Comparative Chloroplast genomes of Gynura species:Sequence Variation, Genome Rearrangement and Divergence studies

doi:10.21203/rs.2.9989/v1

Download PDF

Research article

Comparative Chloroplast genomes of Gynura species:Sequence Variation, Genome Rearrangement and Divergence studies

https://doi.org/10.21203/rs.2.9989/v1

This work is licensed under a CC BY 4.0 License

Journal Publication

published 29 Oct, 2019

Read the published version in BMC Genomics →

You are reading this older preprint version

Read the latest preprint version →

Background

Some Gynura species were reported to be natural anti-diabetic plants. The chloroplast genomes of four Gynura species were sequenced for hybridizations to improve agronomic traits. There are only 4 genera of tribe Senecioneae have published chloroplast genome in Genbank up to now. The internal relationships of the genus Gynura and the relationship of the genus Gynura with other genera in tribe Senecioneae need further researches.

Results

The chloroplast genome of 4 Gynura species were sequenced, assembled and annotated. Comparing with other 12 Senecioneae species, the chloroplast genome features were detailedly analyzed. Subsequently, the differences of the microsatellites and repeats type in the tribe were found. By comparison, the IR expansion and contraction is conserved in the genera Gynura, Dendrosenecio and Ligularia. The region from 25,000 to 50,000 bp is relatively not conservative but the 7 ndh genes in this region are under purifying selection with small change in amino acids. The phylogenetic tree shows two major clades, same as the sequence divergence in region 25,000 to 50,000 bp. Based on the oldest Artemisia pollen fossil, the divergence time were estimated.

Conclusions

Sequencing of chloroplast genome of the 4 Gynura species help us to develop abundant genetic resources. The phylogenetic relationships and divergence time among 4 Gynura and 16 Senecioneae species were sorted out by comparing the chloroplast genomes. The phylogenetic relationship of the genera Gynura and Ligularia is different with former work and further morphology and genome-wide analysis are needed to clarify the genera relationship.

Epigenetics & Genomics

Chloroplast genome

Genus Gynura

Tribe Senecioneae

Phylogenetic relationships

Divergence time

Gynura is a genus of flowering plants in the tribe Senecioneae of family Asteraceae endemic to Asia, which contains 44 species in total [1]. Many species of the genus Gynura have been reported to have medicinal value to diabetes mellitus, such as G. procumbens, G. divaricata and G. medica. The aqueous extract from G. procumbens possessed a significant hypoglycemic effect in streptozotocin-induced diabetic rats [2] and it improved insulin sensitivity and suppressed hepatic gluconeogenesis in C57BL/KsJ-db/db mice [3]. Polysaccharide from G. divaricata couldalleviate the hyperglycemiabymodulating the activities of intestinal disaccharidases in streptozotocin-induced diabetic rats [4] and G. divaricata-lyophilized powder was effectively hypoglycemic by activating insulin signaling and improving antioxidant capacity in mice with type 2 diabetes [5]. Phenolic compounds isolated from G. medica inhibitedyeast α-glucosidase in vitro [6].

Some plants in genus Gynura have also been used as vegetable and tea in people’s daily life of East and South Asia, thus the genus Gynura is a natural treasure trove to treat the increasingly diabetes problem. Although Gynura plants are seemingly useful and harmless, but some shortcomings need improvement such as the medicinal effect to diabetes, potential toxicity and oral tastes [7-8]. Large improvement relies on interspecific hybridizations to increase genetic diversity and introgression of valuable traits. Phylogenetic relationship is useful information for the interspecific hybridizations, but the phylogenetic relationship of the species in genus Gynura is, as yet, unclear.

A whole chloroplast DNA ranges between 120 and 160 kb in size on the circular chromosome in most plants, composing of Large Single Copy (LSC), Small Single Copy (SSC), and two copies of an Inverted Repeat (IRa and IRb) [9-10]. Contrast to mitochondrial and nuclear genomes, chloroplast genomes are more conserved in terms of gene content, organization and structure [11]. The chloroplast genomes of angiosperms generally show slow substitution rates under adaptive evolution [12]. Considering its small size, conserved gene content and simple structure, the chloroplast genome are valid and cost-effective to research phylogenetic relationships and evolution of plants in different taxa. Recently, Forage species of Urochloa [13], marine crop Gracilaria firma [14], Epilithic sister genera Oresitrophe and Mukdenia [15], Family Adoxaceae and Caprifoliaceae of Dipsacales [16] were sequenced the related complete chloroplast genomes to elucidate the diversity, phylogeny and evolution.

In the present study, we sequenced, assembled and annotated the chloroplast genomes of four Gynura species. Combined with other published chloroplast genomes of tribe Senecioneae, the structure features, repeat motifs, adaptive selection, phylogenetic relationships and divergence time were analyzed.

Chloroplast genome features of 16 Senecioneae species

In this study, we focused on the chloroplast genome features of tribe Senecioneae, which is the largest tribe of family Asteraceae. Although the tribe comprises about 500 genera and 3000 species [44], we only found that 4 genera of tribe Senecioneae had published chloroplast genome in Genebank. Five species of genus Dendrosenecio, one species of genus Jacobaea, five species of genus Ligularia, one species of genus Pericallis and four species of genus Gynura were used to find their similarities and differences. The whole sequence length ranges from 150,551 bp (Dendrosenecio brassiciformis) to 151,267 bp (Pericallis hybrida). With the typical quadripartite parts like most land plants, the chloroplast genome has one Large single copy (LSC), one Short single copy (SSC), two Inverted regions (IRa and IRb) (Fig 1). The LSC length ranges from 82,816 bp (Jacobaea vulgaris) to 83,458 bp (Dendrosenecio cheranganiensis), the SSC length ranges from 17,749 bp (D. brassiciformis) to 18,331 bp (P. hybrida) and the IRs length both range 24,688 bp (D. brassiciformis) to 24,845 bp (P. hybrida) (Table 1). Changes in each region are not consistent with changes in whole chloroplast genome. J. vulgaris has the shortest chloroplast genome in length but its SSR region is longer than 4 Gynura species. In addition, there are 95 coding genes in the chloroplast genome of P. hybrida and 87 coding genes in the J. vulgaris. GCcontent varies between 37.2% and 37.5%. Only the rRNA number is conserved in chloroplast genome of tribe Senecioneae, which is same as family Adoxaceae and Caprifoliaceae [16], but different from genus Oresitrophe and Mukdenia [15].

Microsatellites and Repeats type

Number of micosatellites with mono-,di- and tri-nucleotide repeat motifs varies in the tribe. D. brassiciformis, J. vulgaris and L. hodgsonii do not have tri-nucleotide repeat motifs while four Gynura species have 4 to 5 tri-nucleotide repeat motifs. The number of mono-nucleotide repeat motif is 28 to 38, accounting for the largest proportion (Fig 2a). The unit size of microsatellites is significantly different in four Urochloa species [13], which has tetra-nucleotide repeat motif and the tri-nucleotide is the largest in the proportion. The total number of repeats types is consistent with those in the four Gynura species, but the number of each repeat type is different. Palindromic repeats are the most abundant and complement repeats are secondary in 16 Senecioneae species (Fig 2b). Compared with the Oresitrophe species [15], the Senecioneae species have 5 to 12 reverse repeats, but the Oresitrophe species do not have reverse repeats. In addition to this, forward and palindromic repeats number is similar in the Oresitrophe species.

Contraction and Expansion of Inverted Repeats

The chloroplast genome is highly conserved in land plants, but the IR expansion and contraction leads to the different genome sizes of different plants [41].16 species of Senecioneae tribe were analyzed the LSC/IRb/SSC/IRa/LSC border and adjacent genes (Fig 3). rps19 and rpl2 gene locate in the LSC/IRb and IRa/LSC border in pairs. In 16 Senecioneae species, the two copies of rps19 have no change in position to the border and the two copies of rpl2 are relatively conserved with 1-3 base position changes except the IRa/LSC border of P. hybrida.One copy of ycf1 spans the border of LSC/IRb, another copy is different. The start position is just on the border in the four Gynura species, but the others also span the border of IRa/LSC. By comparison, the IR expansion and contraction is conserved in the genera Gynura, Dendrosenecio and Ligularia.

Sequence Variation and Adaptive selection

The whole chloroplast genome sequences of 16 Senecioneae species were aligned by MAFFT program to find the sequence variation. The alignment result was used to calculate the DNA polymorphism by DnaSP program. The base sequence has a Pi value (nucleotide diversity) of 0.2-0.3 at 25,000 bp to 50,000 bp, and other positions below 0.1(Fig 4A). This shows that this region is less conservative than other regions of chloroplast genome. For further analysis of the results, the chloroplast genome sequences of four Gynura species, D. cheranganiensis, L. hodgsonii and P. hybrida werealigned and visualized by mVISTA program. The overall result is consistent with the DNA ploymoriphism result (Fig S1). The four Gynura species are conserved in 25,000 bp to 50,000 bp region and similar with L. hodgsonii. In that region, D.cheranganiensis is close to P. hybrida , but different from the four Gynura species and L. hodgsonii (Fig 4B). That region has total 12 genes and 7 genes are coding the NAD(P)H dehydrogenase (NDH) complex subunit. The function of NAD(P)H dehydrogenase (NDH) complex is well-known in the photosystem I (PSI) cyclic electron flow (CEF) and chlororespiration [42-43], so the substitution of ndh genes was further studied. The ratio of non-synonymous(dN)/synonymous substitution (dS) rate were calculated by PAML program. The ratio > 1 indicates positive selection, the ration < 1 indicates purifying selection and the ratio = 1 indicates neutral evolution. All the dN/dS ratio of 7 genes below 1 indicates that they are under purifying selection and little amino acid change happened (Table 2). That means the functions of 7 ndh genes are conservative during evolution, although they are not located in a conservative area.

Phylogenetic Relationships

The sequence alignment of 16 Senecioneae species was used to construct the ML (Fig 5) and BI (Fig S2) tree. In ML tree, two major clades were constructed with 100% bootstrap value. One clade includes the genera Gynura and Ligularia, and the other clade includes the genera Dendrosenecio, Pericallis and Jacobaea. In genus Gynura, G. bicolor was the first to differentiate, followed by G. divaricata, at last were the G. formosana and G. pseudochina. The two clades divergence result is consistent with the sequence divergence in 25,000 to 50,000 bp region. The former systemic phylogenies of tribe Senecioneae based on ITS region (nuclear) and plastid fragment sequences show a significant different with the phylogenetic tree [44]. In the former phylogenetic tree, genus Ligularia belongs to Tussilagininae grade, which was in the earlier diverging lineage than other genus. The sequence between four Gynura species and five Ligularia species is relatively conserved and the Pi value of most sequence locations are below 0.1 (Fig S3), significantly lower than the 16 species alignment. From the perspective of whole chloroplast genomes, genus Ligularia is close to genus Gynura.

Divergence Time Estimation

For the divergence time estimation of the 16 Senecioneae species, Artemisia gmelinii and Chrysanthemum boreale (Tribe Anthemideae) were selected as outgroup due to oldest Artemisia fossil pollen [38-39]. The divergence time of 16 Senecioneae species were estimated by BEAST2.0 program (Fig 6). The divergence clades of these genera are same with ML tree. The two major clades were expected to differentiate at 37.4 mya (late Eocene). Both Gynura and Ligularia differentiated at 5.8 mya (late Miocene). Dendrosenecio and Pericallis also differentiated at5.8 mya. The divergence time of tribe Senecioneae and Anthemideae was at 51.39 mya (early Eocene) and the result was consistent with previous study on the evolution and phylogenetic of family Asteroideae basing on the plastid fragment sequences [39]. The traditional view on divergence time of the genus Gynura is in the Old World after the Atlantic opening. In that time, the Senecioid species were transferred to South America and the divergence began[45]. The divergence time of Gynura species was about 0.3 mya and the result showed that the divergence time of genus Gynura was much earlier than the traditional views. The divergence time of genus Gynura could not start at hundreds or thousands years ago[45] and the divergence time estimated by BEAST program was in the same time period with other genera of land plants[13-16].

This study analyzes the chloroplast genome of four Gynura species used as herbal medicine in parts of Asia. By comparing with other plants in tribe Senecioneae, the repeat motifs, detailed structure feature, phylogenetic relationships and divergence time estimation were identified. The phylogenetic relationship of genera Gynura, Ligularia and others are still in doubt. The tribe Senecioneae contains 155 genera and almost distributes throughout the world [44]. The phylogenetic relationship is difficult to determine by chloroplast fragment or genome. Morphology and genome-wide analysis are needed to further clarify the genera relationship. Determining interspecific relationships and intergeneric relationships will facilitate the hybrid breeding of Gynura species.

Plant materials, Genome sequencing and assembly

Gynura bicolor, cultivated plant, the voucher specimen (510918-1), collected from Nanjing Botanical Garden Mem. Sun Yet-Sen. Gynura divaricata, cultivated plant, the voucher specimen (510918-6), collected from Nanjing Botanical Garden Mem. Sun Yet-Sen.Gynura formosana, cultivated plant, the voucher specimen (512019-3), collected from Kunming Botanical Garden.Gynura pseudochina, wild plant, the voucher specimen (512019-8), collected from Wenshan Zhuang and Miao Autonomous Prefecture, Yunnan Province, all the plants were collected by Prof. Bingru Ren, and the specimens were deposited in the Herbarium of Institute of Botany, Jiangsu Province and Chinese Academy of Sciences.

The Gynura bicolor, G. divaricata, G. formosana and G. pseudochina plants grow in greenhouse with normal sunlight and temperature. The DNA was extracted from their fresh leaves by CTAB method [17] and DNA degradation and contamination was monitored on 1% agarose gels.

About 1.5μg DNA sample was fragmented by sonication to a size of 350bp, then DNA fragments were end polished, A-tailed, and ligated with the full-length adapter for Illumina sequencing with further PCR amplification. After PCR products purification (AMPure XP system), libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified by using real-time PCR.

The libraries constructed above were sequenced by Illumina HiSeq X Ten platform and 150bp paired-end reads (PE150) were generated with insert size around 350bp. Quality control (QC) is removing reads with ≥10% unidentified nucleotides (N), > 50% bases having phred quality < 5 and > 10 nt aligned to the adapter, allowing ≤10% mismatches.

The perl script NOVOPlasty 2.7.2 [18] was used to assemble the chloroplast genome sequence with 50 K-mer. The chloroplast genome sequence of Dendrosenecio cheranganiensis (Tribe Senecioneae) was selected as the reference genomes. The family Asteraceae plants used in the study were downloaded from Genebank, as follows: Dendrosenecio brassiciformis (NC_037960.1), Dendrosenecio cheranganiensis (NC_037956.1), Dendrosenecio johnstonii (NC_037959.1), Dendrosenecio kilimanjari (NC_037957.1), Dendrosenecio meruensis (NC_037958.1), Jacobaea vulgaris (NC_037957.1), Ligularia hodgsonii (NC_039381.1), Ligularia intermedia (NC_039382.1), Ligularia jaluensis (NC_039383.1), Ligularia mongolica (NC_039384.1), Ligularia veitchiana (NC_039385.1), Artemisia gmelinii (NC_031399.1), Chrysanthemum boreale (NC_037388.1).

Chloroplast genome annotation

The whole chloroplast genome sequences were annotated by Dual Organellar Genome Annotator [19] and GeSeq [20] with default parameters. Chloroplast genome sequences of tribe Senecioneae plants Dendrosenecio cheranganiensis and Pericallis hybrida were used as reference sequences. Subsequently, all tRNAs were verified by ARAGORN v1.2.38 [21] and tRNAscan-SE v2.0 [22]. Four chloroplast genomes( Gynura bicolor, G. divaricata, G. formosana and G. pseudochina ) with annotation were submitted into GenBank and the submission ID is 2222634 . Schematic diagram of chloroplast genome with annotations were obtained by OGDRAW [23].

Repeat structure analysis

The microsatellite regions is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 1-6 or more base pairs) are repeated, typically 5-50 times [24-25]. The perl script Microsatellite identification tool (MISA, http://pgrc.ipk-gatersleben.de/misa/misa.html) were used to find the microsatellite regions of chloroplast genome. Considering the features of plant chloroplasts, the numbers of each unit of continuous DNA motifs is set to 1-6, and the minus DNA motifs of each unit is 1-10, 2-6, 3-5, 4-5, 5-5, 6-5. Forward, reverse, complement and palindromic repeats type were detected by online tool REPuter [26]. The Hamming distance was setting as 1 and the minimum repeat size was 30bp.

Chloroplast genome analysis

All the chloroplast genome sequences was aligned by MAFFT7.427 [27] on FFT-NS-2 module. Alignments of 7 selected genome sequences were visualized by mVISTA [28]. The DNA polymorphism (nucleotide diversity) was calculated by DnaSPv5 [29] based on alignment results.

The molecular evolutionary rates (ω) between orthologous genes were estimated by calculating the ratio of non-synonymous (dN)/synonymous substitution (dS) rate. The coding gene sequences of selected region were extracted by using the Artemis [30]. The gene sequences of each species were aligned by Clustal X [31] with default parameters, and the alignment results (dnd format) were converted to PML format by DAMBE [32] for next analysis. The dN/dS value was calculated by the codeml module (seqtype=1, model=0, Nsites=1,7,8) in PAML4.9i [33]. Significant differences were calculated by Likelihood-ratio test.

Phylogenetic analysis

The 16 chloroplast genome sequences of tribe Senecioneae (family Asteraceae ) were aligned by MAFFT and the results was used to analyze the phylogenetic relationships. RAxML8 [34] was used to build the Maximum likelihood tree with GTRGAMMAI module and 1000 bootstrap replicates. Mrbayes3.2.7a [35] was used to build the Bayesian inference tree. The parameter settings are as follows: nst=6, rates=invgamma, burnin=500, Ngen=20000, Samplefreq=10, Printfreq=100. Both the results of ML tree and BI tree were visualized by FigTree V1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/).

Divergence time estimation

The divergence time of 16 species was estimated by BEAST2 [36]. The oldest Artemisia fossil pollen has been recorded from the Eocene–Oligocene boundary [37-38]. The Asteraceae family plant Artemisia gmelinii and Chrysanthemum boreale were selected as outgroup and the node Artemisia–Chrysanthemum was constrained by using a lognormal distribution with an offset of 31 Ma and a mean and standard deviation of 0.5 [39]. The HKY nucleotide substitution model and priors tree Yule model was selected with strict clock. Each MCMC run had a chain length of 100,000,000 with sampling every 10,000 steps. Tracer [40] was used to read the ESS and Trace value of logged statistics to access the results. Then, the divergence time was accessed by Treeannotator program of BEAST2. The detailed settings are: Burnin percentage=50, Posterior probability limit=0.0, Target tree type=Maximum clade credibility tree, Node heights=Mean heights.

Funding

This research was funded by the National Natural Science Foundation of China (No. 31770366；No. 81773885；No. 81703224). The authors are also indebted to the supports from Jiangsu Scientific and Technological Innovations Platform (Jiangsu Provincial Service Center for Antidiabetic Drug Screening).

Availability of data and materials

All the data and materials are available from the corresponding authors upon request.

Authors’ contributions

Jiawei Li and Han Lv obtained the samples. Tianyu Han and Bingru Ren analyzed the data. Mimi Li , Jian Chen and Tianyu Han conceived and wrote the manuscript. All authors read and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests.

Consent for publication

Not applicable.

Ethics approval and consent to participate

Not applicable.

Author details

¹Co-Innovation Center for Sustainable Forestry in Southern China, forestry College, Nanjing Forestry University, Nanjing 210037, China

² Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China

1. Vanijajiva O. A revision of Gynura (Asteraceae: Senecioneae). Journal of Systematics & Evolution, 2011, 49(4):285-314.

2. Hassan Z, Yam MF, Ahmad M, et al. Antidiabetic Properties and Mechanism of Action of Gynura procumbens Water Extract in Streptozotocin-Induced Diabetic Rats. Molecules, 2010, 15(12):9008-9023.

3. Choi SI, Lee HA, Han JS. Gynura procumbens extract improves insulin sensitivity and suppresses hepatic gluconeogenesis in C57BL/KsJ-db/db mice. Nutrition Research and Practice, 2016, 10.

4. Deng YX , Chen YS , Zhang WR , et al. Polysaccharide from Gynura divaricata modulates the activities of intestinal disaccharidases in streptozotocin-induced diabetic rats. The British journal of nutrition, 2011, 106(9):1323-1329.

5. Xu BQ , Yang P , Zhang YQ . Hypoglycemic activities of lyophilized powder of Gynura divaricata by improving antioxidant potential and insulin signaling in type 2 diabetic mice. Food & Nutrition Research, 2015, 59(1):29652.

6. Tan C , Wang Q , Luo C , et al. Yeast α-Glucosidase Inhibitory Phenolic Compounds Isolated from Gynura medica Leaf. International Journal of Molecular Sciences, 2013, 14(2):2551-2558.

7. Rosidah, Yam MF , Sadikun A , et al. Toxicology evaluation of standardized methanol extract of Gynura procumbens. Journal of Ethnopharmacology, 2009, 123(2):0-249.

8. Zhang F , Zhou Y , Yang X , et al. Gynura Rhizoma containing pyrrolizidine alkaloids induces the hepatic sinusoidal obstruction syndrome in mice via upregulating fibrosis-related factors. Acta Pharmacologica Sinica, 2018.

9. Palmer, DJ . Comparative Organization of Chloroplast Genomes. Annual Review of Genetics, 1985, 19(1):325-354.

10. Palmer JD, Jansen RK, Michaels HJ, et al. Chloroplast DNA variation and plant phylogeny. Annals of the Missouri Botanical Garden, 1988, 75(4):1180-1206.

11. Raubeson LA, Jansen RK, Henry RJ. Chloroplast genomes of plants. 2005.

12. Erixon P, Oxelman B. Reticulate or tree-like chloroplast DNA evolution in Sileneae (Caryophyllaceae)?. Molecular Phylogenetics & Evolution, 2008, 48(1):313-325.

13. Marco PF, Martins AM and Ferreira ME. Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes. BMC Genomics, 2017, 18(1):516-.

14. Ng PK, Lin SM, Lim PE, et al. Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae. BMC Genomics, 2017, 18(1):40.

15. Liu L , Wang Y , He P , et al. Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data. BMC Genomics, 2018, 19(1):235.

16. Fang WB, Ying W, Jiao Y, et al. Comparative Chloroplast Genomics of Dipsacales Species: Insights Into Sequence Variation, Adaptive Evolution, and Phylogenetic Relationships. Frontiers in Plant Science, 2018, 9:689.

17. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987;19:11–5.

18. Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 2016,45(4):e18.

19. Wyman SK, Jansen RK, Boore JL. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 2004, 20(17):3252-3255.

20. Tillich M , Lehwark P , Pellizzer T , et al. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Research, 2017, 45(1):3.

21. Laslett, D. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research, 2004, 32(1):11-16.

22. Lowe T M , Chan P P . tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research, 2016,44: W54-57.

23. 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. Current Genetics, 2007, 52(5-6):267-274.

24. Richard GF, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev, 2008, 72(4): 686–727.

25. Gulcher J. Microsatellite markers for linkage and association studies. Cold Spring Harbor Protocols, 2012, 7(4):425-432.

26. Kurtz S, Choudhuri JV, Ohlebusch E, et al. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 2001, 29(22):4633-42.

27. Nakamura T, Yamada KD, Tomii K, et al. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics, 2018.

28. Frazer KA, Pachter L, Poliakov A, et al. VISTA: computational tools for comparative genomics. Nucleic Acids Res, 2004, 1:32 (Web Server issue):W273-9

29. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 2009, 25(11):1451-1452.

30. Carver T, Harris SR, Berriman M, et al. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics, 2012, 28(4):464-469.

31. Larkin MA , Blackshields G , Brown NP , et al. Clustal W and Clustal X version 2.0. Bioinformatics, 2007, 23(21):2947-2948.

32. Xia X, Kumar S. DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution. Molecular Biology and Evolution, 2018.

33. Yang ZH. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology & Evolution, 2007, 24(8):1586-1591.

34. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 2014, 30(9):1312-1313.

35. Ronquist F, Teslenko M, van der Mark P, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61(3):539-42.

36. Bouckaert R, Heled J, Denise K, et al. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Computational Biology, 2014, 10(4): e1003537.

37. Wang WM. On the origin and development of Artemisia (Asteraceae) in the geological past. Botanical Journal of the Linnean Society, 2004, 145(3):331-336.

38. Hobbs CR, Baldwin BG. Asian origin and upslope migration of Hawaiian Artemisia (Compositae—Anthemideae). Journal of Biogeography, 2013, 40(3):442-454.

39. Panero JL, Crozier BS. Macroevolutionary dynamics in the early diversification of Asteraceae. Molecular Phylogenetics and Evolution, 2016:S105579031600083X.

40. Rambaut A, Drummond AJ, Xie D, et al. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Systematic Biology, 2018, 67(5):??-??.

41. Wang RJ, Cheng CL, Chang CC, et al. Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evolutionary Biology, 2008, 8(1):36-0.

42. Burrows PA, Sazanov LA, Svab Z, et al. Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes. Embo Journal, 1998, 17(4):868-876.

43. Shikanai T. Cyclic Electron Transport Around Photosystem I: Genetic Approaches. Annual Review of Plant Biology, 2007, 58(1):199-217.

44. Pelser PB, Kennedy AH, Tepe EJ, et al. Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies. American Journal of Botany, 2010, 97(5):856-873.

45. Davies FG. The Genus Gynura (Compositae) in Malesia and Australia. Kew Bulletin, 1980, 35(4):711-734.

Table 1 Overview of chloroplast genome of 16 Senecioneae species.

Speices	Size(bp)	LSC(bp)	SSC(bp)	IR(bp)	GC%	Protein	rRNA	tRNA	Total genes
Gynura bicolor	150930	83258	18128	24772	37.2	91	8	35	134
Gynura divaricata	150723	82998	18163	24781	37.2	91	8	35	134
Gynura formosana	151104	83368	18164	24786	37.2	91	8	35	134
Gynura pseudochina	151023	83330	18131	24781	37.2	91	8	35	134
Dendrosenecio brassiciformis	150551	83426	17749	24688	37.5	89	8	37	134
Dendrosenecio cheranganiensis	150606	83458	17768	24690	37.5	89	8	37	134
Dendrosenecio johnstonii	150607	83471	17756	24690	37.4	89	8	37	134
Dendrosenecio kilimanjari	150593	83457	17756	24690	37.5	89	8	37	134
Dendrosenecio meruensis	150587	83450	17757	24690	37.5	89	8	37	134
Jacobaea vulgaris	150689	82816	18277	24798	37.3	87	8	37	132
Ligularia hodgsonii	151136	83254	18218	24832	37.5	94	8	36	138
Ligularia intermedia	151152	83259	18233	24830	37.5	94	8	36	138
Ligularia jaluensis	151148	83264	18226	24829	37.5	94	8	36	138
Ligularia mongolica	151118	83245	18215	24829	37.5	93	8	36	137
Ligularia veitchiana	151253	83331	18248	24837	37.5	94	8	36	138
Pericallis hybrida	151267	83246	18331	24845	37.3	95	8	36	139

Table 2 Molecular evolutionary rate of 7 ndh genes in 16 Senecioneae species.

Gene	ndhA	ndhB	ndhC	ndhD	ndhE	ndhF	ndhG	ndhH	ndhI	ndhJ	ndhK
dN/dS	0.05971	0.71728	0.16003	0.34997	0.0001	0.33121	0.39231	0.13607	0.0001	0.06077	0.3433

Download PDF

Journal Publication

published 29 Oct, 2019

Read the published version in BMC Genomics →

Editorial decision: Major revision
01 Jul, 2019
Review #3 received at journal
28 Jun, 2019
Review #1 received at journal
23 Jun, 2019
Review #2 received at journal
21 Jun, 2019
Reviewer #3 agreed at journal
19 Jun, 2019
Reviewer #1 agreed at journal
06 Jun, 2019
Reviewer #2 agreed at journal
06 Jun, 2019
Reviewers invited by journal
01 Jun, 2019
Submission checks completed at journal
30 May, 2019
Editor invited by journal
30 May, 2019
Editor assigned by journal
28 May, 2019
First submitted to journal
22 May, 2019

You are reading this older preprint version

Read the latest preprint version →

Comparative Chloroplast genomes of Gynura species:Sequence Variation, Genome Rearrangement and Divergence studies

Status:

Journal Publication

Version 1

Abstract

Figures

Background

Results and Discussion

Chloroplast genome features of 16 Senecioneae species

Microsatellites and Repeats type

Contraction and Expansion of Inverted Repeats

Sequence Variation and Adaptive selection

Phylogenetic Relationships

Divergence Time Estimation

Conclusion

Methods

Plant materials, Genome sequencing and assembly

Chloroplast genome annotation

Repeat structure analysis

Chloroplast genome analysis

Phylogenetic analysis

Divergence time estimation

Declarations

Funding

Availability of data and materials

Authors’ contributions

Competing interests

Consent for publication

Ethics approval and consent to participate

Author details

References

Tables

Supplementary Files

Status:

Journal Publication

Version 1