostolova, E.; Yahubyan, G.; Baev, V. Chloroplast Genome Analysis of Resurrection Tertiary Relict Haberlea rhodopensis Highlights Genes Important for Desiccation Stress Response. Front. Plant Sci. 2017, 8, 204. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  42. Kalyaanamoorthy, S.; Minh, B.Q.; Wong, T.K.F.; von Haeseler, A.; Jermiin, L.S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods 2017, 14, 587–589. [Google Scholar] [CrossRef] [Green Version]
  43. Nguyen, L.T.; Schmidt, H.A.; von Haeseler, A.; Minh, B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015, 32, 268–274. [Google Scholar] [CrossRef]
  44. Hoang, D.T.; Chernomor, O.; von Haeseler, A.; Minh, B.Q.; Vinh, L.S. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol. Biol. Evol. 2018, 35, 518–522. [Google Scholar] [CrossRef]
  45. Gu, C.; Tembrock, L.R.; Zheng, S.; Wu, Z. The Complete Chloroplast Genome of Catha edulis: A Comparative Analysis of Genome Features with Related Species. Int. J. Mol. Sci. 2018, 19, 525. [Google Scholar] [CrossRef] [Green Version]
  46. Jansen, R.K.; Cai, Z.; Raubeson, L.A.; Daniell, H.; Depamphilis, C.W.; Leebens-Mack, J.; Müller, K.F.; Guisinger-Bellian, M.; Haberle, R.C.; Hansen, A.K.; et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc. Natl. Acad. Sci. USA 2007, 104, 19369–19374. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  47. Ng, W.L.; Cai, Y.; Wu, W.; Zhou, R. The complete chloroplast genome sequence of Melastoma candidum (Melastomataceae). Mitochondrial DNA Part B Resour. 2017, 2, 242–243. [Google Scholar] [CrossRef] [Green Version]
  48. Fu, J.; Liu, H.; Hu, J.; Liang, Y.; Liang, J.; Wuyun, T.; Tan, X. Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis. PLoS ONE 2016, 11, e0159566. [Google Scholar] [CrossRef] [Green Version]
  49. Mariotti, R.; Cultrera, N.G.; Díez, C.M.; Baldoni, L.; Rubini, A. Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison. BMC Plant Biol. 2010, 10, 211. [Google Scholar] [CrossRef] [Green Version]
  50. Yi, D.K.; Kim, K.J. Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L. PLoS ONE 2012, 7, e35872. [Google Scholar] [CrossRef] [Green Version]
  51. Schmid, P.; Flegel, W.A. Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations. J. Transl. Med. 2011, 9, 87. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  52. Ghada; Baraket; and; Saddoud; Olfa; and; Chatti; Khaled; and; Mars. Chloroplast DNA analysis in Tunisian fig cultivars (Ficus carica L.): Sequence variations of the trnL-trnF intergenic spacer. Biochem. Syst. Ecol. 2008, 36, 828–835. [Google Scholar] [CrossRef]
  53. Wang, J.; Shi, D.; Bai, Y.; Liu, Y. High-throughput sequencing uncover Ficus tikoua Bur. chloroplast genome. J. Plant Biochem. Biotechnol. 2019, 29, 171–182. [Google Scholar] [CrossRef]
  54. Doorduin, L.; Gravendeel, B.; Lammers, Y.; Ariyurek, Y.; Chin, A.W.T.; Vrieling, K. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res. Int. J. Rapid Publ. Rep. Genes Genomes 2011, 18, 93–105. [Google Scholar] [CrossRef]
  55. Asano, T.; Tsudzuki, T.; Takahashi, S.; Shimada, H.; Kadowaki, K. Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: A comparative analysis of four monocot chloroplast genomes. DNA Res. 2004, 11, 93–99. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  56. Weng, M.L.; Blazier, J.C.; Govindu, M.; Jansen, R.K. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Mol. Biol. Evol. 2014, 31, 645–659. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  57. Gómez, A.; González-Martínez, S.C.; Collada, C.; Climent, J.; Gil, L. Complex population genetic structure in the endemic Canary Island pine revealed using chloroplast microsatellite markers. TAG Theor. Appl. Genet. 2003, 107, 1123–1131. [Google Scholar] [CrossRef]
  58. Ruhsam, M.; Rai, H.S.; Mathews, S.; Ross, T.G.; Graham, S.W.; Raubeson, L.A.; Mei, W.; Thomas, P.I.; Gardner, M.F.; Ennos, R.A.; et al. Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria? Mol. Ecol. Resour. 2015, 15, 1067–1078. [Google Scholar] [CrossRef]
  59. Urbaniak, L.; Wojnicka-Pótorak, A.; Celiński, K.; Lesiczka, P.; Pawlaczyk, E.; Aučina, A. Genetic resources of relict populations of Pinus sylvestris (L.) in Western Carpathians assessed by chloroplast microsatellites. Biologia 2019, 74, 1077–1086. [Google Scholar] [CrossRef] [Green Version]
  60. Zhou, T.; Zhu, H.; Wang, J.; Xu, Y.; Xu, F.; Wang, X. Complete chloroplast genome sequence determination of Rheum species and comparative chloroplast genomics for the members of Rumiceae. Plant Cell Rep. 2020, 39, 811–824. [Google Scholar] [CrossRef]
  61. Zhang, D.F.; Li, S.X.; Xia, T. Characterization of EST-SSR Among Six Genera of Rosaceae. Bull. Bot. Res. 2014, 34, 810–815. [Google Scholar]
  62. He, L.; Qian, J.; Li, X.; Sun, Z.; Xu, X.; Chen, S. Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies. Molecules 2017, 22, 249. [Google Scholar] [CrossRef]
  63. Wang, W.; Chen, S.; Zhang, X. Whole-Genome Comparison Reveals Divergent IR Borders and Mutation Hotspots in Chloroplast Genomes of Herbaceous Bamboos (Bambusoideae: Olyreae). Molecules 2018, 23, 1537. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  64. Huotari, T.; Korpelainen, H. Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genome. Gene 2012, 508, 96–105. [Google Scholar] [CrossRef]
  65. Du, X.; Zeng, T.; Feng, Q.; Hu, L.; 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]
  66. Lin, C.P.; Wu, C.S.; Huang, Y.Y.; Chaw, S.M. The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction. Genome Biol. Evol. 2012, 4, 374–381. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  67. Zhang, Y.; Zhang, J.W.; Yang, Y.; Li, X.N. Structural and comparative analysis of the complete chloroplast genome of a mangrove plant: Scyphiphora hydrophyllacea Gaertn. f. and related Rubiaceae species. Forest 2019, 10, 1000. [Google Scholar] [CrossRef] [Green Version]
  68. Abdullah; Mehmood, F.; Shahzadi, I.; Waseem, S.; Mirza, B.; Ahmed, I.; Waheed, M.T. Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots. Genomics 2020, 112, 581–591. [Google Scholar] [CrossRef]
  69. Kuang, D.Y.; Wu, H.; Wang, Y.L.; Gao, L.M.; Zhang, S.Z.; Lu, L. Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): Implication for DNA barcoding and population genetics. Genome 2011, 54, 663–673. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  70. Clegg, M.T.; Gaut, B.S.; Learn, G.H., Jr.; Morton, B.R. Rates and patterns of chloroplast DNA evolution. Proc. Natl. Acad. Sci. USA 1994, 91, 6795–6801. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  71. Huang, H.; Shi, C.; Liu, Y.; Mao, S.Y.; Gao, L.Z. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: Genome structure and phylogenetic relationships. BMC Evol. Biol. 2014, 14, 151. [Google Scholar] [CrossRef] [Green Version]
  72. Perry, A.S.; Wolfe, K.H. Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat. J. Mol. Evol. 2002, 55, 501–508. [Google Scholar] [CrossRef] [PubMed]
  73. Dong, W.; Liu, H.; Xu, C.; Zuo, Y.; Chen, Z.; Zhou, S. A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: A case study on ginsengs. BMC Genet. 2014, 15, 138. [Google Scholar] [CrossRef] [Green Version]
  74. Shen, X.; Wu, M.; Liao, B.; Liu, Z.; Bai, R.; Xiao, S.; Li, X.; Zhang, B.; Xu, J.; Chen, S. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua. Molecules 2017, 22, 1330. [Google Scholar] [CrossRef]
  75. Hu, C.Y.; Zheng, X.Y.; Teng, Y.W. Characterization and phylogenetic utility of non-coding chloroplast regions trnL-trnF and accD-psaI in Pyrus. Acta Horticult. Sin. 2011, 38, 2261–2272. [Google Scholar]
  76. Scarcelli, N.; Barnaud, A.; Eiserhardt, W.; Treier, U.A.; Seveno, M.; D'Anfray, A.; Vigouroux, Y.; Pintaud, J.C. A Set of 100 Chloroplast DNA Primer Pairs to Study Population Genetics and Phylogeny in Monocotyledons. PLoS ONE 2011, 6, e19954. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  77. Shen, J.S.; Li, X.Q.; Zhu, X.T.; Huang, X.L.; Jin, S.H. The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species. Forests 2020, 11, 158. [Google Scholar] [CrossRef] [Green Version]
  78. Nazareno, A.G.; Carlsen, M.; Lohmann, L.G. Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome. PLoS ONE 2015, 10, e0129930. [Google Scholar] [CrossRef] [Green Version]
  79. Yang, Z.; Nielsen, R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 2000, 17, 32–43. [Google Scholar] [CrossRef] [Green Version]
  80. Zeb, U.; Dong, W.L.; Zhang, T.T.; Wang, R.N.; Li, Z.H. Comparative plastid genomics of Pinus species: Insights into sequence variations and phylogenetic relationships. J. Syst. Evol. 2019, 58, 118–132. [Google Scholar] [CrossRef]
  81. Ge, Y.; Dong, X.; Wu, B.; Wang, N.; Chen, D.; Chen, H.; Zou, M.; Xu, Z.; Tan, L.; Zhan, R. Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships. PLoS ONE 2019, 14, e0221827. [Google Scholar] [CrossRef]
  82. Zhang, Y.; Wang, Z.; Guo, Y.; Chen, S.; Xu, X.; Wang, R. Complete chloroplast genomes of Leptodermis scabrida complex: Comparative genomic analyses and phylogenetic relationships. Gene 2021, 791, 145715. [Google Scholar] [CrossRef] [PubMed]
  83. Kim, G.B.; Lim, C.E.; Kim, J.S.; Kim, K.; Lee, J.H.; Yu, H.J.; Mun, J.H. Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: Insights into evolutionary divergence and phylogenomic implications. BMC Genom. 2020, 21, 415. [Google Scholar] [CrossRef] [PubMed]
  84. Rønsted, N.; Weiblen, G.D.; Cook, J.M.; Salamin, N.; Machado, C.A.; Savolainen, V. 60 million years of co-divergence in the fig-wasp symbiosis. Proc. Biol. Sci. 2005, 272, 2593–2599. [Google Scholar] [CrossRef] [Green Version]
  85. Gui, P. Morphological and Anatomical Studies on Ficus subg. Ficus (Moraceae) in China. Master’s Thesis, East China Normal University, Shanghai, China, 2013; pp. 61–62. [Google Scholar]
  86. Zhang, L.F. Phylogeny and Taxonomy of the Ficus auriculata Complex. Master’s Thesis, East China Normal University, Shanghai, China, 2016; pp. 40–42. [Google Scholar]
  87. Zhou, Q.M. Using SSR to Characterize the Ficus gasparriniana-F. heteromorpha Complex of Sect. Ficus (Ficus, Moraceae) in China. Master’s Thesis, East China Normal University, Shanghai, China, 2014; pp. 34–36. [Google Scholar]
Life 12 00848 g001 550
Figure 1. The complete chloroplast genome of eight Ficus species. Genes shown outside the circle are transcribed clockwise and those inside counterclockwise. Different colors represent different kinds of functional genes. The dark gray area and light gray area of inner circle represent the ratio of GC content to AT content of the genome respectively.
Figure 1. The complete chloroplast genome of eight Ficus species. Genes shown outside the circle are transcribed clockwise and those inside counterclockwise. Different colors represent different kinds of functional genes. The dark gray area and light gray area of inner circle represent the ratio of GC content to AT content of the genome respectively.
Life 12 00848 g001
Life 12 00848 g002 550
Figure 2. The number and type of simple sequence repeats (SSRs) and repeat sequences in the chloroplast genomes of eight Ficus species. (a) Frequency of eight SSR types, (b) Frequency of SSR motifs in different repeat class types, (c) Frequency of five repeat types, (d) Frequency of dispersed repeat sequences by length.
Figure 2. The number and type of simple sequence repeats (SSRs) and repeat sequences in the chloroplast genomes of eight Ficus species. (a) Frequency of eight SSR types, (b) Frequency of SSR motifs in different repeat class types, (c) Frequency of five repeat types, (d) Frequency of dispersed repeat sequences by length.
Life 12 00848 g002
Life 12 00848 g003 550
Figure 3. Comparison of the borders of LSC, IR and SSC in the chloroplast genomes of eight Ficus species.
Figure 3. Comparison of the borders of LSC, IR and SSC in the chloroplast genomes of eight Ficus species.
Life 12 00848 g003
Life 12 00848 g004 550
Figure 4. Sequence alignment of the chloroplast genomes of eight Ficus species, with F. religiosa as a reference. The X-axis represents the coordinates in the chloroplast genome, and the Y-axis represents the percentage of homogeneity, ranging from 50% to 100%.
Figure 4. Sequence alignment of the chloroplast genomes of eight Ficus species, with F. religiosa as a reference. The X-axis represents the coordinates in the chloroplast genome, and the Y-axis represents the percentage of homogeneity, ranging from 50% to 100%.
Life 12 00848 g004
Life 12 00848 g005 550
Figure 5. Nucleotide variability (Pi) in the coding region of eight Ficus species.
Figure 5. Nucleotide variability (Pi) in the coding region of eight Ficus species.
Life 12 00848 g005
Life 12 00848 g006 550
Figure 6. The Ka/Ks ratio of 53 protein-coding genes of eight cp genomes for comparison with F. religiosa.
Figure 6. The Ka/Ks ratio of 53 protein-coding genes of eight cp genomes for comparison with F. religiosa.
Life 12 00848 g006
Life 12 00848 g007 550
Figure 7. Phylogenetic tree inferred from maximum likelihood (ML) based on the 34 taxa complete chloroplast genomes.
Figure 7. Phylogenetic tree inferred from maximum likelihood (ML) based on the 34 taxa complete chloroplast genomes.
Life 12 00848 g007
Table
Table 1. List of genes encoded by eight species of Ficus chloroplast genome. (×2) indicates that the gene has two copies. * and ** indicate genes containing one/two introns.
Table 1. List of genes encoded by eight species of Ficus chloroplast genome. (×2) indicates that the gene has two copies. * and ** indicate genes containing one/two introns.
CategoryGene GroupsGene NamesNumber
Self-replicationLarge subunit of ribosomal proteinsrpl14, rpl16 *, rpl2 (×2) *, rpl20, rpl22, rpl23 (×2), rpl32, rpl33, rpl3611
Small subunit of ribosomal proteinsrps11, rps12 **, rps14, rps15, rps16 *, rps18, rps19, rps2, rps3, rps4, rps7 (×2), rps813
DNA dependent RNA polymeraserpoA, rpoB, rpoC1 *, rpoC24
ribosomal RNAsrrn16 (×2), rrn23 (×2), rrn4.5 (×2), rrn5, (×2)8
transfer RNAstrnA-UGC (×2) *, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC *, trnH-GUG, trnI-CAU (×2), trnI-GAU (×2) *, trnK-UUU *, trnL-CAA (×2), trnL-UAA *, trnL-UAG, trnM-CAU, trnN-GUU (×2), trnP-UGG, trnQ-UUG, trnR-ACG (×2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC, (×2), trnV-UAC *, trnW-CCA, trnY-GUA36
PhotosynthesisPhotosystem IpsaA, psaB, psaC, psaI, psaJ5
Photosystem IIpsbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbM, psbN, psbT, psbZ14
NADP dehydrogenasendhA *, ndhB (×2) *, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK12
Cytochrome b6/f complexpetA, petB *, petD *, petG, petL, petN6
ATP synthaseatpA, atpB, atpE, atpF *, atpH, atpI6
RubiscorbcL1
Other genesMaturasematK1
ProteaseclpP **1
Envelop membrane proteincemA1
Subunit Acetyl- CoA-CarboxylateaccD1
c-type cytochrome synthesis geneccsA1
UnknownConserved Open reading framesycf1 (×2), ycf2, (×2), ycf3 **, ycf46
127
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Xia, X.; Peng, J.; Yang, L.; Zhao, X.; Duan, A.; Wang, D. Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus. Life 2022, 12, 848. https://doi.org/10.3390/life12060848

AMA Style

Xia X, Peng J, Yang L, Zhao X, Duan A, Wang D. Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus. Life. 2022; 12(6):848. https://doi.org/10.3390/life12060848

Chicago/Turabian Style

Xia, Xi, Jingyu Peng, Lin Yang, Xueli Zhao, Anan Duan, and Dawei Wang. 2022. "Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus" Life 12, no. 6: 848. https://doi.org/10.3390/life12060848

APA Style

Xia, X., Peng, J., Yang, L., Zhao, X., Duan, A., & Wang, D. (2022). Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus. Life, 12(6), 848. https://doi.org/10.3390/life12060848

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop