Purbojati RW, Putra A, Drautz-Moses DI, Schuster SC, Herrera-Estrella L, Albert VA (2017)
Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome. Proc Natl Acad
Sci USA 114(22):E4435–E4441
Landolt E (1986) The family of Lemnaceae - a monographic study, vol 1. Veroffentlichungen des Geobotanischen Institutes der Eidgenossischen Technischen
Hochschule, Stiftung Rubel
Li C, Lin F, An D, Wang W, Huang R (2017) Genome
sequencing and assembly by long reads in plants.
Genes (Basel) 9(1)
Li J, Jain M, Vunsh R, Vishnevetsky J, Hanania U,
Flaishman M, Perl A, Edelman M (2004) Callus
induction and regeneration in Spirodela and Lemna.
Plant Cell Rep 22(7):457–464
Mardanov AV, Ravin NV, Kuznetsov BB,
Samigullin TH, Antonov AS, Kolganova TV,
Skyabin KG (2008) Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural
organization and phylogenetic relationships to other
angiosperms. J Mol Evol 66(6):555–564
Murray MG, Thompson WF (1980) Rapid isolation of
high molecular weight plant DNA. Nucleic Acids Res
8(19):4321–4325
Nock CJ, Waters DL, Edwards MA, Bowen SG, Rice N,
Cordeiro GM, Henry RJ (2011) Chloroplast genome
sequences from total DNA for plant identification.
Plant Biotechnol J 9(3):328–333
Palmer JD (1986) Isolation and structural analysis of
chloroplast DNA. Methods Enzymol 118(2):167–186
Sanger F (1988) Sequences, sequences, and sequences.
Annu Rev Biochem 57:1–28
Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5(1):16–18
Shi C, Hu N, Huang H, Gao J, Zhao YJ, Gao LZ (2012)
An improved chloroplast DNA extraction procedure
for whole plastid genome sequencing. PLoS ONE 7
(2):e31468
Soorni A, Haak D, Zaitlin D, Bombarely A (2017)
Organelle_PBA, a pipeline for assembling chloroplast
and mitochondrial genomes from PacBio DNA
sequencing data. BMC Genom 18(1):49
Stomp A-M, El-Gewely MR (2005) The duckweeds: a
valuable plant for biomanufacturing. In: Biotechnology annual review, vol 11. Elsevier, pp 69–99
Timmis JN, Ayliffe MA, Huang CY, Martin W (2004)
Endosymbiotic gene transfer: organelle genomes forge
eukaryotic chromosomes. Nat Rev Genet 5(2):123–
135
VanBuren R, Bryant D, Edger PP, Tang H, Burgess D,
Challabathula D, Spittle K, Hall R, Gu J, Lyons E,
Freeling M, Bartels D, Ten Hallers B, Hastie A,
Michael TP, Mockler TC (2015) Single-molecule
sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 527(7579):508–511
Vieira Ldo N, Faoro H, Fraga HP, Rogalski M, de
Souza EM, de Oliveira Pedrosa F, Nodari RO,
Guerra MP (2014) An improved protocol for intact
chloroplasts and cpDNA isolation in conifers.
PLoS ONE 9(1):e84792
Vunsh R, Li J, Hanania U, Edelman M, Flaishman M,
Perl A, Wisniewski JP, Freyssinet G (2007) High
expression of transgene protein in Spirodela. Plant
Cell Rep 26(9):1511
Wang W, Messing J (2011) High-throughput sequencing
of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PLoS ONE 6(9):e24670
Wang W, Wu Y, Messing J (2012) The mitochondrial
genome of an aquatic plant Spirodela polyrhiza. PLoS
One 7(10):e46747
Wang W, Wu Y, Yan Y, Ermakova M, Kerstetter R,
Messing J (2010) DNA barcoding of the Lemnaceae, a
family of aquatic monocots. BMC Plant Biol 10:205
Wu J, Liu B, Cheng F, Ramchiary N, Choi SR, Lim YP,
Wang XW (2012) Sequencing of chloroplast genome
using whole cellular DNA and solexa sequencing
technology. Front Plant Sci 3:243
Wyman SK, Jansen RK, Boore JL (2004) Automatic
annotation of organellar genomes with DOGMA.
Bioinformatics 20(17):3252–3255
Yamamoto YT, Rajbhandari N, Lin X, Bergmann BA,
Nishimura Y, Stomp AM (2000) Genetic transformation of duckweed Lemna gibba and Lemna minor.
Vitro Cell Dev Plant 37:349–353
Yang JB, Li DZ, Li HT (2014) Highly effective
sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol
Res 14(5):1024–1031
Zerbino DR, Birney E (2008) Velvet: algorithms for de
novo short read assembly using de Bruijn graphs.
Genome Res 18(5):821–829
114
Y. Zhang and W. Wang
Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome. Proc Natl Acad
Sci USA 114(22):E4435–E4441
Landolt E (1986) The family of Lemnaceae - a monographic study, vol 1. Veroffentlichungen des Geobotanischen Institutes der Eidgenossischen Technischen
Hochschule, Stiftung Rubel
Li C, Lin F, An D, Wang W, Huang R (2017) Genome
sequencing and assembly by long reads in plants.
Genes (Basel) 9(1)
Li J, Jain M, Vunsh R, Vishnevetsky J, Hanania U,
Flaishman M, Perl A, Edelman M (2004) Callus
induction and regeneration in Spirodela and Lemna.
Plant Cell Rep 22(7):457–464
Mardanov AV, Ravin NV, Kuznetsov BB,
Samigullin TH, Antonov AS, Kolganova TV,
Skyabin KG (2008) Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural
organization and phylogenetic relationships to other
angiosperms. J Mol Evol 66(6):555–564
Murray MG, Thompson WF (1980) Rapid isolation of
high molecular weight plant DNA. Nucleic Acids Res
8(19):4321–4325
Nock CJ, Waters DL, Edwards MA, Bowen SG, Rice N,
Cordeiro GM, Henry RJ (2011) Chloroplast genome
sequences from total DNA for plant identification.
Plant Biotechnol J 9(3):328–333
Palmer JD (1986) Isolation and structural analysis of
chloroplast DNA. Methods Enzymol 118(2):167–186
Sanger F (1988) Sequences, sequences, and sequences.
Annu Rev Biochem 57:1–28
Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5(1):16–18
Shi C, Hu N, Huang H, Gao J, Zhao YJ, Gao LZ (2012)
An improved chloroplast DNA extraction procedure
for whole plastid genome sequencing. PLoS ONE 7
(2):e31468
Soorni A, Haak D, Zaitlin D, Bombarely A (2017)
Organelle_PBA, a pipeline for assembling chloroplast
and mitochondrial genomes from PacBio DNA
sequencing data. BMC Genom 18(1):49
Stomp A-M, El-Gewely MR (2005) The duckweeds: a
valuable plant for biomanufacturing. In: Biotechnology annual review, vol 11. Elsevier, pp 69–99
Timmis JN, Ayliffe MA, Huang CY, Martin W (2004)
Endosymbiotic gene transfer: organelle genomes forge
eukaryotic chromosomes. Nat Rev Genet 5(2):123–
135
VanBuren R, Bryant D, Edger PP, Tang H, Burgess D,
Challabathula D, Spittle K, Hall R, Gu J, Lyons E,
Freeling M, Bartels D, Ten Hallers B, Hastie A,
Michael TP, Mockler TC (2015) Single-molecule
sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 527(7579):508–511
Vieira Ldo N, Faoro H, Fraga HP, Rogalski M, de
Souza EM, de Oliveira Pedrosa F, Nodari RO,
Guerra MP (2014) An improved protocol for intact
chloroplasts and cpDNA isolation in conifers.
PLoS ONE 9(1):e84792
Vunsh R, Li J, Hanania U, Edelman M, Flaishman M,
Perl A, Wisniewski JP, Freyssinet G (2007) High
expression of transgene protein in Spirodela. Plant
Cell Rep 26(9):1511
Wang W, Messing J (2011) High-throughput sequencing
of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PLoS ONE 6(9):e24670
Wang W, Wu Y, Messing J (2012) The mitochondrial
genome of an aquatic plant Spirodela polyrhiza. PLoS
One 7(10):e46747
Wang W, Wu Y, Yan Y, Ermakova M, Kerstetter R,
Messing J (2010) DNA barcoding of the Lemnaceae, a
family of aquatic monocots. BMC Plant Biol 10:205
Wu J, Liu B, Cheng F, Ramchiary N, Choi SR, Lim YP,
Wang XW (2012) Sequencing of chloroplast genome
using whole cellular DNA and solexa sequencing
technology. Front Plant Sci 3:243
Wyman SK, Jansen RK, Boore JL (2004) Automatic
annotation of organellar genomes with DOGMA.
Bioinformatics 20(17):3252–3255
Yamamoto YT, Rajbhandari N, Lin X, Bergmann BA,
Nishimura Y, Stomp AM (2000) Genetic transformation of duckweed Lemna gibba and Lemna minor.
Vitro Cell Dev Plant 37:349–353
Yang JB, Li DZ, Li HT (2014) Highly effective
sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol
Res 14(5):1024–1031
Zerbino DR, Birney E (2008) Velvet: algorithms for de
novo short read assembly using de Bruijn graphs.
Genome Res 18(5):821–829
114
Y. Zhang and W. Wang