Complete chloroplast genome of the Wollemi pine (Wollemia nobilis): Structure and evolution

PLoS ONE

Volumn 10, Issue 6, 2015, Pages

  Yap, Jia Yee S ^a,b   Rohner, Thore ^c,d   Greenfield, Abigail ^a,b   Van Der Merwe, Marlien ^a   McPherson, Hannah ^a   Glenn, Wendy ^b   Kornfeld, Geoff ^b   Marendy, Elessa ^b   Pan, Annie Y H ^b,e   Wilton, Alan ^b   Wilkins, Marc R ^b   Rossetto, Maurizio ^a   Delaney, Sven K ^b,f  

^a ROYAL BOTANIC GARDENS AND DOMAIN TRUST   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c HANZE UNIVERSITY OF APPLIED SCIENCES   (Netherlands)

^d UNIVERSITY OF HAMBURG   (Germany)

^e UNIVERSITY OF SYDNEY   (Australia)

^f FLINDERS UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

ACCD GENE; AGATHIS; ARAUCARIACEAE; ARTICLE; CHLB GENE; CHLOROPLAST GENOME; CONIFER; CONTROLLED STUDY; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENE INSERTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; GYMNOSPERM; INTRON; NONHUMAN; PINE; PLANT EVOLUTION; PLANT GENE; PLANT GENOME; PODOCARPACEAE; PSEUDOGENE; RNA ANALYSIS; RPS16 GENE; SEQUENCE ANALYSIS; SHORT TANDEM REPEAT; SISTER GROUP; SPECIES DIFFERENCE; TANDEM REPEAT; TRNK GENE; WOLLEMIA NOBILIS; AUSTRALIA; DNA SEQUENCE; EVOLUTION; GENETIC VARIATION; GENETICS;

AGATHIS (CONIFER); ARAUCARIACEAE; CONIFEROPHYTA; PODOCARPACEAE; WOLLEMIA NOBILIS;

AUSTRALIA; BIOLOGICAL EVOLUTION; CONIFEROPHYTA; GENETIC VARIATION; GENOME, CHLOROPLAST; SEQUENCE ANALYSIS, DNA;

EID: 84936767163     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0128126     Document Type: Article

References (65)

1. Jones W, Hill K, Allen J. Wollemia nobilis, a new living Australian genus and species in the Araucariaceae. Telopea (Syd). 1995; 6: 173-176.
2. Chambers TC, Drinnan AN, McLoughlin S. Some morphological features of Wollemi pine (Wollemia nobilis: Araucariaceae) and their comparison to Cretaceous plant fossils. Int J Plant Sci. 1998: 160-171.
3. Macphail M, Hill K, Partridge A, Truswell E, Foster C. Wollemi Pine-old pollen records for a newly discovered genus of gymnosperm. Geology Today. 1995; 11: 48-50.
4. Gilmore S, Hill K. Relationships of the Wollemi Pine (Wollemia nobilis) and a molecular phylogeny of the Araucariaceae. Telopea (Syd). 1997; 7: 275-291.
5. Stefanoviac S, Jager M, Deutsch J, Broutin J, Masselot M. Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences. Am J Bot. 1998; 85: 688-688. PMID: 21684951
6. Conran JG, Wood GM, Martin PG, Dowd JM, Quinn CJ, Gadek AP, et al. Generic relationships within and between the gymnosperm families Podocarpaceae and Phyllocladaceae based on an analysis of the chloroplast gene rbcL. Aust J Bot. 2000; 48: 715-724.
7. Quinn C, Price R, Gadek P. Familial concepts and relationships in the conifer based on rbcL and matK sequence comparisons. Kew Bulletin. 2002: 513-531.
8. Kershaw P, Wagstaff W. The Southern conifer family Araucariaceae: history, status and value for palaeoenvironmental reconstruction. Annu Rev Ecol Syst. 2001; 32: 397-414.
9. Enright N, Hill R. Ecology of the Southern Conifers. Melbourne: Melbourne University Press; 1995.
10. Burrows G, Offord C, Meagher P, Ashton K. Axillary meristems and the development of epicormic buds in Wollemi pine (Wollemia nobilis). Ann Bot. 2003; 92: 835-844. PMID: 14612379
11. Burrows G, Meagher P, Heady R. An anatomical assessment of branch abscission and branch-base hydraulic architecture in the endangered Wollemia nobilis. Ann Bot. 2007; 99: 609-623. PMID: 17272303
12. Zonneveld B. Genome sizes of all 19 Araucaria species are correlated with their geographical distribution. Plant Syst Evol. 2012; 298: 1249-1255.
13. Kranitz ML, Biffin E, Clark A, Hollingsworth ML, Ruhsam M, Gardner MF, et al. Evolutionary diversification of New Caledonian Araucaria. PloS One. 2014; 9: e110308. doi: 10.1371/journal.pone.0110308 PMID: 25340350
14. Biffin E, Hill RS, Lowe AJ. Did kauri (Agathis: Araucariaceae) really survive the Oligocene drowning of New Zealand? Systematic Biology. 2010; 59: 594-602. doi: 10.1093/sysbio/syq030 PMID: 20530131
15. Hill RS, Lewis T, Carpenter RJ, Whang SS. Agathis (Araucariaceae) macrofossils from Cainozoic sediments in south-eastern Australia. Aust J Bot. 2008; 21: 162-177.
16. Knapp M, Mudaliar R, Havell D, Wagstaff SJ, Lockhart PJ. The drowning of New Zealand and the problem of Agathis. Syst Biol. 2007; 56: 862-870. PMID: 17957581
17. Lee DE, Bannister JM, Lindqvist JK. Late Oligocene-early Miocene leaf macrofossils confirm a long history of Agathis in New Zealand. New Zealand J Bot. 2007; 45: 565-578.
18. Timmis JN, Ayliffe MA, Huang CY, Martin W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet. 2004; 5: 123-135. PMID: 14735123
19. Pyke KA. Plastid division and development. Plant Cell. 1999; 11: 549-556. PMID: 10213777
20. Reboud X, Zeyl C. Organelle inheritance in plants. Heredity. 1994; 72: 132-140.
21. Mogensen HL. The hows and whys of cytoplasmic inheritance in seed plants. Am J Bot. 1996; 83: 383-404.
22. Jansen RK, Ruhlman TA. Plastid genomes of seed plants. Genomics of chloroplasts and mitochondria: Springer.2012 pp. 103-126.
23. do Nascimento Vieira L, Faoro H, Rogalski M, de Freitas Fraga HP, Cardoso RLA, de Souza EM, et al. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection. PLoS One. 2014; 9: e90618. doi: 10.1371/journal.pone.0090618 PMID: 24594889
24. Wu C-S, Wang Y-N, Hsu C-Y, Lin C-P, Chaw S-M. Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny. Genome Biol Evol. 2011; 3: 1284-1295. doi: 10.1093/gbe/evr095 PMID: 21933779
25. Wu CS, Chaw SM. Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers. Plant Biotechnol J. 2014; 12: 344-353. doi: 10.1111/pbi.12141 PMID: 24283260
26. Hirao T, Watanabe A, Kurita M, Kondo T, Takata K. Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC Plant Biol. 2008; 8: 70. doi: 10.1186/1471-2229-8-70 PMID: 18570682
27. Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S. Plant DNA barcoding: from gene to genome. Biol Rev. 2015; 90: 157-166. doi: 10.1111/brv.12104 PMID: 24666563
28. Peakall R, Ebert D, Scott LJ, Meagher PF, Offord CA. Comparative genetic study confirms exceptionally low genetic variation in the ancient and endangered relictual conifer, Wollemia nobilis (Araucariaceae). Mol Ecol. 2003; 12: 2331-2343. PMID: 12919472
29. McPherson H, van der Merwe M, Delaney SK, Edwards MA, Henry RJ, McIntosh E, et al. Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. BMC Ecol. 2013; 13: 8. doi: 10.1186/1472-6785-13-8 PMID: 23497206
30. Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue. Focus. 1990; 12: 13-15.
31. Blanca JM, Pascual L, Ziarsolo P, Nuez F, Cañizares J. ngs-backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics. 2011; 12: 285. doi: 10.1186/1471-2164-12-285 PMID: 21635747
32. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18: 821-829. doi: 10.1101/gr.074492.107 PMID: 18349386
33. Chevreux B. MIRA: an automated genome and EST assembler. PhD Thesis, Ruprecht-Karls University. 2005. Available: http://www.chevreux.org/uploads/media/chevreux-thesis-MIRA.pdf
34. Sommer DD, Delcher AL, Salzberg SL, Pop M. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics. 2007; 8: 64. PMID: 17324286
35. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinform. 2009; 25: 1754-1760.
36. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010; 5: e11147. doi: 10.1371/journal.pone.0011147 PMID: 20593022
37. Wyman SK, Jansen RK, Boore JL Automatic annotation of organellar genomes with DOGMA. Bioinform. 2004; 20: 3252-3255.
38. Katoh K, Kuma K-i, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005; 33: 511-518. PMID: 15661851
39. Schattner P, A.F. B, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005; 33: W686-689. PMID: 15980563
40. 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. Curr Genet. 2007; 52: 267-274. PMID: 17957369
41. Mayer C, Leese F, Tollrian R. Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach. BMC Genomics. 2010; 11: 277. doi: 10.1186/1471-2164-11-277 PMID: 20433735
42. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27: 573. PMID: 9862982
43. 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. PMID: 11713313
44. Wu C-S, Wang Y-N, Liu S-M, Chaw S-M. Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. Mol Biol Evol. 2007; 24: 1366-1379. PMID: 17383970
45. Morton BR. The role of context-dependent mutations in generating compositional and codon usage bias in grass chloroplast DNA. J Mol Evol. 2003; 56: 616-629. PMID: 12698298
46. Rouwendal GJ, Mendes O, Wolbert EJ, De Boer AD. Enhanced expression in tobacco of the gene encoding green fluorescent protein by modification of its codon usage. Plant Mol Biol. 1997; 33: 989-999. PMID: 9154981
47. Steane DA. Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae). DNA Res. 2005; 12: 215-220. PMID: 16303753
48. Fleischmann TT, Scharff LB, Alkatib S, Hasdorf S, Schöttler MA, Bock R. Nonessential plastid-encoded ribosomal proteins in tobacco: a developmental role for plastid translation and implications for reductive genome evolution. Plant Cell. 2011; 23: 3137-3155. doi: 10.1105/tpc.111.088906 PMID: 21934145
49. Yi X, Gao L, Wang B, Su Y-J, Wang T. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of Cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms. Genome Biol Evol. 2013; 5: 688-698. doi: 10.1093/gbe/evt042 PMID: 23538991
50. Doyle JJ, Doyle JL, Palmer JD. Multiple independent losses of two genes and one intron from legume chloroplast genomes. Syst Bot. 1995: 272-294.
51. Chaw S-M, Walters TW, Chang C-C, Hu S-H, Chen S-H. A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region. Mol Phylogenet Evol. 2005; 37: 214-234. PMID: 16182153
52. Hausner G, Olson R, Simon D, Johnson I, Sanders ER, Karol KG, et al. Origin and evolution of the chloroplast trnK (matK) intron: a model for evolution of group II intron RNA structures. Mol Biol Evol. 2006; 23: 380-391. PMID: 16267141
53. Kress WJ, Erickson DL. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One. 2007; 2: e508. PMID: 17551588
54. Shaw J, Lickey EB, Schilling EE, Small RL. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot. 2007; 94: 275-288. doi: 10.3732/ajb.94.3.275 PMID: 21636401
55. Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, et al. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot. 2005; 92: 142-166. doi: 10.3732/ajb.92.1.142 PMID: 21652394
56. Sugiura C, Sugita M. Plastid transformation reveals that moss tRNAArg-CCG is not essential for plastid function. Plant J. 2004; 40: 314-321. PMID: 15447656
57. Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci. 1994; 91: 9794-9798. PMID: 7937893
58. Escapa IH, Catalano SA. Phylogenetic analysis of Araucariaceae: Integrating molecules, morphology, and fossils. Int J Plant Sci. 2013; 174: 1153-1170.
59. Stöckler K, Daniel IL, Lockhart PJ. New Zealand kauri (Agathis australis (D. Don) Lindl., Araucariaceae) survives Oligocene drowning. Syst Biol. 2002: 827-832.
60. Do HDK, Kim JS, Kim J-H. A trnI-CAU Triplication Event in the Complete Chloroplast Genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales). Genome Biol Evol. 2014; 6: 1699-1706. doi: 10.1093/gbe/evu138 PMID: 24951560
61. Cosner ME, Jansen RK, Palmer JD, Downie SR. The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Curr Genet. 1997; 31: 419-429. PMID: 9162114
62. Kikuchi S, Bédard J, Hirano M, Hirabayashi Y, Oishi M, Imai M, et al. Uncovering the protein translocon at the chloroplast inner envelope membrane. Science. 2013; 339: 571-574. doi: 10.1126/science.1229262 PMID: 23372012
63. Echt CS, DeVerno L, Anzidei M, Vendramin G. Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait. Mol Ecol. 1998; 7: 307-316.
64. Leclercq S, Rivals E, Jarne P. Detecting microsatellites within genomes: significant variation among algorithms. BMC Bioinformatics. 2007; 8: 125. PMID: 17442102
65. Merkel A, Gemmell N. Detecting microsatellites in genome data: variance in definitions and bioinformatic approaches cause systematic bias. Evol Bioinform 2008; 4: 1-6.