Background Podocarpus lambertii (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. Methodology/Principal Findings The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA (trnN-GUU), which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi) and Araucariaceae (Agathis dammara). Structurally, P. lambertii shows 4 inversions of a large DNA fragment ~20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. Conclusion The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus.
References
[1]
Murray BG (2013) Karyotype variation and evolution in gymnosperms. In Leitch IJ, Greilhuber J, Dolezel J, Wendel JF, editors. Plant genome diversity 2: physical structure, behaviour and evolution of plant genomes. Springer231243.
[2]
Kelch DG (1998) Phylogeny of Podocarpaceae: comparison of evidence from morphology and 18S rDNA. Am J Bot 85: 986–996. doi: 10.2307/2446365
[3]
Farjon A (1998) World checklist and bibliography of conifers. Kew The Royal Botanical Gardens1316
[4]
Biffin E, Conran J, Lowe A (2011) Podocarp Evolution: A Molecular Phylogenetic Perspective. In: Turner BL, Cernusak LA, editors. Ecology of the Podocarpaceae in Tropical Forests. Washington: Smithsonian Institution Scholarly Press. pp 1–20.
[5]
Page CN (1990) Coniferophytina. In: Kramer KU, Green PS, editors. The families and genera of vascular plants, Pteridophytous and Gymnosperms: Springer. pp 332–346.
[6]
Ledru M, Salatino MLF, Ceccantini G, Salatino A, Pinheiro F, et al. (2007) Regional assessment of the impact of climatic change on the distribution of a tropical conifer in the lowlands of South America. Diversity Distrib 13: 761–771. doi: 10.1111/j.1472-4642.2007.00389.x
[7]
de Laubenfels DJD (1985) A taxonomic revision of the genus Podocarpus. Blumea 30: 251–278.
[8]
Myers N, Mittermeier RA, Mittermeier CG, Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853–858. doi: 10.1038/35002501
[9]
Longhi SJ, Brena DA, Ribeiro SB, Gracioli CR, Longhi RV, et al. (2010) Fatores ecológicos deteminantes na ocorrência de Araucaria angustifolia e Podocarpus lambertii, na floresta Ombrófila mista da FLONA de S？o Francisco de Paula, RS, Brasil. Cienc Rural 40: 57–63. doi: 10.1590/s0103-84782009005000220
[10]
Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7: 84. doi: 10.1186/1741-7007-7-84
[11]
Yi X, Gao L, Wang B, Su Y, Wang T (2013) 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 5: 688–698. doi: 10.1093/gbe/evt042
[12]
Hirao T, Watanabe A, Kurita M, Kondo T, Takata K (2008) Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC Plant Biol 8: 70. doi: 10.1186/1471-2229-8-70
[13]
Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, et al. (1994) Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA 91: 9794–9798. doi: 10.1073/pnas.91.21.9794
[14]
Cronn R, Liston A, Parks M, Gernandt DS, Shen R, et al. (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36(19): e122. doi: 10.1093/nar/gkn502
[15]
Lin C, Huang J, Wu C, Hsu C, Chaw S (2010) Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies. Genome Biol Evol 2: 504–517. doi: 10.1093/gbe/evq036
[16]
Wu CS, Chaw SM (2013) Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers. Plant Biotechnol J doi: 10.1111/pbi.12141
[17]
Moore MJ, Bell CD, Soltis PS, Soltis DE (2007) Using plastid genomic-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci USA 104: 19363–19368. doi: 10.1073/pnas.0708072104
[18]
Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE (2010) Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci USA 107: 4623–4628. doi: 10.1073/pnas.0907801107
[19]
Jansen RK, Cai Z, Raubeson LA, Daniell H, dePamphilis CW, 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. doi: 10.1073/pnas.0709121104
[20]
Wu CS, Wang YN, Hsu CY, Lin CP, Chaw SM (2011) 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 3: 1284–1295. doi: 10.1093/gbe/evr095
[21]
Palmer JD, Thompson WF (1982) Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell 29: 537–550. doi: 10.1016/0092-8674(82)90170-2
[22]
Strauss SH, Palmer JD, Howe GT, Doerksen AH (1988) Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proc Natl Acad Sci 85: 3898–3902. doi: 10.1073/pnas.85.11.3898
[23]
Wu CS, Lai YT, Lin CP, Wang YN, Chaw SM (2009) Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection towards a lower cost strategy. Mol Phylogent Evol 52: 115–124. doi: 10.1016/j.ympev.2008.12.026
[24]
Vieira LN, Faoro H, Fraga HPF, Rogalski M, Souza EM, et al. (2014) An improved protocol for intact chloroplasts and cpDNA isolation in conifers. PLoS ONE 9(1): e84792 doi:10.1371/journal.pone.0084792.
[25]
Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252–3255. doi: 10.1093/bioinformatics/bth352
[26]
Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33: W686–689. doi: 10.1093/nar/gki366
[27]
Lohse M, Drechsel O, Kahlau S, Bock R (2013) OrganellarGenomeDRAW: a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucl Acids Res doi: 10.1093/nar/gkt289
[28]
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12. doi: 10.1186/gb-2004-5-2-r12
[29]
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucl Acids Res 27: 573–580. doi: 10.1093/nar/27.2.573
[30]
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et al. (2001) REPuter: The manifold applications of repeat analysis on a genomic scale. Nucl Acids Res 29: 4633–4642. doi: 10.1093/nar/29.22.4633
[31]
Wu CS, Lin CP, Hsu CY, Wang RJ, Chaw SM (2011) Comparative chloroplast genomes of Pinaceae: insights into the mechanism of diversified genomic organizations. Genome Biol Evol 3: 309–319. doi: 10.1093/gbe/evr026
[32]
Wu CS, Wang YN, Liu SM, Chaw SM (2007) 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 24: 1366–1379. doi: 10.1093/molbev/msm059
[33]
Tsudzuki J, Nakashima K, Tsudzuki T, Hiratsuka J, Shibata M, et al. (1992) Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16. Mol Gen Genet 232: 206–214.
[34]
Guo X, Castillo-Ramírez S, González V, Bustos P, Fernández-Vázquez JL, et al. (2007) Rapid evolutionary change of common bean (Phaseolus vulgaris L.) plastome, and the genomic diversification of legume chloroplasts. BMC Genomics 8: 228. doi: 10.1186/1471-2164-8-228
[35]
Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, et al. (2009) The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res 17: 11–22. doi: 10.1093/dnares/dsp025
[36]
Fleischmann TT, Scharff LB, Alkatib S, Hasdorf S, Schottler MA, et al. (2011) Nonessential plastid-encoded ribosomal proteins in tobacco: a developmental role for plastid translation and implications for reductive genome evolution. Plant Cell 23: 3137–3155. doi: 10.1105/tpc.111.088906
[37]
Sugiura C, Sugita M (2004) Plastid transformation reveals that moss tRNA(Arg)-CCG is not essential for plastid function. The Plant J 40: 314–321. doi: 10.1111/j.1365-313x.2004.02202.x
[38]
Schmidt M, Schneider-Poetsch HA (2002) The evolution of gymnosperms redrawn by phytochrome genes: the Gnetatae appear at the base of the gymnosperms. J Mol Evol 54: 715–724. doi: 10.1007/s00239-001-0042-9
[39]
Alkatib S, Scharff LB, Rogalski M, Fleischmann TT, Matthes A, et al. (2012) The contributions of wobbling and superwobbling to the reading of the genetic code. PLoS Genet. 8(11): e1003076. doi: 10.1371/journal.pgen.1003076
[40]
Ambrogelly A, Palioura S, Soll D (2007) Natural expansion of the genetic code. Nat Chem Biol 3: 29–35. doi: 10.1038/nchembio847
[41]
Weixlbaumer A, Murphy FV, Dziergowska A, Malkiewicz A, Vendeix FA, et al. (2007) Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat Struct Mol Biol 14: 498–502. doi: 10.1038/nsmb1242
[42]
Rogalski M, Karcher D, Bock R (2008) Superwobbling facilitates translation with reduced tRNA sets. Nat Struct Mol Biol 15: 192–198. doi: 10.1038/nsmb.1370
[43]
Terakami S, Matsumura Y, Kurita K, Kanamori H, Katayose Y, et al. (2012) Complete sequence of the chloroplast genome from pear (Pyrus pyrifolia): genome structure and comparative analysis. Tree Genet Genomes 8: 841–854. doi: 10.1007/s11295-012-0469-8
[44]
Hill RS, Brodribb TJ (1999) Southern Conifers in Time and Space. Aust J Bot 47: 639–696. doi: 10.1071/bt98093
[45]
Farjon A (2008) A natural history of conifers. Portland: . Timber Press1304
[46]
Morley RJ (2011) Dispersal and paleoecology of tropical podocarps. In: Turner BL, Cernusak LA, editors. Ecology of the Podocarpaceae in tropical forests. Washington: Smithsonian Institute Scholarly Press. pp 21–42.
[47]
Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16: 142–147. doi: 10.1016/s0169-5347(00)02097-8
[48]
Provan J, Corbett G, McNicol JW, Powell W (1997) Chloroplast variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats. Genome 40: 104–110. doi: 10.1139/g97-014
[49]
Provan J, Russell JR, Booth A, Powell W (1999) Polymorphic chloroplast simple-sequence repeat primers for systematic and population studies in the genus Hordeum. Mol Ecol 8: 505–511. doi: 10.1046/j.1365-294x.1999.00545.x
[50]
Kikuchi S, Bédard J, Hirano M, Hirabayashi Y, Oishi M, et al. (2013) Uncovering the protein translocon at the chloroplast inner envelope membrane. Science 339: 571–574. doi: 10.1126/science.1229262
[51]
Huang Y-Y, Matzke AJM, Matzke M (2013) Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera). PLoS ONE 8(8): e74736. doi: 10.1371/journal.pone.0074736
[52]
Qian J, Song J, Gao H, Zhu Y, Xu J, et al. (2013) The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS ONE 8(2): e57607. doi: 10.1371/journal.pone.0057607
