Le Paslier MC, Lippi Y, Lorenzon L, Mandel JR,
Marage G, Marchand G, Marquand E, Bret-Mestries
E, Morien E, Nambeesan S, Nguyen T,
Pegot-Espagnet P, Pouilly N, Raftis F, Sallet E,
Schiex T, Thomas J, Vandecasteele C, Vares D,
Vear F, Vautrin S, Crespi M, Mangin B, Burke JM,
Salse J, Munos S, Vincourt P, Rieseberg LH,
Langlade NB (2017) The sunflower genome provides
insights into oil metabolism, flowering and Asterid
evolution. Nature 546(7656):148–152
Bi Y, Zhang MF, Xue J, Dong R, Du YP, Zhang XH
(2018) Chloroplast genomic resources for phylogeny
and DNA barcoding: a case study on Fritillaria. Sci
Rep 8(1):1184
Bog M, Schneider P, Hellwig F, Sachse S, Kochieva EZ,
Martyrosian E, Landolt E, Appenroth KJ (2013) Genetic
characterization and barcoding of taxa in the genus
Wolffia Horkel ex Schleid. (Lemnaceae) as revealed by
two plastidic markers and amplified fragment length
polymorphism (AFLP). Planta 237(1):1–13
Bookjans G, Stummann BM, Henningsen KW (1984)
Preparation of chloroplast DNA from pea plastids
isolated in a medium of high ionic strength. Anal
Biochem 141(1):244–247
Canto-Pastor A, Molla-Morales A, Ernst E, Dahl W,
Zhai J, Yan Y, Meyers BC, Shanklin J, Martienssen R
(2015) Efficient transformation and artificial miRNA
gene silencing in Lemna minor. Plant Biol (Stuttg) 17
(Suppl 1):59–65
Cheng JJ, Stomp AM (2009) Growing duckweed to
recover nutrients from wastewaters and for production
of fuel ethanol and animal feed. CLEAN Soil Air
Water 37(1):17–26
Cronn R, Liston A, Parks M, Gernandt DS, Shen R,
Mockler T (2008) Multiplex sequencing of plant
chloroplast
genomes
using
Solexa
sequencing-by-synthesis technology. Nucleic Acids
Res 36(19):e122
Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast
genomes: diversity, evolution, and applications in
genetic engineering. Genome Biol 17(1):134
Dean FB, Hosono S, Fang L, Wu X, Faruqi AF,
Bray-Ward P, Sun Z, Zong Q, Du Y, Du J,
Driscoll M, Song W, Kingsmore SF, Egholm M,
Lasken RS (2002) Comprehensive human genome
amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99(8):5261–5266
Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008)
Substantial biases in ultra-short read data sets from
high-throughput DNA sequencing. Nucleic Acids Res
36(16):e105
Douglas SE (1998) Plastid evolution: origins, diversity,
trends. Curr Opin Genet Dev 8(6):655–661
E Landolt (1994) Taxonomy and ecology of the section
Wolffia of the genus Wolffia (Lemnaceae). Ber Geobot
Inst ETH
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P,
Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S,
Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A,
Hardenbol P, Heiner C, Hester K, Holden D,
Kearns G, Kong X, Kuse R, Lacroix Y, Lin S,
Lundquist P, Ma C, Marks P, Maxham M, Murphy D,
Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G,
Sorenson J, Tomaney A, Travers K, Trulson M,
Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D,
Zhao P, Zhong F, Korlach J, Turner S (2009)
Real-time DNA sequencing from single polymerase
molecules. Science (80) 323(5910):133–138
Ferrarini M, Moretto M, Ward JA, Surbanovski N,
Stevanovic V, Giongo L, Viola R, Cavalieri D,
Velasco R, Cestaro A, Sargent DJ (2013) An evaluation of the PacBio RS platform for sequencing and de
novo assembly of a chloroplast genome. BMC Genom
14:670
Group CPW (2009) A DNA barcode for land plants. Proc
Natl Acad Sci USA 106(31):12794–12797
Heinze B (2007) A database of PCR primers for the
chloroplast genomes of higher plants. Plant Methods
3:4
Jansen RK, Raubeson LA, Boore JL, dePamphilis CW,
Chumley TW, Haberle RC, Wyman SK, Alverson AJ,
Peery R, Herman SJ, Fourcade HM, Kuehl JV,
McNeal JR, Leebens-Mack J, Cui L (2005) Methods
for obtaining and analyzing whole chloroplast genome
sequences. Methods Enzymol 395:348–384
Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B,
Borm TJA, Ohyanagi H, Mineta K, Michell CT,
Saber N, Kharbatia NM, Rupper RR, Sharp AR,
Dally N, Boughton BA, Woo YH, Gao G, Schijlen EGWM, Guo X, Momin AA, Negrão S, Al-Babili
S, Gehring C, Roessner U, Jung C, Murphy K,
Arold ST, Gojobori T, van der Linden CG, van
Loo EN, Jellen EN, Maughan PJ, Tester M (2017) The
genome of Chenopodium quinoa. Nature:1–20
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B,
Campbell MS, Stein JC, Wei X, Chin C-S, Guill K,
Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM,
Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR,
Ware D (2017) Improved maize reference genome
with single-molecule technologies. Nature 546:524–
527
Kolodner R, Tewari KK (1979) Inverted repeats in
chloroplast DNA from higher plants. Proc Natl Acad
Sci USA 76(1):41–45
Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM,
McVey SD, Radune D, Bergman NH, Phillippy AM
(2013) Reducing assembly complexity of microbial
genomes with single-molecule sequencing. Genome
Biol 14(9):R101
Ku C, Chung WC, Chen LL, Kuo CH (2013) The
complete plastid genome sequence of Madagascar
Periwinkle Catharanthus roseus (L.) G. Don: plastid
genome evolution, molecular marker identification,
and phylogenetic implications in Asterids. PLoS One
8(6):e68518
Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang TH,
Cervantes-Perez SA, Zheng C, Sankoff D, Tang H,
10 Duckweed Chloroplast Genome Sequencing and Annotation
113
Marage G, Marchand G, Marquand E, Bret-Mestries
E, Morien E, Nambeesan S, Nguyen T,
Pegot-Espagnet P, Pouilly N, Raftis F, Sallet E,
Schiex T, Thomas J, Vandecasteele C, Vares D,
Vear F, Vautrin S, Crespi M, Mangin B, Burke JM,
Salse J, Munos S, Vincourt P, Rieseberg LH,
Langlade NB (2017) The sunflower genome provides
insights into oil metabolism, flowering and Asterid
evolution. Nature 546(7656):148–152
Bi Y, Zhang MF, Xue J, Dong R, Du YP, Zhang XH
(2018) Chloroplast genomic resources for phylogeny
and DNA barcoding: a case study on Fritillaria. Sci
Rep 8(1):1184
Bog M, Schneider P, Hellwig F, Sachse S, Kochieva EZ,
Martyrosian E, Landolt E, Appenroth KJ (2013) Genetic
characterization and barcoding of taxa in the genus
Wolffia Horkel ex Schleid. (Lemnaceae) as revealed by
two plastidic markers and amplified fragment length
polymorphism (AFLP). Planta 237(1):1–13
Bookjans G, Stummann BM, Henningsen KW (1984)
Preparation of chloroplast DNA from pea plastids
isolated in a medium of high ionic strength. Anal
Biochem 141(1):244–247
Canto-Pastor A, Molla-Morales A, Ernst E, Dahl W,
Zhai J, Yan Y, Meyers BC, Shanklin J, Martienssen R
(2015) Efficient transformation and artificial miRNA
gene silencing in Lemna minor. Plant Biol (Stuttg) 17
(Suppl 1):59–65
Cheng JJ, Stomp AM (2009) Growing duckweed to
recover nutrients from wastewaters and for production
of fuel ethanol and animal feed. CLEAN Soil Air
Water 37(1):17–26
Cronn R, Liston A, Parks M, Gernandt DS, Shen R,
Mockler T (2008) Multiplex sequencing of plant
chloroplast
genomes
using
Solexa
sequencing-by-synthesis technology. Nucleic Acids
Res 36(19):e122
Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast
genomes: diversity, evolution, and applications in
genetic engineering. Genome Biol 17(1):134
Dean FB, Hosono S, Fang L, Wu X, Faruqi AF,
Bray-Ward P, Sun Z, Zong Q, Du Y, Du J,
Driscoll M, Song W, Kingsmore SF, Egholm M,
Lasken RS (2002) Comprehensive human genome
amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99(8):5261–5266
Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008)
Substantial biases in ultra-short read data sets from
high-throughput DNA sequencing. Nucleic Acids Res
36(16):e105
Douglas SE (1998) Plastid evolution: origins, diversity,
trends. Curr Opin Genet Dev 8(6):655–661
E Landolt (1994) Taxonomy and ecology of the section
Wolffia of the genus Wolffia (Lemnaceae). Ber Geobot
Inst ETH
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P,
Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S,
Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A,
Hardenbol P, Heiner C, Hester K, Holden D,
Kearns G, Kong X, Kuse R, Lacroix Y, Lin S,
Lundquist P, Ma C, Marks P, Maxham M, Murphy D,
Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G,
Sorenson J, Tomaney A, Travers K, Trulson M,
Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D,
Zhao P, Zhong F, Korlach J, Turner S (2009)
Real-time DNA sequencing from single polymerase
molecules. Science (80) 323(5910):133–138
Ferrarini M, Moretto M, Ward JA, Surbanovski N,
Stevanovic V, Giongo L, Viola R, Cavalieri D,
Velasco R, Cestaro A, Sargent DJ (2013) An evaluation of the PacBio RS platform for sequencing and de
novo assembly of a chloroplast genome. BMC Genom
14:670
Group CPW (2009) A DNA barcode for land plants. Proc
Natl Acad Sci USA 106(31):12794–12797
Heinze B (2007) A database of PCR primers for the
chloroplast genomes of higher plants. Plant Methods
3:4
Jansen RK, Raubeson LA, Boore JL, dePamphilis CW,
Chumley TW, Haberle RC, Wyman SK, Alverson AJ,
Peery R, Herman SJ, Fourcade HM, Kuehl JV,
McNeal JR, Leebens-Mack J, Cui L (2005) Methods
for obtaining and analyzing whole chloroplast genome
sequences. Methods Enzymol 395:348–384
Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B,
Borm TJA, Ohyanagi H, Mineta K, Michell CT,
Saber N, Kharbatia NM, Rupper RR, Sharp AR,
Dally N, Boughton BA, Woo YH, Gao G, Schijlen EGWM, Guo X, Momin AA, Negrão S, Al-Babili
S, Gehring C, Roessner U, Jung C, Murphy K,
Arold ST, Gojobori T, van der Linden CG, van
Loo EN, Jellen EN, Maughan PJ, Tester M (2017) The
genome of Chenopodium quinoa. Nature:1–20
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B,
Campbell MS, Stein JC, Wei X, Chin C-S, Guill K,
Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM,
Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR,
Ware D (2017) Improved maize reference genome
with single-molecule technologies. Nature 546:524–
527
Kolodner R, Tewari KK (1979) Inverted repeats in
chloroplast DNA from higher plants. Proc Natl Acad
Sci USA 76(1):41–45
Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM,
McVey SD, Radune D, Bergman NH, Phillippy AM
(2013) Reducing assembly complexity of microbial
genomes with single-molecule sequencing. Genome
Biol 14(9):R101
Ku C, Chung WC, Chen LL, Kuo CH (2013) The
complete plastid genome sequence of Madagascar
Periwinkle Catharanthus roseus (L.) G. Don: plastid
genome evolution, molecular marker identification,
and phylogenetic implications in Asterids. PLoS One
8(6):e68518
Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang TH,
Cervantes-Perez SA, Zheng C, Sankoff D, Tang H,
10 Duckweed Chloroplast Genome Sequencing and Annotation
113