Skip to main content
SpringerLink
Log in

Citrus Genomes: From Sequence Variations to Epigenetic Modifications

  • Chapter
  • First Online:
The Citrus Genome

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

Abstract

Genome platform is critical to the basic molecular biological research and to the molecular marker assisted breeding. Genomics data of citrus species have accumulated rapidly after the first publication of sweet orange in 2013. With the cost of sequencing decreased dramatically, each individual research group can afford to sequence many genomes. This chapter summarizes methods for genome assembly and annotation, how we identify genes by comparative genomics, linkage mapping and association analysis, how we apply SNP markers in cultivar identification and breeding, and the current knowledge on epigenetic regulations in Citrus. This chapter also anticipates future genomic researches in Citrus.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Aritua V, Achor D, Gmitter FG, Albrigo G, Wang N (2013) Transcriptional and microscopic analyses of citrus stem and root responses to Candidatus Liberibacter asiaticus infection. PLoS ONE 8(9):e73742

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28:45–48

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Birney E, Clamp M, Durbin R (2004) GeneWise and genomewise. Genome Res 14:988–995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579

    Article  CAS  PubMed  Google Scholar 

  • Butelli E et al (2012) Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell 24:1242–1255

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chin CS et al (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569

    Article  CAS  PubMed  Google Scholar 

  • Chuck G, O’Connor D (2010) Small RNAs going the distance during plant development. Curr Opin Plant Biol 13:40–45

    Article  CAS  PubMed  Google Scholar 

  • Chumsakul O, Nakamua K, Kurata T et al (2013) High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq/ DNA Res. 20:325–338

    CAS  PubMed  Google Scholar 

  • Consortium TTG (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641

    Article  CAS  Google Scholar 

  • Curk F et al (2015) Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties. PLoS ONE 10:e0125628

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Curk F, Ollitrault F, Garcia-Lore A, Luro F, Navarro L, Ollitrault P (2016) Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers. Ann Bot 117:565–583

    Article  PubMed  PubMed Central  Google Scholar 

  • Daccord N, Celton J-M, Linsmith G et al (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet 49:1099–1106

    Article  CAS  PubMed  Google Scholar 

  • Danecek P et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dardick C, Callahan A, Horn R, Ruiz KB, Zhebentyayeva T, Hollender C, Whitaker M, Abbott A, Scorza R (2013) PpeTAC1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species. Plant J. 75:618–630

    Article  CAS  PubMed  Google Scholar 

  • Delaneau O, Marchini J, Zagury JF (2011) A linear complexity phasing method for thousands of genomes. Nat Methods 9:179–181

    Article  PubMed  CAS  Google Scholar 

  • D’Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengelle J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, McKain MR, Leebens-Mack J, Burgess D, Freeling M, Mbeguie AMD, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quetier F, Yahiaoui N, Wincker P (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–217

    Article  PubMed  CAS  Google Scholar 

  • Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:64–70

    Article  CAS  Google Scholar 

  • Ellinghaus D, Kurtz S, Willhoeft U (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinform 9:18

    Article  CAS  Google Scholar 

  • Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP Related Tools. Nat Protoc 2:953–971

    Article  CAS  PubMed  Google Scholar 

  • Fang J-G, Song C-N, Qian J-L, Zhang X-Y, Shangguan L-F, Yu H-P, Wang X-C (2010) Variation of cytosine methylation in 57 sweet orange cultivars. Acta Physiol Plant 32:1023–1030

    Article  CAS  Google Scholar 

  • Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM (2010) Transposon-induced gene activation as a mechanism generating cluster shape somatic variation in grapevine. Plant J 61:545–557

    Article  CAS  PubMed  Google Scholar 

  • Fujii H, Shimada T, Nonaka K, Kita M, Kuniga T, Endo T, Ikoma Y, Omura M (2013) High-throughput genotyping in citrus accessions using an SNP genotyping array. Tree Genet Genomes 9:145–153

    Article  CAS  Google Scholar 

  • Gao L, McCarthy EM, Ganko EW, McDonald JF (2004) Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genom 5:18

    Article  Google Scholar 

  • Garcia D (2008) A miRacle in plant development: role of microRNAs in cell differentiation and patterning. Sem Cell Dev Biol 19:586–595

    Article  CAS  Google Scholar 

  • Garcia-Lor A et al (2013) A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species. Ann Bot 111:1–19

    Article  CAS  PubMed  Google Scholar 

  • Garciamas J, Benjak A, Sanseverino W et al (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci USA 109:11872–11877

    Google Scholar 

  • Ge XX, Chai LJ, Liu Z, Wu XM, Deng XX, Guo WW (2012) Transcriptional profiling of genes involved in embryogenic, non-embryogenic calluses and somatic embryogenesis of Valencia sweet orange by SSH-based microarray. Planta 236:1107–1124

    Article  CAS  PubMed  Google Scholar 

  • Guerra M (1993) Cytogenetics of Rutaceae. V. High chromosomal variability in citrus species revealed by CMA/DAPI staining. Heredity 71:234–241

    Article  Google Scholar 

  • Guo S, Zhang J, Sun H et al (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51–58

    Article  CAS  PubMed  Google Scholar 

  • Haas BJ et al (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31:5654–5666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Han YH, Zhang ZH, Liu JH, Huang SW, Jin WW (2008) Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis Sativus L.) by fluorescence in situ hybridization. Cytogenet Genome Res 122:80–88

    Google Scholar 

  • Hao Y, Deng X (2002) Stress treatments and DNA methylation affected the somatic embryogenesis of citrus callus. Acta Bot Sin 44:673–677

    CAS  Google Scholar 

  • Hao Y, Wen X, Deng X (2004) Genetic and epigenetic evaluations of citrus calluses recovered from slow-growth culture. J Plant Physiol 161:479–484

    Google Scholar 

  • He G, Elling AA, Deng XW (2011) The epigenome and plant development. Ann Rev Plant Biol 62:411–435

    Article  CAS  Google Scholar 

  • Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 447:418–424

    Article  CAS  PubMed  Google Scholar 

  • Hong L, Deng X (2005) Analysis of DNA methylation in navel oranges based on MSAP marker. Zhongguo Nongye Kexue 38:2301–2307

    CAS  Google Scholar 

  • Jaillon O et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467

    Article  CAS  PubMed  Google Scholar 

  • Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92:4487–4491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaeppler SM, Kaeppler HF, Rhee Y (2000) Epigenetic aspects of somaclonal variation in plants. In: Matzke MA, Matzke AJM (eds) Plant gene silencing. Springer, Dordrecht, pp 59–68

    Chapter  Google Scholar 

  • Kaity A, Ashmore SE, Drew RA, Dulloo ME (2008) Assessment of genetic and epigenetic changes following cryopreservation in papaya. Plant Cell Rep 27:1529–1539

    Article  CAS  PubMed  Google Scholar 

  • Kalisz S, Purugganan MD (2004) Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol Evol 19:309–314

    Article  PubMed  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kelley DR, Schatz MC, Salzberg Quake SL (2009) Quality-aware detection and correction of sequencing errors. Genome Biol 11:1–13

    Google Scholar 

  • Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304:982

    Article  PubMed  Google Scholar 

  • Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580

    Article  CAS  PubMed  Google Scholar 

  • Lang P, Zhang C, Ebel RC, Dane F, Dozier WA (2005) Identification of cold acclimated genes in leaves of Citrus unshiu by mRNA differential display. Gene 359:111–118

    Article  CAS  PubMed  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li X, Xu M, Korban SS (2002) DNA methylation profiles differ between field- and in vitro-grown leaves of apple. J Plant Physiol 159:1229–1234

    Article  Google Scholar 

  • Lim KY (2004) Karyotype and ribosomal gene mapping in Fragaria vesca L. Acta Hort 649:103–106

    Article  CAS  Google Scholar 

  • Liu B, Davis TM (2011) Conservation and loss of ribosomal RNA gene sites in diploid and polyploid Fragaria (Rosaceae). BMC Plant Biol 11:157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Q, Zhu A, Chai L, Zhou W, Yu K, Ding J, Xu J, Deng X (2009) Transcriptome analysis of a spontaneous mutant in sweet orange [Citrus sinensis (L.) Osbeck] during fruit development. J Exp Bot 60:801–813

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Wang G, Wang Z, Yang F, Wu G, Hong N (2012) Identification of differentially expressed genes in response to infection of a mild Citrus tristeza virus isolate in Citrus aurantifolia by suppression subtractive hybridization. Sci Hortic 134:144–149

    Article  CAS  Google Scholar 

  • Liu Y, Ke L, Wu G, Xu Y, Wu X, Xia R, Deng X, Xu Q (2017) miR3954 is a trigger of phasiRNAs that affects flowering time in citrus. Plant J 92:263–275

    Article  CAS  PubMed  Google Scholar 

  • Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ (2005) Elucidation of the small RNA component of the transcriptome. Science 309:1567–1569

    Article  CAS  PubMed  Google Scholar 

  • Luo R et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:1–6

    Article  Google Scholar 

  • Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20:2878–2879

    Article  CAS  PubMed  Google Scholar 

  • Marcais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martinelli F, Uratsu SL, Albrecht U, Reagan RL, Phu ML et al (2012) Transcriptome profiling of Citrus Fruit Response to Huanglongbing Disease. PLoS ONE 7(5):e38039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ming R et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–996

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moraes AP, Mirkov TE, Guerra M (2008) Mapping the chromosomes of Poncirus trifoliata Raf. by BAC-FISH. Cytogenet Genome Res 121:277–281

    Google Scholar 

  • Novelli VM, Takita MA, Machado MA (2004) Identification and analysis of single nucleotide polymorphisms (SNPs) in citrus. Euphytica 138:227–237

    Article  CAS  Google Scholar 

  • Ollitrault P et al (2012a) A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping. BMC Genomics 13:593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ollitrault P (2012b) SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping. BMC Genomics 13:170–170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Otto TD, Sanders M, Berriman M, Newbold C (2010) Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 26:1704–1707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pasentsis K, Falara V, Pateraki I, Gerasopoulos D, Kanellis AK (2007) Identification and expression profiling of low oxygen regulated genes from Citrus flavedo tissues using RT-PCR differential display. J Exp Bot 58:2203–2216

    Article  CAS  PubMed  Google Scholar 

  • Peng T, Zhu XF, Fan QJ, Sun PP, Liu JH (2012) Identification and characterization of low temperature stress responsive genes in Poncirus trifoliata by suppression subtractive hybridization. Gene 492:220–228

    Article  CAS  PubMed  Google Scholar 

  • Peraza-Echeverria S, Herrera-Valencia VA, Kay A (2001) Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP). Plant Sci 161:359–367

    Article  CAS  PubMed  Google Scholar 

  • Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21:i351–i358

    Article  CAS  PubMed  Google Scholar 

  • Purcell S et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575

    Article  CAS  PubMed  Google Scholar 

  • Rho M, Choi JH, Kim S, Lynch M, Tang H De (2007) novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genom 8:90

    Article  CAS  Google Scholar 

  • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277

    Article  CAS  PubMed  Google Scholar 

  • Schuster M, Fuchs J, Schubert I (1997) Cytogenetics in fruit breeding—localization of ribosomal RNA genes on chromosomes of apple (Malus x domestica Borkh.). Theor Appl Genet 94:322–324

    Article  CAS  Google Scholar 

  • Selmer KK et al (2009) Genome-wide linkage analysis with clustered SNP markers. J Biomol Screen 14:92–96

    Article  CAS  PubMed  Google Scholar 

  • Shulaev V et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–116

    Article  CAS  PubMed  Google Scholar 

  • Song C, Wang C, Zhang C, Korir NK, Yu H, Ma Z, Fang J (2010) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 111:431

    Article  CAS  Google Scholar 

  • Sun L-M, Ai X-Y, Li W-Y, Guo W-W, Deng X, Hu C-G, Zhang J-Z (2012) Identification and comparative profiling of miRNAs in an early flowering mutant of trifoliate orange and its wild type by genome-wide deep sequencing. PLoS ONE 7(8):e43760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Szinay D et al (2008) High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome. Plant J 56:6

    Article  CAS  Google Scholar 

  • Telias A, Lin-Wang K, Stevenson DE et al (2011) Apple skin patterning is associated with differential expression of MYB10. BMC Plant Biol 11:93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell C et al (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Valledor L, Hasbun R, Meijon M et al (2007) Involvement of DNA methylation in tree development and micropropagation. Plant Cell, Tissue, Organ Cult 91:75–86

    Google Scholar 

  • Velasco R et al (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42:833–839

    Google Scholar 

  • Verde I, Abbott AG, Scalabrin S et al (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494

    Article  CAS  PubMed  Google Scholar 

  • Walling JG, Jiang J (2011) DNA and chromatin fiber-based plant cytogenetics. Plant cytogenetics, pp 121–130. In: Bass H, Birchler J (eds) Plant cytogenetics. Plant genetics and genomics: crops and models, vol 4. Springer, New York, NY

    Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev Genet 10:56–63

    Article  CAS  Google Scholar 

  • Wang Z, Meng D, Wang A, Li T, Jiang S, Cong P, Li T (2013) The methylation of the PcMYB10 promoter is associated with green-skinned sport in Max Red Bartlett pear. Plant Physiol 162:885–896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang X, Xu Y, Zhang S et al (2017) Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nat Genet 49:765–772

    Article  CAS  PubMed  Google Scholar 

  • Wu GA et al (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 32:656–662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu X-M, Kou S-J, Liu Y-L, Fang Y-N, Xu Q, Guo W-W (2015) Genomewide analysis of small RNAs in non-embryogenic and embryogenic tissues of citrus: microRNA-and siRNA-mediated transcript cleavage involved in somatic embryogenesis. Plant Biotech J 13:383–394

    Article  CAS  Google Scholar 

  • Xu Q, Yu KQ, Deng XX et al (2009) Comparative transcripts profiling reveals new insight into molecular processes regulating lycopene accumulation in a sweet orange (Citrus sinensis) red-flesh mutant. BMC Genom 10:1–15

    Article  CAS  Google Scholar 

  • Xu Q, Liu Y, Zhu A, Wu X, Ye J, Yu K, Guo W, Deng X (2010) Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type. BMC Genom 11:246

    Article  CAS  Google Scholar 

  • Xu Q et al (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45:59–66

    Article  CAS  PubMed  Google Scholar 

  • Xu J, Xu H, Xu Q, Deng X (2015) Characterization of DNA methylation variations during fruit development and ripening of sweet orange. Plant Mol Biol Rep 33:1–11

    Article  CAS  Google Scholar 

  • Yao J-L, Dong Y-H, Morris BAM (2001) Parthenocarpic apple fruit production conferred by transposon insertion mutations in a MADS-box transcription factor. Proc Nat Acad Sci USA 98:1306–1311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zdobnov EM, Apweiler R (2001) InterProScan–an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847–848

    Article  CAS  PubMed  Google Scholar 

  • Zenoni S, Ferrarini A, Giacomelli E, Xumerle L, Fasoli M, Malerba G, Bellin D, Pezzotti M, Delledonne M (2010) Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol 152:1787–1795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang J-Z, Li Z-M, Liu L, Mei L, Yao J-L, Hu C-G (2008) Identification of early-flower-related ESTs in an early-flowering mutant of trifoliate orange (Poncirus trifoliata) by suppression subtractive hybridization and macroarray analysis. Tree Physiol 28:1449–1457

    Article  CAS  PubMed  Google Scholar 

  • Zhang W, Wai CM, Ming R, Yu Q, Jiang J (2010) Integration of genetic and cytological maps and development of a pachytene chromosome-based karyotype in papaya. Tropical Plant Biol 3:166–170

    Article  Google Scholar 

  • Zhang X-N, Li X, Liu J-H (2014) Identification of conserved and novel cold-responsive microRNAs in trifoliate orange (Poncirus trifoliata (L.) Raf.) using high-throughput sequencing. Plant Mol Biol Report 32:328–341

    Article  CAS  Google Scholar 

  • Zheng and Zhao (2013) Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to ‘Candidatus Liberibacter asiaticus’ infection. BMC Genomic 14:27

    Article  CAS  Google Scholar 

  • Zhong S, Fei Z, Chen Y-R, Zheng Y et al (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotech 31:154–159

    Article  CAS  PubMed  Google Scholar 

  • Zhou RN, Hu ZM (2007) The development of chromosome microdissection and microcloning technique and its applications in genomic research. Curr Genomics 8:67–72

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu AD (2012) Citrus genome evolution and transcriptomic studies on postharvest fruits. PhD dissertation, Huazhong Agricultural University, Wuhan (in Chinese)

    Google Scholar 

Download references

Acknowledgements

The authors are grateful to Dr. Xia Wang, Dr. Yue Huang, and Chunli Chen for contribution and beneficial discussions on the population genomics, genome assembly and cytogenomics. We thank the funding by the National Key Research and Development Program of China (2018YFD1000100), and USDA-NIFA grant 2013-67013-21110

Author information

Authors and Affiliations

  1. Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China

    Qiang Xu

  2. Department of Botany and Plant Sciences, University of California, Riverside, 92521, USA

    Mikeal L. Roose

Authors
  1. Qiang Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mikeal L. Roose
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Qiang Xu or Mikeal L. Roose .

Editor information

Editors and Affiliations

  1. Department of Agriculture, Food and Environment, University of Catania, Catania, Italy

    Alessandra Gentile

  2. Department of Agriculture, Food and Environment, University of Catania, Catania, Italy

    Stefano La Malfa

  3. Horticulture and Landscape College, Hunan Agricultural University, Changsha, China

    Ziniu Deng

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Xu, Q., Roose, M.L. (2020). Citrus Genomes: From Sequence Variations to Epigenetic Modifications. In: Gentile, A., La Malfa, S., Deng, Z. (eds) The Citrus Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-15308-3_8

Download citation

Publish with us

Policies and ethics

Search

Navigation