Fisher JB. The vegetative and reproductive structure of papaya (Carica papaya). Harold L Lyon Arboretum. 1980;1(4):191–208.
Google Scholar
Ming R, Moore PH. Genetics and Genomics of Papaya. In: Plant Genetics & Genomics Crops & Models: Springer; 2014.
Gonsalves D. Control of papaya ringspot virus in papaya: a case study. Annu Rev Phytopathol. 1998;36(1):415–37.
Article
CAS
PubMed
Google Scholar
Storey W, Ferwerda F, Wit F. Outlines of Perennial Crop Breeding in the Tropics. Veenman & Zonen, Wageningen: Landbouwhogeschool Wageningen, Netherlands; 1969. p. 389–408.
Google Scholar
Fitch MM, Manshardt RM, Gonsalves D, Slightom JL, Sanford JC. Stable transformation of papaya via microprojectile bombardment. Plant Cell Rep. 1990;9(4):189–94.
Article
CAS
PubMed
Google Scholar
Fitch MM, Manshardt RM, Gonsalves D, Slightom JL, Sanford JC. Virus resistant papaya plants derived from tissues bombarded with the coat protein gene of papaya ringspot virus. Nat Biotechnol. 1992;10(11):1466–72.
Article
CAS
Google Scholar
Suzuki JY, Tripathi S, Fermín GA, Jan F-J, Hou S, Saw JH, Ackerman CM, Yu Q, Schatz MC, Pitz KY. Characterization of insertion sites in Rainbow papaya, the first commercialized transgenic fruit crop. Trop Plant Biol. 2008;1(3–4):293–309.
Article
CAS
Google Scholar
Zhang S, Chen W, Xin L, Gao Z, Hou Y, Yu X, Zhang Z, Qu S. Genomic variants of genes associated with three horticultural traits in apple revealed by genome re-sequencing. Horticulture Res. 2014;1:14045. https://doi.org/10.1038/hortres.2014.45.
Article
CAS
Google Scholar
Timmis JN, Scott NS. Sequence homology between spinach nuclear and chloroplast genomes. Nature. 1983;305(5929):65–7.
Article
CAS
Google Scholar
Baldauf SL, Palmer J. Evolutionary transfer of the chloroplast tufA gene to the nucleus. Nature. 1990;344(6263):262–5.
Article
CAS
PubMed
Google Scholar
Martin W, Herrmann RG. Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol. 1998;118(1):9–17.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kleine T, Maier UG, Leister D. DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annu Rev Plant Biol. 2009;60:115–38.
Article
CAS
PubMed
Google Scholar
VanBuren R, Ming R. Organelle DNA accumulation in the recently evolved papaya sex chromosomes. Mol Gen Genomics. 2013;288(5–6):277–84.
Article
CAS
Google Scholar
Sheppard AE, Timmis JN. Instability of plastid DNA in the nuclear genome. PLoS Genet. 2009;5(1):e1000323.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yoshida T, Furihata HY, Kawabe A. Analysis of nuclear mitochondrial DNAs and factors affecting patterns of integration in plant species. Genes Genet Syst. 2017;92(1):27–33.
Article
CAS
PubMed
Google Scholar
Michalovova M, Vyskot B, Kejnovsky E. Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization. Heredity. 2013;111(4):314–20.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yoshida T, Furihata HY, Kawabe A. Patterns of genomic integration of nuclear chloroplast DNA fragments in plant species. DNA Res. 2014;21(2):127–40.
Article
CAS
PubMed
Google Scholar
Leister D. Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends in Genetics Tig. 2005;21(12):655–63.
Article
CAS
PubMed
Google Scholar
Yoshida T, Furihata HY, To TK, Kakutani T, Kawabe A. Genome defense against integrated organellar DNA fragments from plastids into plant nuclear genomes through DNA methylation. Sci Rep. 2019;9:2060 doi: 10.1038/s41598–41019–38607-41596.
Article
PubMed Central
CAS
PubMed
Google Scholar
Noutsos C. Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants. Genome Res. 2005;15(5):616–28.
Article
CAS
PubMed Central
PubMed
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60.
Article
CAS
PubMed Central
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6(2):80–92.
Article
CAS
PubMed Central
PubMed
Google Scholar
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674–6.
Article
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
Google Scholar
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6.
Article
CAS
PubMed Central
PubMed
Google Scholar
Neelakandan AK, Wang K. Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications. Plant Cell Rep. 2012;31(4):597–620.
Article
CAS
PubMed
Google Scholar
Kovalic D, Garnaat C, Guo L, Yan Y, Groat J, Silvanovich A, Ralston L, Huang M, Tian Q, Christian A. The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology. Plant Genome. 2012;5(3):149–63.
Article
CAS
Google Scholar
Kawakatsu T, Kawahara Y, Itoh T, Takaiwa F. A whole-genome analysis of a transgenic rice seed-based edible vaccine against cedar pollen allergy. DNA Res. 2013;20(6):623–31.
Article
CAS
PubMed Central
PubMed
Google Scholar
Endo M, Kumagai M, Motoyama R, Sasaki-Yamagata H, Mori-Hosokawa S, Hamada M, Kanamori H, Nagamura Y, Katayose Y, Itoh T. Whole-genome analysis of herbicide-tolerant mutant rice generated by Agrobacterium-mediated gene targeting. Plant Cell Physiol. 2015;56(1):116–25.
Article
CAS
PubMed
Google Scholar
Kim M, Moore P, Zee F, Fitch MM, Steiger D, Manshardt R, Paull R, Drew RA, Sekioka T, Ming R. Genetic diversity of Carica papaya as revealed by AFLP markers. Genome. 2002;45(3):503–12.
Article
CAS
PubMed
Google Scholar
Blas AL, Ming R, Liu Z, Veatch OJ, Paull RE, Moore PH, Yu Q. Cloning of the papaya chromoplast-specific lycopene β-Cyclase, CpCYC-b, controlling fruit flesh color reveals conserved microsynteny and a recombination hot spot. Plant Physiol. 2010;152(4):2013–22.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008;452(7190):991–6.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yu Q, Navajas-Pérez R, Tong E, Robertson J, Moore PH, Paterson AH, Ming R. Recent origin of dioecious and gynodioecious Y chromosomes in papaya. Trop Plant Biol. 2008;1(1):49–57.
Article
Google Scholar
Yadav CB, Bhareti P, Muthamilarasan M, Mukherjee M, Khan Y, Rathi P, Prasad M. Genome-wide SNP identification and characterization in two soybean cultivars with contrasting Mungbean Yellow Mosaic India Virus disease resistance traits. PLoS One. 2015;10(4):e0123897.
Article
PubMed Central
CAS
PubMed
Google Scholar
Project IRGS. The map-based sequence of the rice genome. Nature. 2005;436(7052):793–800.
Article
CAS
Google Scholar
Jiang C, Mithani A, Gan X, Belfield EJ, Klingler JP, Zhu J-K, Ragoussis J, Mott R, Harberd NP. Regenerant Arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes. Curr Biol. 2011;21(16):1385–90.
Article
CAS
PubMed Central
PubMed
Google Scholar
Miyao A, Nakagome M, Ohnuma T, Yamagata H, Kanamori H, Katayose Y, Takahashi A, Matsumoto T, Hirochika H: Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. Plant Cell Physiol 2012, 53(1):256–264.
Anderson JE, Michno JM, TJY K, Stec AO, Campbell BW, Curtin SJ, Stupar RM. Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnol. 2016;16:41. https://doi.org/10.1186/s12896-016-0271-z.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science. 2010;327(5961):92–4.
Article
CAS
PubMed
Google Scholar
Fang J, Wood A, Chen R, Ming R. Molecular basis of off-type microsatellite markers in papaya. Euphytica. 2016;209(2):323–39.
Article
CAS
Google Scholar
Fang J, Lin A, Qiu W, Cai H, Umar M, Chen R, Ming R. Transcriptome profiling revealed stress-induced and disease resistance genes up-regulated in PRSV resistant transgenic papaya. Front Plant Sci. 2016;7:855. https://doi.org/10.3389/fpls.2016.00855.
Article
PubMed Central
PubMed
Google Scholar
Doerfler W, Hohlweg U, Müller K, Remus R, Heller H, Hertz J. Foreign DNA integration--perturbations of the genome--oncogenesis. Ann N Y Acad Sci. 2010;945(1):276–88.
Article
Google Scholar
Dai S, Zheng P, Marmey P, Zhang S, Tian W, Chen S, Beachy RN, Fauquet C. Comparative analysis of transgenic rice plants obtained by Agrobacterium-mediated transformation and particle bombardment. Mol Breed. 2001;7(1):25–33.
Article
CAS
Google Scholar
Kohli A, Leech M, Vain P, Laurie DA, Christou P. Transgene organization in rice engineered through direct DNA transfer supports a two-phase integration mechanism mediated by the establishment of integration hot spots. Proc Natl Acad Sci. 1998;95(12):7203–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shirasawa K, Hirakawa H, Nunome T, Tabata S, Isobe S. Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato. Plant Biotechnol J. 2016;14(1):51–60.
Article
CAS
PubMed
Google Scholar
Kashima K, Mejima M, Kurokawa S, Kuroda M, Kiyono H, Yuki Y. Comparative whole-genome analyses of selection marker–free rice-based cholera toxin B-subunit vaccine lines and wild-type lines. BMC Genomics. 2015;16:48. https://doi.org/10.1186/s12864-015-1285-y.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452(7184):215–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Coulondre C, Miller JH, Farabaugh PJ, Gilbert W. Molecular basis of base substitution hotspots in Escherichia coli. Nature. 1978;274(5673):775–80.
Article
CAS
PubMed
Google Scholar
Duncan BK, Miller JH. Mutagenic deamination of cytosine residues in DNA. Nature. 1980;287(5782):560–1.
Article
CAS
PubMed
Google Scholar
Friedberg EC, Walker GC, Siede W, Wood RD. DNA repair and mutagenesis: American Society for Microbiology Press; 2005.
Google Scholar
Cooper JL, Greene EA, Till BJ, Codomo CA, Wakimoto BT, Henikoff S. Retention of induced mutations in a Drosophila reverse-genetic resource. Genetics. 2008;180(1):661–7.
Article
PubMed Central
PubMed
Google Scholar
Liu S, Liu W, Jakubczak JL, Erexson GL, Tindall KR, Chan R, Muller WJ, Adhya S, Garges S, Merlino G. Genetic instability favoring transversions associated with ErbB2-induced mammary tumorigenesis. Proc Natl Acad Sci. 2002;99(6):3770–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng KC, Cahill DS, Kasai H, Nishimura S, Loeb LA. 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G→T and A→C substitutions. J Biol Chem. 1992;267(1):166–72.
CAS
PubMed
Google Scholar
Levinson G, Gutman GA. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol. 1987;4(3):203–21.
CAS
PubMed
Google Scholar
Tachida H, Iizuka M. Persistence of repeated sequences that evolve by replication slippage. Genetics. 1992;131(2):471–8.
CAS
PubMed Central
PubMed
Google Scholar
Jain M, Moharana KC, Shankar R, Kumari R, Garg R. Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotechnol J. 2014;12(2):253–64.
Article
CAS
PubMed
Google Scholar
Timmis JN, Ayliffe MA, Huang CY, Martin W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet. 2004;5(2):123–35.
Article
CAS
PubMed
Google Scholar
Chen H, Yu Y, Chen X, Zhang Z, Gong C, Li J, Wang A. Plastid DNA insertions in plant nuclear genomes: the sites, abundance and ages, and a predicted promoter analysis. Funct Integr Genomics. 2015;15(2):131–9.
Article
CAS
PubMed
Google Scholar
Stegemann S, Bock R. Experimental reconstruction of functional gene transfer from the tobacco plastid genome to the nucleus. Plant Cell. 2006;18(11):2869–78.
Article
CAS
PubMed Central
PubMed
Google Scholar
Noutsos C, Richly E, Leister D. Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants. Genome Res. 2005;15(5):616–28.
Article
CAS
PubMed Central
PubMed
Google Scholar
Khanna KK, Jackson SP. DNA double-strand breaks: signaling, repair and the cancer connection. Nat Genet. 2001;27(3):247–54.
Article
CAS
PubMed
Google Scholar
Huang CY, Ayliffe MA, Timmis JN. Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature. 2003;422(6927):72–6.
Article
CAS
PubMed
Google Scholar
Lutz KA, Wang W, Zdepski A, Michael TP. Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing. BMC Biotechnol. 2011;11:54. https://doi.org/10.1186/1472-6750-11-54.
Article
CAS
PubMed Central
PubMed
Google Scholar
Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7(2):e30619.
Article
CAS
PubMed Central
PubMed
Google Scholar
Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010;38(S2):W64–70.
Article
CAS
PubMed Central
PubMed
Google Scholar
Chen K, Wallis JW, MD ML, Larson DE, Kalicki JM, Pohl CS, SD MG, Wendl MC, Zhang Q, Locke DP. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009;6(9):677–81.
Article
CAS
PubMed Central
PubMed
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010;20(2):265–72.
Article
CAS
PubMed Central
PubMed
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.
Article
CAS
PubMed Central
PubMed
Google Scholar