Trapnell C, Williams B A, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J]. Nat Biotech, 2010, 28(5): 511-515.
[2]
Zhao Y,Li X,Chen W,et al.Whole genome survey and characterization of MADS-box gene family in maize and sorghum[J]. Plant Cell, Tissue and Organ Culture, 2011, 105(2): 159-173.
[3]
Shu Y, Yu D, Wang D,et al.Genome wide survey and expression analysis of the MADS-box gene family in soybean[J]. Molecular Biology Reports, 2013, 40(6): 3901-3911.
[4]
参考文献:
[5]
Theiβen G, Becker A, Di Rosa A,et al. A short history of MADS-box genes in plants[J]. Plant Molecular Biology, 2000, 42(1): 115-149.
[6]
Becker A, Winter K-U, Meyer B,et al. MADS-box gene diversity in seed plants 300 million years ago[J]. Molecular Biology and Evolution, 2000, 17(10): 1425-1434.
[7]
De Bodt S, Raes J, Van de Peer Y,et al. And then there were many:MADS goes genomic[J]. Trends in Plant Science, 2003, 8(10): 475-483.
[8]
Michaels S D, Amasino R M. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering[J]. The Plant Cell, 1999, 11(5): 949-956.
[9]
Hartmann U, Hhmann S, Nettesheim K,et al. Molecular cloning of SVP:a negative regulator of the floral transition in Arabidopsis[J]. The Plant Journal, 2000, 21(4): 351-360.
[10]
Samach A, Onouchi H, Gold S E,et al. Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis[J]. Science, 2000, 288: 1613-1616.
[11]
Scortecci K C, Michaels S D, Amasino R M. Identification of a MADS-box gene, FLOWERING LOCUS M, that represses flowering[J]. The Plant Journal, 2001, 26(2): 229-236.
[12]
Michaels S D, Ditta G, Gustafson-Brown C,et al. AGL24 acts as a promoter of flowering in Arabidopsis and is positively regulated by vernalization[J]. The Plant Journal, 2003, 33(5): 867-874.
[13]
Kaufmann K, Melzer R, Theiβen G. MIKC-type MADS-domain proteins:structural modularity, protein interactions and network evolution in land plants[J]. Gene, 2005, 347(2): 183-198.
[14]
Alejandra Mandel M, Gustafson-Brown C, Savidge B,et al. Molecular characterization of the Arabidopsis floral homeotic gene APETALA1[J]. Nature, 1992, 360: 273-277.
[15]
Bowman J L, Alvarez J, Weigel D,et al. Control of flower development in Arabidopsis thaliana by APETALA1 and interacting genes[J]. Development, 1993, 119(3): 721-743.
[16]
Gu Q, Ferrandiz C, Yanofsky M F,et al. The FRUITFULL MADS-box gene mediates cell differentiation during Arabidopsis fruit development[J]. Development, 1998, 125(8): 1509-1517.
[17]
Pelaz S, Ditta G S, Baumann E,et al. B and C floral organ identity functions require SEPALLATA MADS-box genes[J]. Nature, 2000, 405: 200-203.
[18]
Liljegren S J, Ditta G S, Eshed Y,et al. SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis[J]. Nature, 2000, 404: 766-770.
[19]
Nesi N, Debeaujon I, Jond C,et al. The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat[J]. The Plant Cell, 2002, 14(10): 2463-2479.
Young N D, Debelle F, Oldroyd G E,et al. The Medicago genome provides insight into the evolution of rhizobial symbioses[J]. Nature, 2011, 480: 520-524.
Finn R D, Mistry J, Schuster-Bckler B,et al. Pfam:clans, web tools and services[J]. Nucleic Acids Research, 2006, 34(S1): 247-251.
[26]
Finn R D, Clements J, Eddy S R. HMMER web server:interactive sequence similarity searching[J]. Nucleic Acids Research, 2011, 39(S2): 29-37.
[27]
Thompson J D, Higgins D G, Gibson T J. CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice[J]. Nucleic Acids Research, 1994, 22(22): 4673-4680.
Altschul S F, Madden T L, Schaffer A A,et al. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs[J]. Nucleic Acids Res, 1997, 25(17): 3389-3402.
[30]
Krzywinski M I, Schein J E, Birol I,et al. Circos:An information aesthetic for comparative genomics[J]. Genome Research, 2009, 19(9): 1639-1645.
[31]
Trapnell C, Pachter L, Salzberg S L. TopHat:discovering splice junctions with RNA-Seq[J]. Bioinformatics, 2009, 25(9): 1105-1111.
[32]
Trapnell C, Williams B A, Pertea G,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J]. Nat Biotech, 2010, 28(5): 511-515.
[33]
Zhao Y, Li X, Chen W,et al. Whole-genome survey and characterization of MADS-box gene family in maize and sorghum[J]. Plant Cell, Tissue and Organ Culture, 2011, 105(2): 159-173.
[34]
Shu Y, Yu D, Wang D,et al. Genome-wide survey and expression analysis of the MADS-box gene family in soybean[J]. Molecular Biology Reports, 2013, 40(6): 3901-3911.
[35]
Reference:
[36]
Theiβen G,Becker A,Di Rosa A,et al.A short history of MADS-box genes in plants[J]. Plant Molecular Biology, 2000, 42(1): 115-149.
[37]
Becker A,Winter K-U, Meyer B,et al.MADS-box gene diversity in seed plants 300 million years ago[J]. Molecular Biology and Evolution, 2000, 17(10): 1425-1434.
[38]
De Bodt S, Raes J,Van de Peer Y,et al.And then there were many:MADS goes genomic[J]. Trends in Plant Science, 2003, 8(10): 475-483.
[39]
Michaels S D, Amasino R M. Flowering locus cencodes a novel MADS domain protein that acts as a repressor of flowering[J]. The Plant Cell, 1999, 11(5): 949-956.
[40]
Hartmann U, H hmann S,Nettesheim K,et al. Molecular cloning of SVP:a negative regulator of the floral transition in Arabidopsis[J]. The Plant Journal, 2000, 21(4): 351-360.
[41]
Samach A, Onouchi H,Gold S E,et al. Distinct roles of constans target genes in reproductive development of Arabidopsis[J]. Science, 2000, 288: 1613-1616.
[42]
Scortecci K C,Michaels S D,Amasino R M.Identification of a MADS-box gene, flowering locus M, that represses flowering[J]. The Plant Journal, 2001, 26(2): 229-236.
[43]
Michaels S D,Ditta G,Gustafson Brown C,et al.AGL24 acts as a promoter of flowering in Arabidopsis and is positively regulated by vernalization[J]. The Plant Journal, 2003, 33(5): 867-874.
[44]
Kaufmann K, Melzer R,Theiβen G.MIKC type MADS domain proteins:structural modularity, protein interactions and network evolution in land plants[J]. Gene, 2005, 347(2): 183-198.
[45]
Alejandra Mandel M,Gustafson Brown C,Savidge B,et al. Molecular characterization of the Arabidopsis floral homeotic gene APETALA1[J]. Nature, 1992, 360: 273-277.
[46]
Bowman J L, Alvarez J,Weigel D,et al.Control of flower development in Arabidopsis thaliana by apetala 1 and interacting genes[J]. Development, 1993, 119(3): 721-743.
[47]
Gu Q, Ferrandiz C,Yanofsky M F,et al.The fruitfull MADS-box gene mediates cell differentiation during Arabidopsis fruit development[J]. Development, 1998, 125(8): 1509-1517.
[48]
Pelaz S, Ditta G S,Baumann E,et al. B and C floral organ identity functions require SEPALLATA MADS-box genes[J]. Nature, 2000, 405: 200-203.
[49]
Liljegren S J, Ditta G S, Eshed Y,et al. hatterproofMADS-box genes control seed dispersal in Arabidopsis[J]. Nature, 2000, 404: 766-770.
[50]
Nesi N, Debeaujon I, Jond C,et al.The transparent testa 16 locus encodes the Arabidopsis bsister MADS domain protein and is required for proper development and pigmentation of the seed coat[J]. The Plant Cell, 2002, 14(10): 2463-2479.
[51]
Jiang T,Lin Y X,Liu X,et al.Genome-wide analysis of the WRKY transcription factor family in Medicago truncatula[J]. Acta Prataculturae Sinica, 2011, 20(3): 211-218.
[52]
Liu Z P,Zhang J Y,Wang Y R.Research advances in genetic regulation of gametophyte development in Medicago sativa[J]. Acta Prataculturae Sinica, 2011, 20(4): 270-278.
[53]
Young N D, Debelle F,Oldroyd G E, et al.The medicago genome provides insight into the evolution of rhizobial symbioses[J]. Nature, 2011, 480: 520-524.
[54]
Lv F J,Cui M C,Chen M L.Reproductive biology of polygonum japonicum[J]. Acta Prataculturae Sinica, 2013, 22(3): 196-203.
[55]
Huang L C,Jin L,Zhang S Z,et al. Pollen release mechanisms of papilionaceous plants (Faboideae)[J]. Acta Prataculturae Sinica, 2013, 22(6): 305-314.
[56]
Finn R D, Mistry J, Schuster B ckler B,et al.Pfam: clans, web tools and services[J]. Nucleic Acids Research, 2006, 34(S1): 247-251.
[57]
Finn R D, Clements J, Eddy S R.HMMER web server: interactive sequence similarity searching[J]. Nucleic Acids Research, 2011, 39(S2): 29-37.
[58]
Thompson J D, Higgins D G, Gibson T J. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice[J]. Nucleic Acids Research, 1994, 22(22): 4673-4680.
Altschul S F, Madden T L, Schaffer A A,et al. Gapped blast and pis blast : a new generation of protein database search programs[J]. Nucleic Acids Res, 1997, 25(17): 3389-3402.
[61]
Krzywinski M I, Schein J E, Birol I, et al. Circos:An information aesthetic for comparative genomics[J]. Genome Research, 2009, 19(9): 1639-1645.
[62]
Trapnell C, Pachter L, Salzberg S L.TopHat: discovering splice junctions with RNA-Seq[J]. Bioinformatics, 2009, 25(9): 1105-1111.