Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships
© Huang et al.; licensee BioMed Central Ltd. 2014
Received: 1 January 2014
Accepted: 20 June 2014
Published: 7 July 2014
Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most challengingly difficult taxa in plants. Sequence comparisons of chloroplast (cp) genomes are of great interest to provide a robust evidence for taxonomic studies, species identification and understanding mechanisms that underlie the evolution of the Camellia species.
The eight complete cp genomes and five draft cp genome sequences of Camellia species were determined using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. The Camellia cp genomes exhibited typical circular structure that was rather conserved in genomic structure and the synteny of gene order. Differences of repeat sequences, simple sequence repeats, indels and substitutions were further examined among five complete cp genomes, representing a wide phylogenetic diversity in the genus. A total of fifteen molecular markers were identified with more than 1.5% sequence divergence that may be useful for further phylogenetic analysis and species identification of Camellia. Our results showed that, rather than functional constrains, it is the regional constraints that strongly affect sequence evolution of the cp genomes. In a substantial improvement over prior studies, evolutionary relationships of the section Thea were determined on basis of phylogenomic analyses of cp genome sequences.
Despite a high degree of conservation between the Camellia cp genomes, sequence variation among species could still be detected, representing a wide phylogenetic diversity in the genus. Furthermore, phylogenomic analysis was conducted using 18 complete cp genomes and 5 draft cp genome sequences of Camellia species. Our results support Chang’s taxonomical treatment that C. pubicosta may be classified into sect. Thea, and indicate that taxonomical value of the number of ovaries should be reconsidered when classifying the Camellia species. The availability of these cp genomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of the genus Camellia.
KeywordsCamellia Chloroplast genome Phylogenetic relationships Genomic structure Taxonomic identification
Camellia, comprising more than 200 species, is an economically and phylogenetically important genus in the family Theaceae . Besides the abundance in phenotypic and species diversity, increasing attention has been paid to the genus, as they include several economically important members of their commercial and ornamental values. One of the most economic values of Camellia is the production of tea made from the young leaves of C. sinensis var. sinensis and C. sinensis var. assamica in the section Thea. The other most economically important species is C. oleifera, which has the longest history of cultivation and utilization in China for edible oil used primarily in cooking. Many other species of the genus Camellia were also used locally for seed oil production, such as C. reticulata . Moreover, the Camellia species are of great ornamental values, particularly represented by C. japonica, C. reticulata and C. sasanqua.
As a result of frequent hybridization and polyploidization, Camellia is taxonomically and phylogenetically regarded as one of the most challengingly difficult taxa in plants. Traditional classification of species using a morphology-based system is often dynamic and unreliable, which is often affected by environmental factors. The lack of suitable DNA fragments and polymorphic genetic markers for phylogenic analysis have long obstructed the availability of a reliable phylogeny, adding the controversies about taxonomic classification that prevent us from better understanding the diversification and evolution of the genus Camellia. By using amplified fragment length polymorphisms (AFLPs) , simple sequence repeats (SSRs) , random amplified polymorphic DNA (RAPD) , inter-simple sequence repeat (ISSR) , internal transcribed spacer (ITS) [1, 7] and several DNA loci , a number of previous studies gave further insights into the taxonomy and phylogeny of the Camellia species but still have not reached a satisfied resolution. A recent effort using whole chloroplast (cp) genome sequences of six Camellia species has generated useful data but still failed to determine their phylogenetic relationships, not agreeing with any taxonomic treatments .
The cp genomes could provide valuable information for taxonomic classification and the reconstruction of phylogeny as a result of sequence divergence between plant species and individuals. Owing to the absence of recombination and maternal transmission, the cp genomes are helpful for tracing source populations [10, 11] and phylogenetic studies of higher plants for resolving complex evolutionary relationships [12–14]. It is particularly true for the case of Camellia, given its confusing phylogenetic relationships with large nuclear genomes . Cp-derived markers, e.g. rpl16 gene, psbA-trnH, trnL-F and rpl32-trnL intergenic spacer (IGS), were employed to study evolutionary relationships between tea plants [8, 16]. Repetitive sequences within the cp genomes are also potentially useful for ecological and evolutionary studies of plants . Not only will the information from cp genomes be useful for studying the taxonomy and phylogenetic relationships, but it will also facilitate cp transformation in the economically important plants. The next-generation sequencing techniques have revolutionized DNA sequencing via high-throughput capabilities but relatively low costs. As it is now more convenient to obtain cp genome sequences and promptly extend gene-based phylogenetics to phylogenomics.
In this study, we sequenced the 13 Camellia chloroplast genomes using next-generation Illumina genome analyzer platform. The sequenced Camellia species included up to 10 species and varieties (10/18) from sect. Thea with an emphasis of these species belonging to the section. Three representative species were additionally sampled, each from sect. Camellia, sect. Corallina and sect. Archecamellia, respectively. This study aims to examine global patterns of structural variation of the Camellia cp genomes and reconstruct phylogenetic relationships among the representative species. The complete cp genome sequences of Camellia reported here are prerequisite for classifying the ‘difficult taxa’ and modifying these important economic plants by chloroplast genetic engineering techniques.
Results and discussion
Chloroplast genome sequencing and assembly
Information of the sequenced Camellia chloroplast genomes according Min’s taxonomic treatment 
Camellia crassicolumna var. crassicolumna
Camellia sinensis var. dehungensis
Camellia sinensis var. sinensis
Camellia sinensis var. pubilimba
The sequenced chloroplast genome features
Matched reads (bp)
Genome size (bp)
LSC length (bp)
SSC length (bp)
IR length (bp)
GC content (%)
C. sinensis var. dehungensis
C. sinensis var. sinensis
C. sinensis var. pubilimba
C. sinensis var. assamica
Matched reads (bp)
Predicted genome size (bp)
Number of gaps
Gap length (bp)
C. crassicolumna var. crassicolumna
Conservation of Camelliachloroplast genomes
Genes contained in the sequenced Camellia chloroplast genomes
Group of genes
Name of genes
Large subunit of ribosomal proteins
rpl2b,c, 14, 16b, 20, 22, 23c, 32, 33, 36
Small subunit of ribosomal proteins
rps2, 3, 4, 7c, 8, 11, 12b-d, 14, 15, 16b, 18, 19
DNA dependent RNA polymerase
rpoA, B, C1b, C2
rrn4.5c, 5c, 16c, 23c
trnA-UGCb,c, C-GCA, D-GUC, E-UUC, F-GAA, G-UCC, G-GCCb, H-GUG, I-CAUc, I-GAUb,c, K-UUUb, L-UAG, L-CAAc, L-UAAb, M-CAU, fM-CAU, N-GUUc, P-UGC, Q-UUG, R-ACGc, R-UCU, S-GGA, S-GCU, S-UGA, T-GGU, T-UGU, V-UACb, V-GACc, W-CCA, Y-GUA
psaA, B, C, I, J, ycf3a, ycf4
psbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z
ndhAb, Bb,c, C, D, E, F, G, H, I, J, K
Cytochrome b6/f complex
petA, Bb, Db, G, L, N
atpA, B, E, Fb, H, I
Translational initiation factor
Envelop membrane protein
c-type cytochrom synthesis gene
Conserved Open Reading Frames
ycf1, 2c,15c, orf42
Simple sequence repeats (SSRs) in the five representative Camellia chloroplast genomes
Substitution and indel variation
The numbers and ratios of nucleotide substitutions and indels in the five Camellia chloroplast genomes
Molecular marker identification
Structural constraints on evolutionary divergence
The phylogenetic analyses were performed based on the entire cp genome sequences from 18 Camellia cp genomes (Figure 9C and D), showing that the species of sect.Thea formed a monophyletic clade, except for the three individuals of C. taliensis, which is close to C. yunnanensis. This result indicated that C. taliensis may not be the ancestors of C. sinensis var. assamica  and there might be hybridization between C. taliensis and C. yunnanensis due to chimeric habitats. We observed that C.danzaiensis, C.pitardii and C.reticulata formed a monophyletic clade with strong bootstrap support, which might suggest that C. danzaiensis belongs to Subgen. Camellia, rather than Subgen. Thea. The different positions of C. impressinervis and C. cuspidate in ML and MP tree made more samples to resolve their phylogenetic relationship is essential. Further genomic and taxon sampling and more complete cp genomes of Camellia are deserved in further studies as phylogenomic analysis tends to suffer from the poor sampling .
We reported eight complete and five draft cp genomes in the genus Camellia using Illumina sequencing technology via a combination of de novo and reference-guided assembly. These cp genomes were found highly conserved each other. We investigated the variation of repeat sequences, SSRs, indels and substitutions among the five complete Camellia cp genomes, representing a wide phylogenetic diversity in the genus Camellia. The fifteen rapidly evolving regions were identified across these cp genomes that could serve as potential molecular markers for further phylogenetic studies. This study is undoubtedly the first successful attempt to provide well-supported evolutionary relationships of sect. Thea based on phylogenomic analyses. The obtained cp genomes may facilitate the development of biotechnological applications for these economically important woody plants, and offer useful genetic information for purposes of phylogenetics, taxonomy and species identification in the genus Camellia.
Leaf materials of the Camellia plants used in this study were collected from Kunming Institute of Botany (Chinese Academy of Sciences), Tea Research Institute (Yunnan Academy of Agricultural Sciences) and International Camellia Species Garden (Jinhua, Zhejiang Province, China) in May 2011 (Table 1). The collected plant materials were classified by Min’s taxonomic treatment  (Table 1). C. gymnogyna and C. costata of sect. Thea were unavailable and thus were absent in this study.
DNA sequencing and genome assembly
Approximately 20 g of fresh leaves from each species were harvested for cpDNA isolation using an improved extraction method that includes high ionic strength buffer at low pH (3.8) . After DNA isolation, 5 μg of purified DNA was fragmented by nebulization with compressed nitrogen gas, and constructed short-insert (300 bp) libraries following the manufacturer’s protocol (Illumina). DNA from the different species was indexed by tags and pooled together in one lane of Illumina’s Genome Analyzer for sequencing (2 × 100 bp) at Germplasm Bank of Wild Species in Southwest China, Kunming Institution of Botany, Chinese Academy of Sciences. Raw reads were first filtered to obtain the high-quality clean data by removing adaptor sequences and low-quality reads with Q-value ≤ 20. Then, those reads mixed non-cp DNA from the nucleus and mitochondria were isolated based on the known cp genome sequences. Then, the following three steps were used to assemble cp genomes . First, the filtered reads were assembled into contigs using SOAPdenovo . Second, contigs were aligned to the reference genome of C. sinensis var. assamica (Genbank ID: JQ975030) using BLAST, and aligned contigs (≥90% similarity and query coverage) were ordered according to the reference genome. Third, raw reads were again mapped to the assembled draft cp genomes that were then visualized by Geneious (version 5.1) , and the majority of gaps were filled through local assembly.
Based on the reference genome of C. sinensis var. assamcia, we designed four primer pairs for the verification of the four junctions between the single-copy segments and IRs (as given in Additional file 1: Table S1), respectively. PCR products were then sequenced following standard Sanger protocols on ABI 3730 ×1 instruments. Sanger sequences and assembled genomes were aligned using Geneious assembly software to determine if there were any differences.
Genome annotation, alignment and visualization
The chloroplast genes were annotated using an online DOGMA tool , using default parameters to predict protein-coding genes, transfer RNA (tRNA) genes, and ribosome RNA (rRNA) genes. Start and stop codons of protein-coding genes were searched and determined by BLASTX against the NCBI protein database, with C. sinensis var. assamica as a guide. Genome maps were drawn with OGDraw (version 1.2) . Multiple alignments were made using MAFFT version 5  and adjusted manually where necessary. Full alignments with annotations were visualized using the VISTA viewer .
Characterization of repeat sequences and SSRs
REPuter  was used to identify and locate the repeat sequences, including direct, reverse and palindromic repeats within cp genome. For repeat identification, the following constraints were set to REPuter: (i) minimum repeat size of 30 bp, and (ii) 90% or greater sequence identity, based on Hamming distance of 3.
SSRs were predicted using MISA  with the parameters set to ten repeat units ≥10 for mononucleotide SSRs, six repeat units ≥6 for dinucleotide, five repeat units ≥5 for trinucleotide, four repeat units ≥4 for tetranucleotide, and three repeat units ≥3 for pentanucleotide and hexanucleotide SSRs.
Identification of molecular markers
To identify the divergent regions for phylogenetic analyses, all the regions, including CDS, introns and IGS from the Camellia cp genomes, were sequentially extracted. For each species, homologous regions of cp genomes were aligned using MAFFT version 5 and manual adjustments were made where necessary. Subsequently, the percentage of variable characters for each region was obtained. The proportion of mutational events (or variation%) was calculated by following the modified version of the formula used in Gielly and Taberlet . The proportion of mutation events = [(NS + ID)/L] × 100, where NS = the number of nucleotide substitutions, ID = the number of indels, L = the aligned sequence length.
The Camellia cp genome sequences were aligned using the program MAFFT version 5  and adjusted manually where necessary. The ambiguously aligned loci (e.g., ‘N’) were excluded from the analyses. The unambiguously aligned DNA sequences were used for the reconstruction of phylogenetic trees. The phylogenetic analyses were performed based on the following two data sets: (1) the remaining sequences with lengths from 83,585 to 83,835 bp (including 78.1% coding and 21.9% non-coding regions) after the removal of the ‘N’s in incomplete cp genomes as well as the corresponding orthologous sequences in complete cp genomes from the alignment of the 13 Camellia cp genomes that belong to sect. Thea with C. reticulata as outgroup; (2) the eight complete cp DNA sequences sequenced obtained in this study, three Camellia cp genomes adopted from , and seven Camellia cp genomes retrieved from  with C. arabica as outgroup.
ML analyses were implemented in RAxML version 7.2.6 . RAxML searches relied on the general time reversible (GTR) model of nucleotide substitution with the gamma model of rate heterogeneity. Non-parametric bootstrapping used 1,000 replicates as implemented in the “fast bootstrap” algorithm of RAxML. MP analyses were performed with PAUP*4.0b10. Heuristic tree searches were conducted with 1,000 random-taxon-addition replicates and tree bisection-reconnection (TBR) branch swapping, with “multrees” option in effect. Non-parametric bootstrap analysis was conducted under 1,000 replicates with TBR branch swapping.
Availability of supporting data
These cp genomes sequenced in this study are available the GenBank database under the accession numbers (KJ806274-KJ806286). The alignments and phylogenetic trees supporting the results of this article are available in the TreeBASE repository, http://purl.org/phylo/treebase/phylows/study/TB2:S16027?x-accesscode=e9a8a916b74d332d14f1954ca00a51f6&format=html.
Amplified fragment length polymorphisms
C. sinensis var. assamica
- BS value:
Bootstrap support values
Conserved noncoding sequences
Inter-simple sequence repeat
Internal transcribed spacer
Large single copy
Random amplified polymorphic DNA
Nucleotide substitutions events to indels events
Small single copy
Simple sequence repeats
We thank Zhu Ting, Nan Hu and Chen Qing for their help to sample the Camellia germplasms and experimental assistance, Ju Gao and Qun-Jie Zhang for data analysis, and anonymous reviewers for their valuable comments. This work was supported by National Science Foundation of China (U0936603), Top Talents Program of Yunnan Province (20080A009) and Hundreds of Oversea Talents Program of Yunnan Province to L.Z. GAO and National Science Foundation of China (31200515) and Surface Project of Natural Science Foundation of Yunnan Province (2012FB179) to H. Huang.
- Vijayan K, Zhang WJ, Tsou CH: Molecular taxonomy of Camellia (Theaceae) inferred from nrITS sequences. Am J Bot. 2009, 96: 1348-1360.PubMedView ArticleGoogle Scholar
- Min TL, Bruce B: Flora of China. 2010, Beijing, China: Science PressGoogle Scholar
- Wachira FN, Tanaka J, Takeda Y: Genetic variation and differentiation in tea (Camellia sinensis) germplasm revealed by RAPD and AFLP variation. J Hort Sci Biotech. 2001, 76: 557-563.Google Scholar
- Wang LY, Liu BY, Jiang YY, Duan YS, Cheng H, Zhou J, Tang YC: Phylogenetic analysis of inter species in section Thea through SSR markers. J Tea Sci. 2009, 29: 341-346.Google Scholar
- Chen L, Yamaguchi S, Wang PS, Xu M, Song WX, Tong QQ: Genetic polymorphism and molecular phylogeny analysis of section Thea based on RAPD markers. J Tea Sci. 2002, 22: 19-24.Google Scholar
- Ji PZ, Wang YG, Zhang J, Tang YC, Huang XQ, Wang PS: Genetic relationships between sect. Thea from Yunnan province revealed by inter-simple sequence repeat polymerase China reaction. Southwest China J Agric Sci. 2009, 22: 584-588.Google Scholar
- Tian M, Li JY, Ni S, Fan ZQ, Li XL: Phylogenetic study on section Camellia based on ITS sequences data. Acta Hort Sin. 2008, 35: 1685-1688.Google Scholar
- Fang W, Yang JB, Yang SX, Li DZ: Phylogeny of Camellia sects. Longipedicellata, Chrysantha and Longissima (Theaceae) based on sequence data of four chloroplast DNA Loci. Acta Bot Yunnanica. 2010, 32: 1-13.View ArticleGoogle Scholar
- Yang JB, Yang SX, Li HT, Yang J, Li DZ: Comparative chloroplast genomes of Camellia species. PLoS ONE. 2013, 8: e73053-PubMedPubMed CentralView ArticleGoogle Scholar
- McCauley DE, Stevens JE, Peroni PA, Raveill JA: The spatial distribution of chloroplast DNA and allozyme polymorphisms within a population of Silene alba (Caryophyllaceae). Am J Bot. 1996, 83: 727-31.View ArticleGoogle Scholar
- Small RL, Cronn RC, Wendel JF: Use of nuclear genes for phylogeny reconstruction in plants. Aust Syst Bot. 2004, 17: 145-70.View ArticleGoogle Scholar
- Jansen RK, Cai Z, Raubeson LA, Daniell H, de Pamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee S, Peery R, McNeal JR, Kuehl J, Boore JL: Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A. 2007, 104: 19369-19374.PubMedPubMed CentralView ArticleGoogle Scholar
- Parks M, Cronn R, Liston A: Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol. 2009, 7: 84-PubMedPubMed CentralView ArticleGoogle Scholar
- Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE: Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci U S A. 2010, 107: 4623-4628.PubMedPubMed CentralView ArticleGoogle Scholar
- Huang H, Tong Y, Zhang QJ, Gao LZ: Genome Size Variation among and within Camellia Species by Using Flow Cytometric Analysis. PLoS ONE. 2013, 8: e64981-PubMedPubMed CentralView ArticleGoogle Scholar
- Liu Y, Yang SX, Ji PZ, Gao LZ: Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation. BMC Evol Biol. 2012, 12: 92-105.PubMedPubMed CentralView ArticleGoogle Scholar
- Provan J, Powell W, Hollingsworth PM: Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol. 2001, 16: 142-147.PubMedView ArticleGoogle Scholar
- Shi C, Liu Y, Huang H, Xia EH, Zhang HB, Gao LZ: Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms. PLoS ONE. 2013, 8: e59620-PubMedPubMed CentralView ArticleGoogle Scholar
- Cronn R, Liston A, Parks M, Gernandt DS, Shen RK: Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by- synthesis technology. Nucleic Acids Res. 2008, 36: e122-PubMedPubMed CentralView ArticleGoogle Scholar
- Matsuoka Y, Yamazaki Y, Ogihara Y, Tsunewaki K: Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals. Mol Biol Evol. 2002, 19: 2084-2091.PubMedView ArticleGoogle Scholar
- Xu Q, Xiong GJ, Li PB, He F, Huang Y, Wang KB, Li ZH, Hua JP: Analysis of Complete Nucleotide Sequences of 12 Gossypium Chloroplast Genomes: Origin and Evolution of Allotetraploids. PLoS ONE. 2012, 7: e37128-PubMedPubMed CentralView ArticleGoogle Scholar
- Davis JI, Soreng RJ: Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (Poaceae). Am J Bot. 2010, 97: 874-892.PubMedView ArticleGoogle Scholar
- Kim KJ, Lee HL: Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 2004, 11: 247-261.PubMedView ArticleGoogle Scholar
- Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I: VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 2000, 16: 1046-1047.PubMedView ArticleGoogle Scholar
- Palmer JD: Plastid chromosomes: structure and evolution. the Molecular Biology of Plastids. Edited by: Bogorad L, Vasil IK. 1991, New York: Academic Press, 5-53.View ArticleGoogle Scholar
- Kurtz S, Choudhuri JV, 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.PubMedPubMed CentralView ArticleGoogle Scholar
- Saski C, Lee SB, Fjellheim S, Guda C, Jansen RK, Luo H, Tomkins J, Rognli OA, Daniell H, Clarke JL: Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor Appl Genet. 2007, 115: 571-590.PubMedPubMed CentralView ArticleGoogle Scholar
- Zhang YJ, Ma PF, Li DZ: High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLoS ONE. 2011, 6: e20596-PubMedPubMed CentralView ArticleGoogle Scholar
- Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N, Tragoonrung S: The chloroplast genome sequence of Mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationship. DNA Res. 2010, 17: 11-22.PubMedPubMed CentralView ArticleGoogle Scholar
- 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.PubMedView ArticleGoogle Scholar
- Timme RE, Kuehl JV, Boore JL, Jansen RK: A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: Identification of divergent regions and categorization of shared repeats. Am J Bot. 2007, 94: 302-312.PubMedView ArticleGoogle Scholar
- Cavalier-Smith T: Chloroplast evolution: secondary symbiogenesis and multiple losses. Curr Biol. 2002, 12: 62-64.View ArticleGoogle Scholar
- Gao L, Yi X, Yang YX, Su YJ, Wang T: Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol Biol. 2009, 9: 130-144.PubMedPubMed CentralView ArticleGoogle Scholar
- Echt CS, DeVerno LL, Anzidei M, Vendramin GG: Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait. Mol Ecol. 1998, 7: 307-316.View ArticleGoogle Scholar
- Powell W, Morgante M, Andre C, Mcnicol JW, Machray GC, Doyle JJ, Tingey SV, Rafalski JA: Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Curr Biol. 1995, 5: 1023-1029.PubMedView ArticleGoogle Scholar
- Kuang DY, Wu H, Wang YL, Gao LM, Zhang SZ, Lu L: Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. Genome. 2011, 54: 663-673.PubMedView ArticleGoogle Scholar
- Yi D-K, Kim K-J: Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L. PLoS ONE. 2012, 7: e35872-PubMedPubMed CentralView ArticleGoogle Scholar
- Jakobsson M, Sall T, Lind-Hallden C, Hallden C: Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana. Theor Appl Genet. 2007, 114: 223-235.PubMedView ArticleGoogle Scholar
- Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S: Genetic structure and diversity in Oryza sativa L. Genetics. 2005, 169: 1631-1638.PubMedPubMed CentralView ArticleGoogle Scholar
- Xu DH, Abe J, Gai JY, Shimamoto Y: Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean. Theor Appl Genet. 2002, 105: 645-653.PubMedView ArticleGoogle Scholar
- Leseberg CH, Duvall MR: The complete chloroplast genome of Coix lacryma-jobi and a comparative molecular evolutionary analysis of plastomes in cereals. J Mol Evol. 2009, 69: 311-318.PubMedView ArticleGoogle Scholar
- Grover CE, Yu Y, Wing RA, Paterson AH, Wendel JF: A phylogenetic analysis of indel dynamics in the cotton genus. Mol Biol Evol. 2008, 25: 1415-1428.PubMedView ArticleGoogle Scholar
- Britten RJ, Rowen L, Williams J, Cameron RA: Majority of divergence between closely related DNA samples is due to indels. Proc Natl Acad Sci U S A. 2003, 100: 4661-4665.PubMedPubMed CentralView ArticleGoogle Scholar
- Chen JQ, Wu Y, Yang H, Bergelson J, Kreitman M, Tian D: Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol. 2009, 26: 1523-1531.PubMedView ArticleGoogle Scholar
- Yamane K, Yano K, Kawahara T: Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice. DNA Res. 2006, 13: 197-204.PubMedView ArticleGoogle Scholar
- McCluskey K, Wiest AE, Grigoriev IV, Lipzen A, Martin J, Schackwitz W, Baker SE: Rediscovery by whole genome sequencing: classical mutations and genome polymorphisms in Neurospora crassa. G3 (Bethesda). 2011, 1: 303-316.View ArticleGoogle Scholar
- Smith SA, Donoghue MJ: Rates of molecular evolution are linked to life history in flowering plants. Science. 2008, 322: 86-89.PubMedView ArticleGoogle Scholar
- Perry AS, Wolfe KH: Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat. J Mol Evol. 2002, 55: 501-508.PubMedView ArticleGoogle Scholar
- Clegg MT, Gaut BS, Learn GH, Morton BR: Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci U S A. 1994, 91: 6795-6801.PubMedPubMed CentralView ArticleGoogle Scholar
- Wolfe KH, Gouy ML, Yang YW, Sharp PM, Li WH: Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci U S A. 1989, 86: 6201-6205.PubMedPubMed CentralView ArticleGoogle Scholar
- Moore MJ, Bell CD, Soltis PS, Soltis DE: Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci U S A. 2007, 104: 19363-19368.PubMedPubMed CentralView ArticleGoogle Scholar
- Chang HD, Ren SX: Flora of China. Science Press. Tomus. 1998, 49 (3): 1-251.Google Scholar
- Min TL: A revision of Camellia sect. Thea Acta Bot Yunnanica. 1992, 14: 115-132.Google Scholar
- Li XH, Zhang CZ, Liu CL, Shi ZP, Luo JW, Chen X: RAPD analysis of the genetic diversity in Chinese tea germplasm. Acta Hort Sin. 2007, 34: 507-508.Google Scholar
- Peng ZH, Lu TT, Li LB, Liu XH, Gao ZM, Hu T, Yang XW, Feng Q, Guan JP, Weng QJ, Fan DL, Zhu CR, Lu Y, Han B, Jiang ZH: Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences. BMC Plant Biol. 2010, 10: 116-129.PubMedPubMed CentralView ArticleGoogle Scholar
- Bapteste E, Philippe H: The potential value of indels as phylogenetic markers: position of Trichomonads as a case study. Mol Biol Evol. 2002, 19: 972-977.PubMedView ArticleGoogle Scholar
- Simmons MP, Ochoterena H, Carr TG: Incorporation, relative homoplasy, and effect of Gap characters in sequence -based phylogenetic analyses. Syst Biol. 2001, 50: 454-462.PubMedView ArticleGoogle Scholar
- Shi C, Hu N, Huang H, Gao J, Zhao Y-J, Gao LZ: An Improved Chloroplast DNA Extraction Procedure for Whole Plastid Genome Sequencing. PLoS ONE. 2012, 7: e31468-PubMedPubMed CentralView ArticleGoogle Scholar
- Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J: De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010, 20: 265-272.PubMedPubMed CentralView ArticleGoogle Scholar
- Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A: Geneious v5. 2011, 4: Available from http://www.geneious.comGoogle Scholar
- Wyman SK, Jansen RK, Boore JL: Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 2004, 20: 3252-3255.PubMedView ArticleGoogle Scholar
- Lohse M, Drechsel O, Bock R: Organellar Genome DRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet. 2007, 52: 267-274.PubMedView ArticleGoogle Scholar
- Katoh K, Kuma K, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005, 33: 511-518.PubMedPubMed CentralView ArticleGoogle Scholar
- Thiel T, Michalek W, Varshney RK, Graner A: Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet. 2003, 106: 411-422.PubMedGoogle Scholar
- Gielly L, Taberlet P: The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Mol Biol Evol. 1994, 11: 769-777.PubMedGoogle Scholar
- Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006, 22: 2688-2690.PubMedView ArticleGoogle Scholar
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