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Duckweed Chloroplast Genome Sequencing and Annotation

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The Duckweed Genomes

Part of the book series: Compendium of Plant Genomes ((CPG))

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Abstract

Duckweed chloroplasts make great contributions to their rapid growth and abundant starch accumulation. The availability of chloroplast genomes will greatly facilitate the understanding of duckweed traits and further genetic chloroplast bioengineering. Here, we summarized the progress of duckweed chloroplast genome sequencing, together with the developments of sequencing technology and bioinformatics tools. The high-quality chloroplast DNA preparation was specifically emphasized in this chapter due to the key of genome sequencing. We also highlighted the potential applications of chloroplast genomes in the phylogenetic studies and the improvement of plant desirable traits.

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References

  • Ardui S, Ameur A, Vermeesch JR, Hestand MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46(5):2159–2168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE, Cottret L, Lelandais-Briere C, Owens GL, Carrere S, Mayjonade B, Legrand L, Gill N, Kane NC, Bowers JE, Hubner S, Bellec A, Berard A, Berges H, Blanchet N, Boniface MC, Brunel D, Catrice O, Chaidir N, Claudel C, Donnadieu C, Faraut T, Fievet G, Helmstetter N, King M, Knapp SJ, Lai Z, 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17(1):134

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Douglas SE (1998) Plastid evolution: origins, diversity, trends. Curr Opin Genet Dev 8(6):655–661

    Article  CAS  PubMed  Google Scholar 

  • E Landolt (1994) Taxonomy and ecology of the section Wolffia of the genus Wolffia (Lemnaceae). Ber Geobot Inst ETH

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Group CPW (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106(31):12794–12797

    Article  Google Scholar 

  • Heinze B (2007) A database of PCR primers for the chloroplast genomes of higher plants. Plant Methods 3:4

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kolodner R, Tewari KK (1979) Inverted repeats in chloroplast DNA from higher plants. Proc Natl Acad Sci USA 76(1):41–45

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang TH, Cervantes-Perez SA, Zheng C, Sankoff D, Tang H, 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Landolt E (1986) The family of Lemnaceae - a monographic study, vol 1. Veroffentlichungen des Geobotanischen Institutes der Eidgenossischen Technischen Hochschule, Stiftung Rubel

    Google Scholar 

  • Li C, Lin F, An D, Wang W, Huang R (2017) Genome sequencing and assembly by long reads in plants. Genes (Basel) 9(1)

    Article  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8(19):4321–4325

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Palmer JD (1986) Isolation and structural analysis of chloroplast DNA. Methods Enzymol 118(2):167–186

    Article  CAS  Google Scholar 

  • Sanger F (1988) Sequences, sequences, and sequences. Annu Rev Biochem 57:1–28

    Article  CAS  PubMed  Google Scholar 

  • Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5(1):16–18

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Stomp A-M, El-Gewely MR (2005) The duckweeds: a valuable plant for biomanufacturing. In: Biotechnology annual review, vol 11. Elsevier, pp 69–99

    Google Scholar 

  • Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5(2):123–135

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Wang W, Messing J (2011) High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PLoS ONE 6(9):e24670

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang W, Wu Y, Messing J (2012) The mitochondrial genome of an aquatic plant Spirodela polyrhiza. PLoS One 7(10):e46747

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17):3252–3255

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, 200240, China

    Yating Zhang & Wenqin Wang

Authors
  1. Yating Zhang
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  2. Wenqin Wang
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Correspondence to Wenqin Wang .

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Editors and Affiliations

  1. Department of Plant Physiology, Institute of Biology, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany

    Xuan Hieu Cao

  2. Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA

    Paul Fourounjian

  3. School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China

    Wenqin Wang

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Zhang, Y., Wang, W. (2020). Duckweed Chloroplast Genome Sequencing and Annotation. In: Cao, X., Fourounjian, P., Wang, W. (eds) The Duckweed Genomes. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-11045-1_10

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