Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'

Autoři: Xiao-Fei Liu aff001;  Gen-Fa Zhu aff002;  Dong-Mei Li aff002;  Xiao-Jing Wang aff001
Působiště autorů: Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou, Guangdong, China aff001;  Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China aff002
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0224038


Spathiphyllum is a very important tropical plant used as a small, potted, ornamental plant in South China, with an annual output value of hundreds of millions of yuan. In this study, we sequenced and analyzed the complete nucleotide sequence of the Spathiphyllum 'Parrish' chloroplast genome. The whole chloroplast genome is 168,493 bp in length, and includes a pair of inverted repeat (IR) regions (IRa and IRb, each 31,600 bp), separated by a small single-copy (SSC, 15,799 bp) region and a large single-copy (LSC, 89,494 bp) region. Our annotation revealed that the S. 'Parrish' chloroplast genome contained 132 genes, including 87 protein coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. In the repeat structure analysis, we detected 281 simple sequence repeats (SSRs) which included mononucleotides (223), dinucleotides (28), trinucleotides (12), tetranucleotides (11), pentanucleotides (6), and hexanucleotides (1), in the S. 'Parrish' chloroplast genome. In addition, we identified 50 long repeats, comprising 18 forward repeats, 13 reverse repeats, 17 palindromic repeats, and 2 complementary repeats. Single nucleotide polymorphism (SNP) and insertion/deletion (indel) analyses of the chloroplast genome of the S. 'Parrish' relative S. cannifolium revealed 962 SNPs in S. 'Parrish'. There were 158 indels (90 insertions and 68 deletions) in the S. 'Parrish' chloroplast genome relative to the S. cannifolium chloroplast genome. Phylogenetic analysis of five species found S. 'Parrish' to be more closely related to S. kochii than to S. cannifolium. This study identified the characteristics of the S. 'Parrish' chloroplast genome, which will facilitate species identification and phylogenetic analysis within the genus Spathiphyllum.

Klíčová slova:

DNA sequence analysis – Chloroplast genome – Introns – Molecular genetics – Phylogenetic analysis – Sequence alignment – Sequence assembly tools – Transfer RNA


1. Mayo SJ, Bogner J, Boyce PC. The genera of Araceae[M]. Royal Botanic Gardens Kew, UK. 1997; 110.

2. Manos PS, Cannon CH, Oh SH. Phylogenetic relationships and taxonomic status of the paleoendemic Fagaceae of western North America: Recognition of a new genus, Notholithocarpus. Madroño. 2008; 55, 181–190.

3. Oh SH, Manos PS. Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear crabs claw sequences. Taxon. 2008; 57, 434–451.

4. Li X, Li Y, Zang M, Li M, Fang Y. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima. Int. J. Mol. Sci. 2018; 19, 2443.

5. Ravi V, Khurana JP, Tyagi AK, Khurana P. An update on chloroplast genomes. Plant Syst Evol. 2008; 271:101–122.

6. Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, et al. Methods for obtaining and analyzing chloroplast genome sequences. Methods Enzymol. 2005; 395: 348–384. doi: 10.1016/S0076-6879(05)95020-9 15865976

7. Wu C, Lai Y, Lin C, Wang Y, Chaw S. Evolution of reduced and compact chloroplastgenomes (chloroplastDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol. 2009; 52(1):115–124 doi: 10.1016/j.ympev.2008.12.026 19166950

8. Kong W, Yang J. The complete chloroplast genome sequence of Morus mongolica and a comparative analysis within the Fabidae clade. Curr Genet. 2016; 62, 165–172. doi: 10.1007/s00294-015-0507-9 26205390

9. Daniell H, Lin CS, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 2016; 17, 134 doi: 10.1186/s13059-016-1004-2 27339192

10. Cazzonelli CI. Carotenoids in nature: Insights from plants and beyond. Funct. Plant Biol. 2011, 38, 833–847.

11. Bobik K, Burch-Smith TM. Chloroplast signaling within, between and beyond cells. Front. Plant Sci. 2015, 6, 781. doi: 10.3389/fpls.2015.00781 26500659

12. Baczkiewicz A, Szczecinska M, Sawicki J, Stebel A, Buczkowska K. DNA barcoding, ecology and geography of the cryptic species of Aneura pinguis and their relationships with Aneura maxima and Aneura mirabilis (Metzgeriales, Marchantiophyta). PLoS ONE 2017, 12, e0188837. doi: 10.1371/journal.pone.0188837 29206876

13. Kang Y, Deng Z, Zang R, Long W. DNA barcoding analysis and phylogenetic relationships of tree species in tropical cloud forests. Sci. Rep. 2017, 7, 12564. doi: 10.1038/s41598-017-13057-0 28970548

14. Song Y, Chen Y, Lv J, Xu J, Zhu S, Li M, Chen N. Development of Chloroplast Genomic Resources for Oryza Species Discrimination. Front. Plant Sci. 2017, 8, 1854. doi: 10.3389/fpls.2017.01854 29118779

15. Liu X, Zhou B, Yang H, Li Y, Yang Q, Lu Y, Gao Y. Sequencing and Analysis of Chrysanthemum carinatum Schousb and Kalimeris indica. The Complete Chloroplast Genomes Reveal Two Inversions and rbcL as Barcoding of the Vegetable. Molecules. 2018, 23, 1358.

16. Hui L, Xie H, Jiang Z, Li C, Zhang G. Photosynthetic response of potted Quercus acutissima Carruth seedlings under different soil moisture conditions. Sci. Soil Water Conserv. 2013; 11, 93–97.

17. Shen X, Wu M, Liao B, Liu Z, Bai R, Xiao S, et al. Complete chloroplast genome sequence and phylogenetic analysis of the medicinal plant Artemisia annua. Molecules. 2017; 22, 1330.

18. Guo S, Guo L, Zhao W, Xu J, Li Y, Zhang X, et al. Complete chloroplast genome sequence and phylogenetic analysis of Paeonia ostii. Molecules. 2018; 23, 246.

19. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986; 5:2043–9. 16453699

20. Han L, Wang B, Wang ZZ. The complete chloroplast genome sequence of Spathiphyllum kochii. Mitochondrial DNA A DNA Mapp Seq Anal. 2016, 27(4):2973–4. doi: 10.3109/19401736.2015.1060466 26134343

21. Asaf S, Khan AL, Khan MA, Waqas M, Kang SM, Yun BW, et al. Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis. Sci. Rep. 2017; 7, 7556. doi: 10.1038/s41598-017-07891-5 28790364

22. Mohammad-Panah N, Shabanian N, Khadivi A, Rahmani M.-S, Emami A. Genetic structure of gall oak (Quercus infectoria) characterized by nuclear and chloroplast SSR markers. Tree Genet. Genomes. 2017; 13, 70–82.

23. Park SH, Sang IP, Gil J, Hwangbo K, Um Y, Kim HB, et al. Development of Chloroplast SSR Markers to Distinguish Codonopsis Species. Korean Soc. Hortic. Sci. 2017; 5, 207–208.

24. Zeng J, Chen X, Wu XF, Jiao FC, Xiao BG, Li YP, et al. Genetic diversity analysis of genus Nicotiana based on SSR markers in chloroplast genome and mitochondria genome. Acta Tab. Sin. 2016; 22, 89–97.

25. Chen J, Henny RJ, Devanand PS, Chao CCT. Genetic Relationships of Spathiphyllum Cultivars Analyzed by AFLP Markers. HortScience: a publication of the American Society for Horticultural Science 41(4) July 2006 with152.

26. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012, 1, 18–24. doi: 10.1186/2047-217X-1-18 23587118

27. Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory. BMC Bioinform. 2012, 13, 238.

28. Wyman SK, Jansen RK, Boore JL. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 2004, 20, 3252–3255. doi: 10.1093/bioinformatics/bth352 15180927

29. 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. doi: 10.1007/s00294-007-0161-y 17957369

30. MISA-MIcroSAtellite identification tool. (accessed on 20 September 2017)

31. Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, et al. MUMmer4: A fast and versatile genome alignment system. PLoS Comput. Biol. 2018,14, e1005944. doi: 10.1371/journal.pcbi.1005944 29373581

32. Bhagwat M, Young L, Robison RR. Using BLAT to find sequence similarity in closely related genomes. Curr. Protoc. Bioinform. 2012, 010, Unit10.8.

33. Liu XF, Zhu GF, Li DM, Wang XJ. The complete chloroplast genome sequence of Spathiphyllumcannifolium, Mitochondrial DNA Part B, 2019, 4:1,

34. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: Computational tools for comparative genomics. Nucleic Acids Res. 2004, 32, 273–279.

35. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 2004, 32(5): 1792–1797. doi: 10.1093/nar/gkh340 15034147

36. Guindon S, Dufayard JF, Lefort V. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology, 2010, 59(3): 307–321. doi: 10.1093/sysbio/syq010 20525638

37. He Y, Xiao H, Deng C, Xiong L, Yang J, Peng C. The complete chloroplast genome sequences of the medicinal plant Pogostemon cablin. Int. J. Mol. Sci. 2016; 17, 820.

38. Boudreau E, Takahashi Y, Lemieux C, Turmel M, Rochaix JD. The chloroplast ycf3 and ycf4 open reading frames of Chlamydomonas reinhardtii are required for the accumulation of the photosystem I complex. EMBO J. 1997; 16, 6095–6104. doi: 10.1093/emboj/16.20.6095 9321389

39. Naver H, Boudreau E, Rochaix JD. Functional studies of Ycf3: Its role in assembly of photosystem I and interactions with some of its subunits. Plant Cell. 2001; 13, 2731–2745. doi: 10.1105/tpc.010253 11752384

40. Guisinger MM, Chumley TW, Kuehl JV, Boore JL, Jansen RK. Implications of the plastid genome sequence of Typha (Typhaceae, Poales) for understanding genome evolution in Poaceae. J. Mol. Evol. 2010; 70, 149–166. doi: 10.1007/s00239-009-9317-3 20091301

41. Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebensmack J, 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. doi: 10.1073/pnas.0709121104 18048330

42. Ueda M, Fujimoto M, Arimura S, Murata J, Tsutsumi N, Kadowaki K. Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus. Gene. 2007; 402, 51–56. doi: 10.1016/j.gene.2007.07.019 17728076

43. Yamane K, Yano K, Kawahara T. Pattern and rate of indels evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice. DNA Res. 2006; 13(5):197–204. doi: 10.1093/dnares/dsl012 17110395

44. Carbonell-Caballero J, Alonso R, Ibanez V, Terol J, Talon M, Dopazo J. A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus citrus. MBE. 2015; doi: 10.1093/molbev/msv082 25873589

45. Shahid Masood M, Nishikawa T, Fukuoka S, Njenga PK, Tsudzuki T, Kadowaki K. The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: First genome wide comparative sequence analysis of wild and cultivated rice. Gene 2004, 340, 133–139. doi: 10.1016/j.gene.2004.06.008 15556301

46. Li DM, Zhao CY, Liu XF. Complete chloroplast genome sequences of Kaempferia galanga and Kaempferia elegans: molecular structures and comparative analysis. Molecules, 2019, 24,474.

47. Xu J, Chu Y, Liao B, Xiao S, Yin Q, Bai R, et al. Panax ginseng genome examination for ginsenoside biosynthesis. Gigascience 2017; 6, 1–15.

48. Chen S, Xu J, Liu C, Zhu Y, Nelson DR, Zhou S, et al. Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nat. Commun. 2012; 3, 913. doi: 10.1038/ncomms1923 22735441

49. Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boorem JL, et al. Comparative chloroplast genomics: Analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genom. 2007; 8, 174–201.

50. Wang RJ, Cheng CL, Chang CC, Wu CL, Su TM, Chaw SM. Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol. Biol. 2008; 8, 36–50. doi: 10.1186/1471-2148-8-36 18237435

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2019 Číslo 10