The first complete chloroplast genome sequences in Actinidiaceae: Genome structure and comparative analysis

PLoS ONE

Volumn 10, Issue 6, 2015, Pages

  Yao, Xiaohong ^a   Tang, Ping ^a   Li, Zuozhou ^a   Li, Dawei ^a   Liu, Yifei ^b   Huang, Hongwen ^a,b  

^a Wuhan Institute of Botany Chinese Academy of Sciences   (China)

^b SOUTH CHINA INSTITUTE OF BOTANY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA; CHLOROPLAST DNA; CHLOROPLAST PROTEIN;

ACTINIDIA CHINENSIS; ACTINIDIA DELICIOSA; ANGIOSPERM; ARTICLE; CHLOROPLAST; CLAP GENE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA SEQUENCE; GENE DUPLICATION; GENE LOCUS; GENE LOSS; GENE STRUCTURE; GENE TRANSFER; GENETIC ENGINEERING; GENETIC RECOMBINATION; INTRON; MITOCHONDRIAL GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHOTOSYNTHESIS; PHYLOGENY; PLANT GENE; PLANT GENOME; PROTEIN ASSEMBLY; PROTEIN LOCALIZATION; ACTINIDIA; ACTINIDIACEAE; CHEMISTRY; CHLOROPLAST GENE; CHLOROPLAST GENOME; CLASSIFICATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE REPEAT;

ACTINIDIA; ACTINIDIA CHINENSIS; ACTINIDIA DELICIOSA; ACTINIDIACEAE; ASTERIDS; ERICALES; MAGNOLIOPHYTA;

ACTINIDIA; ACTINIDIACEAE; CHLOROPLAST PROTEINS; DNA, CHLOROPLAST; GENES, CHLOROPLAST; GENOME, CHLOROPLAST; GENOME, PLANT; MOLECULAR SEQUENCE DATA; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

EID: 84934934823     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0129347     Document Type: Article

References (45)

1. Neuhaus HE, Emes MJ (2000) Nonphotosynthetic Metabolism in Plastids. Annu Rev Plant Physiol Plant Mol Biol 51: 111-140. PMID: 15012188
2. Palmer JD (1991) Plastid chromosomes: structure and evolution. In: Bogorad L, editor. Molecular Biology of Plastids. San Diego, CA: Academic Press. pp. 5-53.
3. Raubeson LA, Jansen RK (2005) Chloroplast genomes of plants. In: Henry RJ, editor. Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants. Cambridge, MA: CABI. pp. 45-68.
4. Lee HL, Jansen RK, Chumley TW, Kim KJ (2007) Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol 24: 1161-1180. PMID: 17329229
5. Shinozaki K, Ohme M, Tanaka M, Wakasugi T. Hayashida N, Matsubyashi T, et al. (1986) The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO J 5: 2043-2049. PMID: 16453699
6. Ku C, Hu JM, Kuo CH (2013) Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS ONE 8(4): e62548. doi: 10.1371/journal.pone.0062548 PMID: 23638113
7. Yang JB, Yang SX, Li HT, Yang J, Li DZ (2013) Comparative chloroplast genomes of Camellia Species. PLoS ONE 8: e73053. doi: 10.1371/journal.pone.0073053 PMID: 24009730
8. Fajardo D, Senalik D, Ames M, Zhu HY, Steffan SA, Harbut R, et al (2013) Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing. Tree Genet Genomes 9: 489-498.
9. Li JQ, Li XW, Soejarto DD (2007) Actinidiaceae. In: Wu ZY, Raven PH, Hong DY, editors. Flora of China. Beijing: Science Press and Missouri: Missouri Botanical Garden. pp. 334-360.
10. Huang H, Zhong C, Jiang Z, Li XW, Yao XH, Li DW, et al. (2013) Actinidia: taxonomy, resources, domestication, cultivation. Beijing, Science Press.
11. Huang H, Ferguson AR (2007) Genetic resources of kiwifruit: domestication and breeding. Hortic Rev 33: 1-121.
12. Belrose, Inc. (2013) World Kiwifruit Review. 2013, editor. Pullman, WA: Belrose, Inc.
13. Scortichini M, Marcelleti S, Ferrante P, Petriccione M, Firrao G (2012) Pseudomonas syringae pv. actinidiae: a re-emerging multi-faceted, pandemic pathogen. Molecular Plant Pathol 13: 631-640. doi: 10.1111/j.1364-3703.2012.00788.x PMID: 22353258
14. Daniell H, Khan MS, Allison L (2002) Milestones in chloroplast genetic engineering: an environmentally friendly era in biotechnology. Trends Plant Sci 7: 84-91. PMID: 11832280
15. Maliga P (2004) Plastid transformation in higher plants. Annu Rev Plant Biol 55: 289-313. PMID: 15377222
16. Li JQ, Huang H, Sang T (2002) Molecular phylogeny and infrageneric classification of Actinidia (Actinidiaceae). Syst Bot 27: 408-415.
17. Chat J, Jauregui B, Petit RJ, Nadot S (2004) Reticulate evolution in kiwifruit (Actinidia, Actinidiaceae) identified by comparing their maternal and paternal phylogenies. Am J Bot 91: 736-747. doi: 10.3732/ajb.91.5.736 PMID: 21653428
18. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829. doi: 10.1101/gr.074492.107 PMID: 18349386
19. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. PMID: 15180927
20. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32: 11-16. PMID: 14704338
21. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964. PMID: 9023104
22. Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52: 267-274. PMID: 17957369
23. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32: 273-279.
24. Kurtz S, Choudhuri JV, Ohlebusch E, Scheleiermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29: 4366-4642.
25. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor and Appl Genet 106: 411-422. PMID: 12589540
26. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 1-19. PMID: 14706121
27. Swofford DL (2003) PAUP∗. Phylogenetic analysis using parsimony (∗and other methods), Version 4b 10. Sunderland, Massachusetts: Sinauer.
28. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818. PMID: 9918953
29. Hudson KR, Gardner RC (1988) Organisation of the chloroplast genome of kiwifruit (Actinidia deliciosa). Curr Genet 13:339-342.
30. Tsudzuki J, Ito S, Tsudzuki T, Wakasugi, Sugiura M (1994) A new gene encoding tRNA (Pro) (GGG) is present in the chloroplast genome of black pine: a compilation of 32 tRNA genes from black pine chloroplasts. Curr Genet 26: 153-158. PMID: 8001170
31. Wakasugi T, Nagai T, Kapoor M, Sugita M, Ito M, Tsudzuki J, et al. (1997) Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Proc Natl Acad Sci USA 94: 5967-5972. PMID: 9159184
32. Khakhlova O, Bock R (2006) Elimination of deleterious mutations in plastid genomes by gene conversion. Plant J 46: 85-94. PMID: 16553897
33. Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski JA (1995) Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci USA 92: 7759-7763. PMID: 7644491
34. Stegemann S, Hartmann S, Ruf S, Bock R (2003) High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci USA. 100: 8828-8833. PMID: 12817081
35. Kleine T., Maier U.G. and Leister D. (2009) DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annu Rev Plant Biol 60: 115-138. doi: 10.1146/annurev.arplant.043008.092119 PMID: 19014347
36. Jansen RK, Saski C, Lee S-B, Hansen AK, Daniell H (2011) Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Mol Biol Evol 28: 835-847. doi: 10.1093/molbev/msq261 PMID: 20935065
37. Gantt JS, Baldauf SL, Calie PJ, Weeden NF, Palmer JD (1991) Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J 10: 3073-3078. PMID: 1915281
38. Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, et al. (2001) Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13: 645-658. PMID: 11251102
39. Cusack BP, Wolfe KH (2007) When gene marriages don't work: divorce by subfunctionalization. Trends Genet 23: 270-272. PMID: 17418444
40. Ueda M, Fujimoto M, Arimura SI, Murata J, Tsutsumi N, Kadowaki KI (2007) Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus. Gene 402: 51-56. PMID: 17728076
41. Magee AM, Aspinall S, Rice DW, Cusack BP, Sémon M, Perry AS, et al. (2010) Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res 20: 1700-1710. doi: 10.1101/gr.111955.110 PMID: 20978141
42. Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D (2011) The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol 76: 273-97. doi: 10.1007/s11103-011-9762-4 PMID: 21424877
43. Jansen RK, Cai Z, Raubeson LA, Daniell H, dePamphilis CW, Leebens-Mack J, et al. (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA 104: 19369-19374. PMID: 18048330
44. Haberle R, Fourcade HM, Boore J, Jansen R (2008) Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J Mol Evol 66: 350-361. doi: 10.1007/s00239-008-9086-4 PMID: 18330485
45. Bremer B, Bremer K, Heidari N, Erixon P, Olmstead RG, Anderberg AA, et al. (2002) Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels. Mol Phylogenet Evol 24: 274-301. PMID: 12144762