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Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology.

Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T.

Nucleic Acids Res. 2008 Nov;36(19):e122. doi: 10.1093/nar/gkn502. Epub 2008 Aug 27.


Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses.

Ma PF, Guo ZH, Li DZ.

PLoS One. 2012;7(1):e30297. doi: 10.1371/journal.pone.0030297. Epub 2012 Jan 17.


High-accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy.

Li Q, Li Y, Song J, Xu H, Xu J, Zhu Y, Li X, Gao H, Dong L, Qian J, Sun C, Chen S.

New Phytol. 2014 Dec;204(4):1041-9. doi: 10.1111/nph.12966. Epub 2014 Aug 8.


Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome.

Jo YD, Park J, Kim J, Song W, Hur CG, Lee YH, Kang BC.

Plant Cell Rep. 2011 Feb;30(2):217-29. doi: 10.1007/s00299-010-0929-2. Epub 2010 Oct 27.


De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Pöggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kück U, Freitag M.

PLoS Genet. 2010 Apr 8;6(4):e1000891. doi: 10.1371/journal.pgen.1000891.


High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.

Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J, Anthouard V, Scarpelli C, Artiguenave F, Wincker P.

BMC Genomics. 2008 Dec 16;9:603. doi: 10.1186/1471-2164-9-603.


Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships.

Huang H, Shi C, Liu Y, Mao SY, Gao LZ.

BMC Evol Biol. 2014 Jul 7;14:151. doi: 10.1186/1471-2148-14-151.


Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae.

Steele PR, Hertweck KL, Mayfield D, McKain MR, Leebens-Mack J, Pires JC.

Am J Bot. 2012 Feb;99(2):330-48. doi: 10.3732/ajb.1100491. Epub 2012 Jan 30.


An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome.

Ferrarini M, Moretto M, Ward JA, Šurbanovski N, Stevanović V, Giongo L, Viola R, Cavalieri D, Velasco R, Cestaro A, Sargent DJ.

BMC Genomics. 2013 Oct 1;14:670. doi: 10.1186/1471-2164-14-670.


Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions.

Su Y, Lin L, Tian G, Chen C, Liu T, Xu X, Qi X, Zhang X, Yang H.

Sci China C Life Sci. 2009 May;52(5):483-91. doi: 10.1007/s11427-009-0066-8. Epub 2009 May 27.


An improved chloroplast DNA extraction procedure for whole plastid genome sequencing.

Shi C, Hu N, Huang H, Gao J, Zhao YJ, Gao LZ.

PLoS One. 2012;7(2):e31468. doi: 10.1371/journal.pone.0031468. Epub 2012 Feb 22.


Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics.

Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A.

Mol Biol Evol. 2009 Dec;26(12):2731-44. doi: 10.1093/molbev/msp188. Epub 2009 Aug 25.


ASAP: amplification, sequencing & annotation of plastomes.

Dhingra A, Folta KM.

BMC Genomics. 2005 Dec 7;6:176.


Comparative chloroplast genomes of camellia species.

Yang JB, Yang SX, Li HT, Yang J, Li DZ.

PLoS One. 2013 Aug 23;8(8):e73053. doi: 10.1371/journal.pone.0073053. eCollection 2013.


Rapid and accurate pyrosequencing of angiosperm plastid genomes.

Moore MJ, Dhingra A, Soltis PS, Shaw R, Farmerie WG, Folta KM, Soltis DE.

BMC Plant Biol. 2006 Aug 25;6:17.


Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines.

Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski JA.

Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7759-63.


Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey.

Kerstens HH, Crooijmans RP, Veenendaal A, Dibbits BW, Chin-A-Woeng TF, den Dunnen JT, Groenen MA.

BMC Genomics. 2009 Oct 16;10:479. doi: 10.1186/1471-2164-10-479.

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