Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica

Theoretical and Applied Genetics

Volumn 127, Issue 9, 2014, Pages 1975-1989

  Jeong, Young Min ^a   Chung, Won Hyong ^b   Chung, Hee ^a   Kim, Namshin ^b   Park, Beom Seok ^c   Lim, Ki Byung ^d   Yu, Hee Ju ^a   Mun, Jeong Hwan ^e  

^a The Catholic University of Korea   (South Korea)

^b Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^c National Institute of Animal Science   (South Korea)

^d Kyungpook National University   (South Korea)

^e Myong Ji University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CROPS; FACSIMILE; MAPPING; PLANTS (BOTANY);

ARABIDOPSIS THALIANA; COMPARATIVE ANALYSIS; ENCODED PROTEINS; EVOLUTIONARY RELATIONSHIPS; GENE-BASED MARKERS; GENOME COMPARISON; GENOME STRUCTURES; SINGLE-COPY GENES;

GENES;

PLANT DNA;

BRASSICA; CHROMOSOME MAP; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENOME; RAPHANUS; SYNTENY;

BRASSICA; CHROMOSOME MAPPING; CONSERVED SEQUENCE; DNA, PLANT; GENOME, PLANT; RAPHANUS; SEQUENCE ANALYSIS, DNA; SYNTENY;

EID: 84927172364     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-014-2354-3     Document Type: Article

References (51)

1. Al-Shehbaz I, Beilstein M, Kellogg E (2006) Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview. Plant Syst Evol 259:89–120
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
3. Arias T, Beilstein M, Tang M, McKain M, Pires J (2014) Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence. Am J Bot 101:86–91
4. Beilstein M, Al-Shehbaz I, Kellogg E (2006) Brassicaceae phylogeny and trichome evolution. Am J Bot 93:607–619
5. Beilstein M, Nagalingum N, Clements M, Manchester S, Mathews S (2010) Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci USA 107:18724–18728
6. Bushakra JM, Sargent DJ, Cabrera A, Crowhurst R, Girona EL, Velasco R, Symonds VV, Knaap E, Troggio M, Gardiner SE, Chagné D (2011) Rosaceae conserved orthologous set (RosCOS) markers as a tool to assess genome synteny between Malus and Fragaria. Tree Genet Genomes 8:643–658
7. Cabrera A, Kozik A, Howad W, Arus P, Iezzoni AF, van der Knaap E (2009) Development and bin mapping of a Rosaceae conserved ortholog set (COS) of markers. BMC Genom 10:562
8. Chapman MA, Chang J, Weisman D, Kesseli RV, Burke JM (2007) Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae). Theor Appl Genet 115:747–755
9. Cheng F, Wu J, Fang L, Wang X (2012) Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Front Plant Sci 3:198
10. Cheng F, Mandakova T, Wu J, Xie Q, Lysak MA, Wang X (2013) Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa. Plant Cell 25:1541–1554
11. Dassanayake M, Oh DH, Haas JS, Hernandez A, Hong H, Ali S, Yun DJ, Bressan RA, Zhu JK, Bohnert HJ, Cheeseman JM (2011) The genome of the extremophile crucifer Thellungiella parvula. Nat Genet 43:913–918
12. Economic Research Service USDA (2008) Vegetables and melons outlook. http://www.ers.usda.gov/Publications/VGS/Tables/World.pdf
13. Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467
14. Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11:725–736
15. Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 43:476–481
16. Huang S, Deng L, Guan M, Li J, Lu K, Wang H, Fu D, Mason A, Liu S, Hua W (2013) Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus. BMC Genom 14:717
17. Kim B, Yu H, Park S, Shin J, Oh M, Kim N, Mun J (2012) Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing. BMC Plant Biol 12:218
18. Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB (2004) Comparative mapping in the Pinaceae. Genetics 168:447–461
19. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645
20. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
21. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
22. Li F, Hasegawa Y, Saito M, Shirasawa S, Fukushima A, Ito T, Fujii H, Kishitani S, Kitashiba H, Nishio T (2011) Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.). DNA Res 18:401–411
23. Liewlaksaneeyanawin C, Zhuang J, Tang M, Farzaneh N, Lueng G, Cullis C, Findlay S, Ritland CE, Bohlmann J, Ritland K (2008) Identification of COS markers in the Pinaceae. Tree Genet Genomes 5:247–255
24. Lü N, Yamane K, Ohnishi O (2008) Genetic diversity of cultivated and wild radish and phylogenetic relationships among Raphanus and Brassica species revealed by the analysis of trnK/matK sequence. Breed Sci 58:15–22
25. Lysak M, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I (2006) Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc Natl Acad Sci USA 103:5224–5229
26. Mun J-H, Kwon S, Yang T, Seol Y, Jin M, Kim J, Lim M, Kim J, Baek S, Choi B, Yu H, Kim D, Kim N, Lim K, Lee S, Hahn J, Lim Y, Bancroft I, Park B (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 10:R111
27. Nelson MN, Parkin IA, Lydiate DJ (2011) The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome. Genome 54:33–41
28. Panjabi P, Jagannath A, Bisht NC, Padmaja KL, Sharma S, Gupta V, Pradhan AK, Pental D (2008) Comparative mapping of Brassica juncea and Arabidopsis thaliana using intron polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genom 9:113
29. Quraishi UM, Abrouk M, Bolot S, Pont C, Throude M, Guilhot N, Confolent C, Bortolini F, Praud S, Murigneux A, Charmet G, Salse J (2009) Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection. Funct Integr Genomics 9:473–484
30. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386
31. Schranz ME, Lysak MA, Mitchell-Olds T (2006) The ABC’s of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends Plant Sci 11:535–542
32. Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M, Kishida Y, Kohara M, Takahashi C, Tsuruoka H, Wada T, Sakai T, Isobe S (2011) An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae. DNA Res 18:221–232
33. Slotte T, Hazzouri K, Ågren J, Koenig D, Maumus F, Guo Y, Steige K, Platts A, Escobar J, Newman L, Wang W, Mandáková T, Vello E, Smith L, Henz S, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu T, Blanchette M, Clark R, Quesneville H, Nordborg M, Gaut B, Lysak M, Jenkins J, Grimwood J, Chapman J, Prochnik S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright S (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45:831–835
34. Song KM, Osborn TC, Williams PH (1988) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs): 2. Preliminary analysis of subspecies within B. rapa (syn. campestris) and B. oleracea. Theor Appl Genet 76:593–600
35. Song K, Osborn TC, Williams PH (1990) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs): 3. Genome relationships in Brassica and related genera and the origin of B. oleracea and B. rapa (syn. campestris). Theor Appl Genet 79:497–506
36. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
37. The Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039
38. Thormann CE, Ferreira ME, Camargo LE, Tivang JG, Osborn TC (1994) Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species. Theor Appl Genet 88:973–980
39. Timms L, Jimenez R, Chase M, Lavelle D, McHale L, Kozik A, Lai Z, Heesacker A, Knapp S, Rieseberg L, Michelmore R, Kesseli R (2006) Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements. Genetics 173:2227–2235
40. ® 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma B. V, Wageningen
41. Warwick S, Black L (1991) Molecular systematics of Brassica and allied genera (Subtribe Brassicinae, Brassiceae)—chloroplast genome and cytodeme congruence. Theor Appl Genet 82:81–92
42. Warwick S, Black L (1997) Phylogenetic implications of chloroplast DNA restriction site variation in subtribes Raphaninae and Cakilinae (Brassicaceae, tribe Brassiceae). Canadian J Bot 75:960–973
43. Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174:1407–1420
44. Wu F, Eannetta NT, Xu Y, Durrett R, Mazourek M, Jahn MM, Tanksley SD (2009a) A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum. Theor Appl Genet 118:1279–1293
45. Wu F, Eannetta NT, Xu Y, Tanksley SD (2009b) A detailed synteny map of the eggplant genome based on conserved ortholog set II (COSII) markers. Theor Appl Genet 118:927–935
46. Wu F, Eannetta NT, Xu Y, Plieske J, Ganal M, Pozzi C, Bakaher N, Tanksley SD (2010) COSII genetic maps of two diploid Nicotiana species provide a detailed picture of synteny with tomato and insights into chromosome evolution in tetraploid N. tabacum. Theor Appl Genet 120:809–827
47. Wu HJ, Zhang Z, Wang JY, Oh DH, Dassanayake M, Liu B, Huang Q, Sun HX, Xia R, Wu Y, Wang YN, Yang Z, Liu Y, Zhang W, Zhang H, Chu J, Yan C, Fang S, Zhang J, Wang Y, Zhang F, Wang G, Lee SY, Cheeseman JM, Yang B, Li B, Min J, Yang L, Wang J, Chu C, Chen SY, Bohnert HJ, Zhu JK, Wang XJ, Xie Q (2012) Insights into salt tolerance from the genome of Thellungiella salsuginea. Proc Natl Acad Sci USA 109:12219–12224
48. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591
49. Yang YW, Lai KN, Tai PY, Ma DP, Li WH (1999) Molecular phylogenetic studies of Brassica, Rrippa, Arabidopsis and allied genera based on the internal transcribed spacer region of 18S–25S rDNA. Mol Phylogenet Evol 13:455–462
50. Yang YW, Tai PY, Chen Y, Li WH (2002) A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA. Mol Phylogene Evol 23:268–275
51. Yang R, Jarvis DE, Chen H, Beilstein MA, Grimwood J, Jenkins J, Shu S, Prochnik S, Xin M, Ma C, Schmutz J, Wing RA, Mitchell-Olds T, Schumaker KS, Wang X (2013) The reference genome of the halophytic plant Eutrema salsugineum. Front Plant Sci 4:46