메뉴 건너뛰기




Volumn 30, Issue , 2016, Pages 19-24

Exploring structural variants in environmentally sensitive gene families

Author keywords

[No Author keywords available]

Indexed keywords

PLANT PROTEIN;

EID: 84957545749     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2015.12.012     Document Type: Review
Times cited : (6)

References (48)
  • 2
    • 84862936211 scopus 로고    scopus 로고
    • Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
    • Xu X., Liu X., Ge S., Jensen J.D., Hu F., Li X., Dong Y., Gutenkunst R.N., Fang L., Huang L., et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 2011, 30:105-111.
    • (2011) Nat Biotechnol , vol.30 , pp. 105-111
    • Xu, X.1    Liu, X.2    Ge, S.3    Jensen, J.D.4    Hu, F.5    Li, X.6    Dong, Y.7    Gutenkunst, R.N.8    Fang, L.9    Huang, L.10
  • 3
    • 73649121258 scopus 로고    scopus 로고
    • Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content
    • Springer N.M., Ying K., Fu Y., Ji T., Yeh C.-T., Jia Y., Wu W., Richmond T., Kitzman J., Rosenbaum H., et al. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 2009, 5:e1000734.
    • (2009) PLoS Genet , vol.5 , pp. e1000734
    • Springer, N.M.1    Ying, K.2    Fu, Y.3    Ji, T.4    Yeh, C.-T.5    Jia, Y.6    Wu, W.7    Richmond, T.8    Kitzman, J.9    Rosenbaum, H.10
  • 6
    • 70449704529 scopus 로고    scopus 로고
    • Computational methods for discovering structural variation with next-generation sequencing
    • Medvedev P., Stanciu M., Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 2009, 6:S13-S20.
    • (2009) Nat Methods , vol.6 , pp. S13-S20
    • Medvedev, P.1    Stanciu, M.2    Brudno, M.3
  • 7
    • 69749122557 scopus 로고    scopus 로고
    • Sensitive and accurate detection of copy number variants using read depth of coverage
    • Yoon S., Xuan Z., Makarov V., Ye K., Sebat J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 2009, 19:1586-1592.
    • (2009) Genome Res , vol.19 , pp. 1586-1592
    • Yoon, S.1    Xuan, Z.2    Makarov, V.3    Ye, K.4    Sebat, J.5
  • 8
    • 79954672317 scopus 로고    scopus 로고
    • Genome structural variation discovery and genotyping
    • Alkan C., Coe B.P., Eichler E.E. Genome structural variation discovery and genotyping. Nat Rev Genet 2011, 12:363-376.
    • (2011) Nat Rev Genet , vol.12 , pp. 363-376
    • Alkan, C.1    Coe, B.P.2    Eichler, E.E.3
  • 9
    • 84927128250 scopus 로고    scopus 로고
    • Whole-genome CNV analysis: advances in computational approaches
    • Pirooznia M., Goes F.S., Zandi P.P. Whole-genome CNV analysis: advances in computational approaches. Front Genet 2015, 6:138.
    • (2015) Front Genet , vol.6 , pp. 138
    • Pirooznia, M.1    Goes, F.S.2    Zandi, P.P.3
  • 10
    • 77958462555 scopus 로고    scopus 로고
    • Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales
    • DeBolt S. Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol Evol 2010, 2:441-453.
    • (2010) Genome Biol Evol , vol.2 , pp. 441-453
    • DeBolt, S.1
  • 12
    • 84868016827 scopus 로고    scopus 로고
    • Statistical challenges associated with detecting copy number variations with next-generation sequencing
    • Teo S.M., Pawitan Y., Ku C.S., Chia K.S., Salim A. Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics 2012, 28:2711-2718.
    • (2012) Bioinformatics , vol.28 , pp. 2711-2718
    • Teo, S.M.1    Pawitan, Y.2    Ku, C.S.3    Chia, K.S.4    Salim, A.5
  • 17
    • 0037390933 scopus 로고    scopus 로고
    • Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis
    • Meyers B.C. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell Online 2003, 15:809-834.
    • (2003) Plant Cell Online , vol.15 , pp. 809-834
    • Meyers, B.C.1
  • 20
    • 57149089296 scopus 로고    scopus 로고
    • Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids
    • Lyons E., Pedersen B., Kane J., Alam M., Ming R., Tang H., Wang X., Bowers J., Paterson A., Lisch D., et al. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol 2008, 148:1772-1781.
    • (2008) Plant Physiol , vol.148 , pp. 1772-1781
    • Lyons, E.1    Pedersen, B.2    Kane, J.3    Alam, M.4    Ming, R.5    Tang, H.6    Wang, X.7    Bowers, J.8    Paterson, A.9    Lisch, D.10
  • 25
    • 84923019049 scopus 로고    scopus 로고
    • De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
    • Li Y., Zhou G., Ma J., Jiang W., Jin L., Zhang Z., Guo Y., Zhang J., Sui Y., Zheng L., et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 2014, 32:1045-1052.
    • (2014) Nat Biotechnol , vol.32 , pp. 1045-1052
    • Li, Y.1    Zhou, G.2    Ma, J.3    Jiang, W.4    Jin, L.5    Zhang, Z.6    Guo, Y.7    Zhang, J.8    Sui, Y.9    Zheng, L.10
  • 27
    • 78049405533 scopus 로고    scopus 로고
    • Bin: numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors
    • Zhang M., Wu Y.H., Lee M.K., Liu Y.H., Rong Y., Santos T.S., Wu C., Xie F., Nelson R.L., Zhang H. Bin: numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors. Nucleic Acids Res 2010, 38:6513-6525.
    • (2010) Nucleic Acids Res , vol.38 , pp. 6513-6525
    • Zhang, M.1    Wu, Y.H.2    Lee, M.K.3    Liu, Y.H.4    Rong, Y.5    Santos, T.S.6    Wu, C.7    Xie, F.8    Nelson, R.L.9    Zhang, H.10
  • 28
    • 80053598318 scopus 로고    scopus 로고
    • Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis
    • Guo Y.-L., Fitz J., Schneeberger K., Ossowski S., Cao J., Weigel D. Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis. Plant Physiol 2011, 157:757-769.
    • (2011) Plant Physiol , vol.157 , pp. 757-769
    • Guo, Y.-L.1    Fitz, J.2    Schneeberger, K.3    Ossowski, S.4    Cao, J.5    Weigel, D.6
  • 29
    • 0038663127 scopus 로고    scopus 로고
    • A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs
    • Mergaert P., Nikovics K., Kelemen Z., Maunoury N., Vaubert D., Kondorosi A., Kondorosi E. A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs. Plant Physiol 2003, 132:161-173.
    • (2003) Plant Physiol , vol.132 , pp. 161-173
    • Mergaert, P.1    Nikovics, K.2    Kelemen, Z.3    Maunoury, N.4    Vaubert, D.5    Kondorosi, A.6    Kondorosi, E.7
  • 30
    • 3543042528 scopus 로고    scopus 로고
    • Computational identification and characterization of novel genes from legumes
    • Graham M.A., Silverstein K.A.T., Cannon S.B., VandenBosch K.A. Computational identification and characterization of novel genes from legumes. Plant Physiol 2004, 135:1179-1197.
    • (2004) Plant Physiol , vol.135 , pp. 1179-1197
    • Graham, M.A.1    Silverstein, K.A.T.2    Cannon, S.B.3    VandenBosch, K.A.4
  • 31
    • 34548017391 scopus 로고    scopus 로고
    • Genomic organization and evolutionary insights on GRP and NCR genes, two large nodule-specific gene families in Medicago truncatula
    • Alunni B., Kevei Z., Redondo-Nieto M., Kondorosi A., Mergaert P., Kondorosi E. Genomic organization and evolutionary insights on GRP and NCR genes, two large nodule-specific gene families in Medicago truncatula. Mol Plant Microbe Interact 2007, 20:1138-1148.
    • (2007) Mol Plant Microbe Interact , vol.20 , pp. 1138-1148
    • Alunni, B.1    Kevei, Z.2    Redondo-Nieto, M.3    Kondorosi, A.4    Mergaert, P.5    Kondorosi, E.6
  • 32
    • 84934993109 scopus 로고    scopus 로고
    • Plant cysteine-rich peptides that inhibit pathogen growth and control rhizobial differentiation in legume nodules
    • Maróti G., Downie J.A., Kondorosi É. Plant cysteine-rich peptides that inhibit pathogen growth and control rhizobial differentiation in legume nodules. Curr Opin Plant Biol 2015, 26:57-63.
    • (2015) Curr Opin Plant Biol , vol.26 , pp. 57-63
    • Maróti, G.1    Downie, J.A.2    Kondorosi, É.3
  • 34
    • 84875639791 scopus 로고    scopus 로고
    • Regulatory patterns of a large family of defensin-like genes expressed in nodules of Medicago truncatula
    • Nallu S., Silverstein K.A.T., Samac D.A., Bucciarelli B., Vance C.P., VandenBosch K.A. Regulatory patterns of a large family of defensin-like genes expressed in nodules of Medicago truncatula. PLoS ONE 2013, 8:e60355.
    • (2013) PLoS ONE , vol.8 , pp. e60355
    • Nallu, S.1    Silverstein, K.A.T.2    Samac, D.A.3    Bucciarelli, B.4    Vance, C.P.5    VandenBosch, K.A.6
  • 37
    • 0000354617 scopus 로고    scopus 로고
    • The Arabidopsis Genome Initiative: analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative: analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 39
    • 3042575125 scopus 로고    scopus 로고
    • Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes
    • Zhou T., Wang Y., Chen J.Q., Araki H., Jing Z., Jiang K., Shen J., Tian D. Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Genet Genomics 2004, 271:402-415.
    • (2004) Mol Genet Genomics , vol.271 , pp. 402-415
    • Zhou, T.1    Wang, Y.2    Chen, J.Q.3    Araki, H.4    Jing, Z.5    Jiang, K.6    Shen, J.7    Tian, D.8
  • 40
    • 84859498261 scopus 로고    scopus 로고
    • Sequencing Consortium TPG: genome sequence and analysis of the tuber crop potato
    • Sequencing Consortium TPG: genome sequence and analysis of the tuber crop potato. Nature 2011, 475:189-195.
    • (2011) Nature , vol.475 , pp. 189-195
  • 42
    • 84942371526 scopus 로고    scopus 로고
    • Exploring the rice dispensable genome using a metagenome-like assembly strategy
    • Yao W., Li G., Zhao H., Wang G., Lian X., Xie W. Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biol 2015, 16:187.
    • (2015) Genome Biol , vol.16 , pp. 187
    • Yao, W.1    Li, G.2    Zhao, H.3    Wang, G.4    Lian, X.5    Xie, W.6
  • 45
    • 84890034912 scopus 로고    scopus 로고
    • Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
    • Burton J.N., Adey A., Patwardhan R.P., Qiu R., Kitzman J.O., Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol 2013, 31:1119-1125.
    • (2013) Nat Biotechnol , vol.31 , pp. 1119-1125
    • Burton, J.N.1    Adey, A.2    Patwardhan, R.P.3    Qiu, R.4    Kitzman, J.O.5    Shendure, J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.