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Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae

  • Ting Zhou,

    Roles Formal analysis, Methodology, Software, Visualization, Writing – original draft

    Affiliation Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China

  • Kun Ning,

    Roles Formal analysis

    Affiliation College of Horticulture, Jinling Institute of Technology, Nanjing City, Jiangsu Province, P.R. China

  • Zhenghai Mo,

    Roles Formal analysis

    Affiliation Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China

  • Fan Zhang,

    Roles Investigation, Supervision

    Affiliation Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China

  • Yanwei Zhou,

    Roles Investigation

    Affiliation Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China

  • Xinran Chong,

    Roles Visualization

    Affiliation Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China

  • Donglin Zhang,

    Roles Writing – review & editing

    Affiliation Department of Horticulture, University of Georgia, Athens, GA, United States of America

  • Yousry A. El-Kassaby,

    Roles Writing – review & editing

    Affiliation Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada

  • Jian Bian,

    Roles Resources

    Affiliation Jiangsu Yufeng Tourism Development Co. Ltd., Yancheng, China

  • Hong Chen

    Roles Formal analysis, Funding acquisition, Methodology, Software, Writing – review & editing

    chenhong@cnbg.net

    Affiliation Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China

Abstract

Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.

Introduction

In green plants, the chloroplast is a photosynthetic organelle with fundamental roles in carbon fixation and energy production [1, 2]. It possesses its own independent genome featuring maternal, paternal, or biparental inheritance and a relatively conserved four-part circular structure consisting of a large single copy (LSC), a small single copy (SSC), and two inverted repeat regions (IRs) [35]. Generally, land plant chloroplast genomes range in size from 120 to 160 kb, encoding 110–130 distinct genes [6, 7]. Due to their small size, reduced recombination, slow evolutionary rate, and mostly maternal transmission, chloroplast genomes of angiosperms have been extensively utilized for species identification, biodiversity evaluation, phylogenetic analysis, origin judgment, and explorations of the genetic basis for climatic adaptation [811]. Recently, sequencing plant chloroplast genomes has become much easier with the rapid development of sequencing technologies, such as the Illumina and PacBio sequencing platforms.

The genus Ilex L. (holly), Aquifoliaceae, is the largest angiosperm woody dioecious genus, cultivated as ornamental, culinary, and pharmaceutical plants [12]. Approximately 600 Ilex species are distributed worldwide from tropical to temperate regions, including China where more than 200 species have been documented [13, 14]. Although the taxonomy of the genus Ilex had been proposed based on biogeography and morphology, conducting species identifications and understanding their evolutionary relationships within and among these putative clades was complicated due to apparent morphological similarities, interspecific hybridization, and genetic introgression [1517]. At least 20 Ilex species chloroplast genomes have already been released in the GenBank database. However, genomic information on many high-value species in the family Aquifoliaceae requires further investigation.

Ilex dabieshanensis K. Yao & M. B. Deng (Yao and Deng, 1987) is not only a highly valued tree species for landscaping, it is also a good material for making Kuding tea due to its anti-inflammatory and lipid-lowering properties. To better understand its genetic information, we sequenced and assembled the complete chloroplast genome of I. dabieshanensis (MW292560) using Illumina and PacBio sequencing technologies. Then, we carried out comparative analyses between the resulting I. dabieshanensis chloroplast genome and previously published genomes of I cornuta (MK335536), I. latifolia (KX426465), and I. paraguariensis (KP016928). The three species were selected because they are pharmaceutical plants used as Kuding tea, like I. dabieshanensis [18]. Our objectives were: 1) exploring the molecular structure of I. dabieshanensis chloroplast genome; 2) examining possible simple sequence and long repeats; 3) discovering hypervariable regions that could be used as specific DNA markers for the genus Ilex; 4) revealing the phylogenetic relationships of I. dabieshanensis within the family Aquifoliaceae; and 5) providing molecular data for Ilex tea germplasm identification, phylogeny, and genetic improvement.

Materials and methods

Plant material, chloroplast DNA extraction and sequencing

Fresh leaves of I. dabieshanensis were collected from one plant in Nanjing Botanical Garden, Jiangsu Province, China, (32°03′N latitude, 118°49′E longitude) and immediately flash-frozen in liquid nitrogen. Total chloroplast DNA was extracted using the improved sucrose gradient centrifugation method [19]. DNA integrity, purity, and concentration were estimated by 1% agarose-gel electrophoresis, a NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA), and a Qubit fluorometer (Life Technologies, Darmstadt, Germany), respectively. Only samples with good purity (OD 260/280≥1.8, OD 260/230≥1.8) were retained for sequencing. After DNA detection, two libraries with insert sizes of 300 bp and 10 kb were constructed. Chloroplast genome sequencing of the two I. dabieshanensis libraries was then performed on an Illumina HiSeq X Ten instrument (Biozeron, Shanghai, China) and a PacBio Sequel platform (Biozeron, Shanghai, China), respectively. The qualities of the resulting Illumina and PacBio raw data were filtered by FastQC.

Chloroplast genome assembly and annotation

Using SOAPdenova software (v2.04), clean Illumina reads were first assembled with the default parameters into principal contigs [20]. Then, all contigs were classified and connected into a single draft sequence using the Geneious (v11.0.4) [21]. The BLASR software was immediately used to compare the PacBio clean data with the single draft sequence and meanwhile to extract the correction and error correction [22]. Next, scaffolds were generated by assembling the corrected PacBio clean data with the default parameters using Celera Assembler (v8.0) [23]. For gap closure, these assembled scaffolds were mapped back to the Illumina clean reads using GapCloser (v1.12) [20]. Finally, the assembled chloroplast genome of I. dabieshanensis was produced.

The chloroplast genome genes, including the predicted protein-coding gens, transfer RNA (tRNA) gens, and ribosomal RNA (rRNA) genes, were annotated using the online tool DOGMA (Dual Organellar Genome Annotator) with the default parameters and manually checked [24]. BLASTn searches against the National Center for Biotechnology Information (NCBI) website and the tRNAscanSE program were further used to determine and confirm both tRNA and rRNA genes [25]. With the default parameters and subsequent manual editing, the circular map of I. dabieshanensis chloroplast genome was drawn using OGDRAWv1.3.1 [26].

I. dabieshanensis SSRs, long repeats, and codon usage analyses

Ilex dabieshanensis simple sequence repeats (SSRs) were identified by MIcroSAtellite (MISA) (http://pgrc.ipk-gatersleben.de/misa/) with the parameters set as follows: 8 for mono-, 5 for di-, 4 for tri-, and 3 for tetra-, penta-, and hexa-nucleotides [27]. Long repeats, including forward, complement, reverse, and palindromic, were analyzed using the online software REPuter with a minimum repeat size of 30 bp and a hamming distance of 3 [28]. Codon usage analysis was performed using a critical parameter of Relative Synonymous Codon Usage (RSCU) calculated by MEGA7 software [29].

Sequence divergence analyses of the four Ilex species

Taking the annotation of I. dabieshanensis as the reference, we compared its complete chloroplast genome with three other Ilex species in the family Aquifoliaceae (I. cornuta, I. latifolia, and I. paraguariensis) using the mVISTA program (http://genome.lbl.gov/vista/mvista/submit.shtml) in Shuffle-LAGAN mode [30]. Variations in LSC/IRB/SSC/IRA region borders were also compared using IRscope (https://irscope.shinyapps.io/irapp/) [31].

The genus Ilex and family Aquifoliaceae phylogeny

To determine the phylogenetic positions of I. dabieshanensis in the genus Ilex and family Aquifoliaceae, 21 plastid genome sequences (including 19 Ilex species) were retrieved from the NCBI GenBank database. Setting Helwingia chinensis and H. himalaica as outgroups, a phylogenetic tree was constructed in MEGAX using the maximum likelihood (ML) method based on the Tamura–Nei nucleotide substitution model [32]. The analysis was performed with 1,000 bootstrap replicates.

Results and discussion

I. dabieshanensis chloroplast genome features

The complete circular chloroplast genome of I. dabieshanensis (157,218 bp in length) exhibited a typical quadripartite structure, consisting of a LSC (86,607 bp), a SSC (18,427 bp), and a pair of IR (IRA and IRB: each of 26,092 bp) regions (Fig 1 and Table 1). Like other Aquifoliaceae chloroplast genomes, it had a low GC content (37.69%) [33]. The IR regions had higher GC contents (42.94%) than the LSC (35.75%) and SSC (31.93%) regions, which is a common phenomenon among plant chloroplast genomes [3436]. The relatively high GC content of the IR regions was mostly attributed to rRNA and tRNA genes as they occupied a greater area than the protein-coding genes [37].

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Fig 1. Circular gene map of I. dabieshanensis chloroplast genome.

The gray arrowheads indicate gene directions. Genes inside and outside the circle represent transcribed clockwisely and counterclockwisely. Different functional genes are color coded. The innermost darker gray conforms to GC content, whereas the lighter gray conforms to AT content. LSC, large single copy region; SSC, small single copy region; IR, inverted repeat.

https://doi.org/10.1371/journal.pone.0268679.g001

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Table 1. Summary of I. dabieshanensis chloroplast genome.

https://doi.org/10.1371/journal.pone.0268679.t001

A total of 121 predicted genes, including 113 unique (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions, were identified in I. dabieshanensis chloroplast genome (Tables 1, 2 and S1 Table). Common to many plants [38, 39], the I. dabieshanensis chloroplast genome had 18 intron-containing genes—6 tRNA and 12 protein-coding genes. Among these, 16 genes contained a single intron and 2 genes, clpP and ycf3, contained two introns (Table 2). Notably, the intron of the trnK-UUU gene, which contains the matK gene, was the longest, reaching up to 2,559 bp. The rps12 gene was a trans-spliced gene with one exon located in the LSC region (5’ end) and the other two exons (separated by an intron) located in both IRs. These findings are in line with those of the Zingiber, Cymbidium, and Forsythia chloroplast genomes [4042].

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Table 2. List of genes in the chloroplast genome of I. dabieshanensis.

https://doi.org/10.1371/journal.pone.0268679.t002

SSR and long repeats identification

Short (1–6 nucleotides) and long (10–100 nucleotides) repeats are distinguished according to the number of nucleotides in the repeat units [43]. SSRs (simple sequence repeats), or microsatellites, are short tandem repeats. Generally, SSRs have been widely used in population genetic and phylogenetic studies for their extensive distribution throughout the chloroplast genome and significant effects on its recombination and rearrangement [4446]. In I. dabieshanensis chloroplast genome, 132 SSRs were determined by MISA, among which, there were 119 mononucleotides, 4 dinucleotides, 5 trinucleotides, and 4 tetranucleotides, with a size of at least 8 bp (Fig 2A and S2 Table). The majority of SSRs were mono- and di-nucleotides, which was supported by previously reported chloroplast genome information [47, 48]. Among these nucleotides, A/T mononucleotides were the most abundant (accounting for 87.12%), similar to reports that short polyadenine (polyA) or polythymine (polyT) repeats are the main types of SSRs in chloroplast genomes (Fig 2B) [49]. Different regions possessed different numbers of SSRs. As shown in Fig 2C, there were 101, 18, and 13 SSRs located in the LSC, SSC, and IR regions, respectively. Shown in Fig 2D, 82, 23, and 27 SSRs were separately detected in intergenic regions, introns, and coding regions. These results corresponded with earlier reports that SSRs identified in Ilex chloroplast genome were primarily located in the LSC regions. SSRs were also enriched in noncoding regions [33, 48]. The SSR primers excavated in I. dabieshanensis chloroplast genome could be applied to future Ilex population genetic studies, polymorphism investigations, and evolution analyses.

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Fig 2. Distribution of SSR Types in I. dabieshanensis chloroplast genome.

A) Number of SSRs detected; B) Number of identified SSRs in different repeat class types; C) Number of identified SSRs in different genomic regions; and D) Number of identified SSRs in intergenic regions, introns, and coding regions.

https://doi.org/10.1371/journal.pone.0268679.g002

For the majority of land plants, long repeats in the chloroplast genome are considered uncommon [38]. In terms of direction and complementarity, these repeats can be divided into four types: forward, reverse, complement, and palindromic [50]. Altogether, 43 long repeats (20 palindromic and 23 forward) were identified in I. dabieshanensis chloroplast genome and 30–40 bp repeats were the most frequent, similar to several other land plants [51, 52]. No reverse or complementary repeats were identified in I. dabieshanensis chloroplast genome, same in I. latifolia chloroplast genome (Fig 3 and S3 Table) [33].

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Fig 3. Analysis of identified long repeat sequences in I. dabieshanensis chloroplast genome.

A) Number of long repeats in four identified types; B) Number of palindromic repeats by length; and C) Number of forward repeats by length.

https://doi.org/10.1371/journal.pone.0268679.g003

Codon preference analysis

Codon usage patterns and nucleotide composition can provide important information on the genetic modification of land plant chloroplast genomes. In general, no bias occurred in codon usage, or synonymous codon usage, when selective pressure was absent [53]. However, during plant evolution, the pattern of synonymous codon usage usually exhibited preference [54]. Relative synonymous codon usage (RSCU) is used as an effective index to determine codon preference [55]. A RSCU≤1.0 indicates no preference, 1.0<RSCU<1.2 signifies a weak preference, 1.2≤RSCU≤1.3 represents a moderate preference, and RSCU>1.3 indicates a strong preference [53]. In I. dabieshanensis chloroplast genome, 64 types of codons (26,932 codons totally) encoded 20 different amino acids. 30 of which had RSCU>1: 1 weak preference (RSCU = 1.16), 9 moderate preference (1.21 ≤ RSCU ≤ 1.28), and 20 strong preference (1.39 ≤ RSCU ≤ 1.85) (Table 3). Interestingly, except for TTG (G-ending), the other preferred codons all ended with the base A or T, which was previously confirmed to be the norm in most chloroplast genomes [56].

Comparative chloroplast genome analysis

The entire chloroplast genomes of four sequenced / published Ilex species were compared, with I. dabieshanensis used as the reference. Regions with sequence variation among the four Ilex species were marked with white peaks. Overall, the mVISTA results revealed high degrees of sequence identity between them, especially in I. dabieshanensis and I. cornuta, suggesting a greatly conserved evolution model. The relatively divergent regions primarily occurred in the non-coding regions rather than in coding regions, which was also previously demonstrated in the families Juglandaceae, Zingiberaceae, and Fabacaeae [8, 40, 57]. In total, seven variable sites, including matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL, were subsequently detected, some of which were validated in Yao et al. (2016) [16] and Cascales et al. (2017) [58]. These variations may promote the generation of potential DNA markers for Ilex species identification and phylogenetic reconstruction (Fig 4).

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Fig 4. Chloroplast genome comparisons among four Ilex species by mVISTA.

The chloroplast genome of I. dabieshanensis was used as a reference. Gray arrows above the alignment represent gene orientation. Different genome regions are color-coded as exons (purple bars), rRNA or tRNA (sky-blue bars), and non-coding sequences (CNS, pink bars). The horizontal axis indicates the coordinates within the chloroplast genome and vertical scale indicates the percentage of identity ranging from 50 to 100%. Regions with sequence variation among the four Ilex species were marked with white peaks.

https://doi.org/10.1371/journal.pone.0268679.g004

IR contraction and expansion

Variations (contraction or expansion) in the IR/SC boundary regions are common, which could give rise to differences in gene size and content among chloroplast genomes, even though the IR regions were often highly conserved [59, 60]. A comparison of IR/SC junctions among the four Ilex chloroplast genomes (I. dabieshanensis, I. cornuta, I. latifolia, and I. paraguariensis) is presented in Fig 5. Overall, JLB (LSC/IRB), JLA (LSC/IRA), and JSA (SSC/IRA) junctions were relatively conserved, whereas JSB (SSC/IRB) junctions were strikingly different. The genes located at the JSA/B and JLA/B junctions included rps19, rpl2, ycf1, ndhF, trnN, and trnH. At the JLA and JLB boundaries, the rpl2 gene of all four Ilex species was entirely located in the IRA and IRB regions, presenting a complete expansion in their IR regions. Except for I. latifolia, the rps19 gene in I. dabieshanensis, I. cornuta, and I. paraguariensis slightly covered the JLB, showing just a partial expansion (4 bp) in the JLB boundary. The ycf1 genes in all four Ilex species were throughout the JSA, which is common in angiosperms whose complete copy of ycf1 spans the IR regions [61]. However, in JSB, it was only detected in I. dabieshanensis and I. latifolia, with an expanded length of 1,056 bp and 981 bp in IRB, respectively. The ndhF gene exhibited the same situation as rps19, separately with 15 bp gaps to the JSB in I. dabieshanensis, I. cornuta, and I. paraguariensis.

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Fig 5. Comparisions of the SSC/IRs and LSC/IRs junctions among four Ilex chloroplast genomes.

Colored boxes above the strip with scaled sequence length represent the denoted genes. Between boxed genes and boundaries are the gaps in base length (bp). JLB, JSB, JSA, and JLA indicate IRB/LSC, IRB/SSC, IRA/SSC, and IRA/LSC junctions, respectively.

https://doi.org/10.1371/journal.pone.0268679.g005

Phylogenetic analysis of Ilex species in the family Aquifoliaceae

To determine the phylogenetic relationships, the entire plastid genome sequences of 19 Ilex species were aligned and a phylogenetic tree was generated by MEGAX using the maximum likelihood (ML) method with 1,000 bootstrap replicates. Helwingia chinensis and H. himalaica were set as out groups in the analyses. As shown in Fig 6, four clades were obtained from the examined Ilex species. Ilex dabieshanensis was clustered with I. cornuta in clade I, which also included five additional Ilex species (I. delavayi, I. integra, I. ficoidea, I. latifolia, and I. intermedia). These species are evergreen trees with leathery leaves that are broadly distributed across subtropical Asia [33]. Our results were in accordance with Shi et al. (2016) [62], who showed that I. dabieshanensis was a natural hybrid of I. cornuta and I. latifolia. Ilex paraguariensis and I. dumosa, which both originated from South America, were grouped in clade II. In clade III, I. trifloral, I. viridis, I. szechwanensis, and I. suaveolens showed close relationships. Clustered in clade IV, I. asprella, I. micrococca and I. polyneura are all deciduous shrubs or trees, while the other three clades contained evergreens. Overall, the plastid phylogeny illustrated that within the family Aquifoliaceae, the Ilex species might originate from more than one ancestor.

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Fig 6. Phylogenetic tree for 19 Ilex species in the family Aquifoliaceae using Maximum Likelihood (ML) method, based on alignments of complete chloroplast genomes.

The genomes of Helwingia chinensis and H. himalaica were set as outgroups. Numbers next to the branches indicated bootstrap values from 1,000 replicates.

https://doi.org/10.1371/journal.pone.0268679.g006

Conclusions

Here, the complete chloroplast genome of I. dabieshanensis (157,218 bp in length) was sequenced and analyzed. It was predicted to encode 121 genes, including 113 unique (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. A total of 132 SSRs and 43 long repeats were detected, which could be utilized as potential molecular markers. Based on the protein-coding genes, the codon usage represented a bias toward A/T-ending. Comparative chloroplast genome analyses of I. dabieshanensis, I. cornuta, I. latifolia, and I. paraguariensis revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.

Supporting information

S1 Table. Genes predicted in I. dabieshanensis cp genome.

https://doi.org/10.1371/journal.pone.0268679.s001

(XLS)

S2 Table. SSRs identified in I. dabieshanensis cp genome.

https://doi.org/10.1371/journal.pone.0268679.s002

(XLS)

S3 Table. Long repeats in the I. dabieshanensis cp genome.

https://doi.org/10.1371/journal.pone.0268679.s003

(XLSX)

Acknowledgments

We thank Ruisen Lu, and members in the Ilex laboratory for their technical support and stimulating discussions.

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