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Future Prospects

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The Brassica rapa Genome

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

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Abstract

Releasing of the Brassica rapa var. Chiifu genome provided a reference for genome evolution research, gene discovery and breeding of Brassica crops. However, because of the limitation of the current technology, there is still a great space for the genome to be improved. These include increasing of the assembled repeat sequences, anchoring of the assemblies, accuracy of the predicted gene models and annotation of functional genome elements. More genomes of relative species were released. Comparative genomics genomes should be conducted to understand the B. rapa genome under a wider background. The reference genome provided possibilities to explore the genetic variation in B. rapa by GWAS. But large scale genome wide SNPs have to be generated. Extensive application of the genome data needs also improvement of the genome database.

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References

  • Branton D, Deamer DW, Marziali A, Bayley H, Benner SA et al (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26:1146–1153

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Cheng F, Liu S, Wu J, Fang L, Sun S et al (2011) BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 11

    Google Scholar 

  • Cheng F, Wu J, Fang L, Sun S, Liu B et al (2012) Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS One 7:e36442

    Google Scholar 

  • Cheng F, Mandakova T, Wu J, Xie Q, Lysak MA et al (2013) Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa. Plant Cell 25:1541–1554

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Dassanayake M, Oh DH, Haas JS, Hernandez A, Hong H et al (2011) The genome of the extremophile crucifer Thellungiella parvula. Nat Genet 43:913–918

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Encode C (2004) The ENCODE (ENCyclopedia Of DNA Elements) project. Science 306:636–640

    Article  Google Scholar 

  • Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN et al (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 108:1513–1518

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gupta PK (2008) Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 26:602–611

    Article  CAS  PubMed  Google Scholar 

  • Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M et al (2013) An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 45:891–898

    Article  CAS  PubMed  Google Scholar 

  • Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF et al (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 43:476–481

    Article  PubMed Central  PubMed  Google Scholar 

  • Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y et al (2014) Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res

    Google Scholar 

  • Ku CS, Roukos DH (2013) From next-generation sequencing to nanopore sequencing technology: paving the way to personalized genomic medicine. Expert Rev Med Devices 10:1–6

    Article  CAS  PubMed  Google Scholar 

  • Lin K, Zhang N, Severing EI, Nijveen H, Cheng F et al (2014) Beyond genomic variation—comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genomics 15

    Google Scholar 

  • Liu S, Liu Y, Yang X, Tong C, Edwards D et al (2014) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun (in press)

    Google Scholar 

  • Luo R, Liu B, Xie Y, Li Z, Huang W et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18

    Article  PubMed Central  PubMed  Google Scholar 

  • Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    Article  CAS  PubMed  Google Scholar 

  • Metzker ML (2009) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46

    Article  PubMed  Google Scholar 

  • Mun JH, Yu HJ, Shin JY, Oh M, Hwang HJ et al (2012) Auxin response factor gene family in Brassica rapa: genomic organization, divergence, expression, and evolution. Mol Genet Genomics 287:765–784

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Paritosh K, Yadava SK, Gupta V, Panjabi-Massand P, Sodhi YS et al (2013) RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapa and their use for genome-wide linkage mapping and specific-region fine mapping. BMC Genomics 14:463

    Article  PubMed Central  PubMed  Google Scholar 

  • Slotte T, Hazzouri KM, Agren JA, Koenig D, Maumus F et al (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45:831–835

    Article  CAS  PubMed  Google Scholar 

  • Song XM, Liu TK, Duan WK, Ma QH, Ren J et al (2013) Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis). Genomics 103:135–146

    Article  PubMed  Google Scholar 

  • Tong C, Wang X, Yu J, Wu J, Li W et al (2013) Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa. BMC Genomics 14:689

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wang X, Wang H, Wang J, Sun R, Wu J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Li L, Li H, Liu L, Zhang Y et al (2012) Transcriptome analysis of rosette and folding leaves in Chinese cabbage using high-throughput RNA sequencing. Genomics 99:299–307

    Article  CAS  PubMed  Google Scholar 

  • Yu X, Wang H, Zhong W, Bai J, Liu P et al (2013) QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa. PLoS ONE 8:e76059

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL et al (2013) The MaSuRCA genome assembler. Bioinformatics 29:2669–2677

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Correspondence to Xiaowu Wang .

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© 2015 Springer-Verlag Berlin Heidelberg

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Wang, X., Cheng, F. (2015). Future Prospects. In: Wang, X., Kole, C. (eds) The Brassica rapa Genome. Compendium of Plant Genomes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-47901-8_15

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