Jiang Lab

2022

Zhao, H.N., Yang, M.Y., Bishop, J., Teng, Y.H., Cao, Y.X., Beall, B.D., Li, S.L., Liu, T.X., Fang, Q.X., Fang, C., Xin, H.Y., Nützmann, H.-W., Osbourn, A., Meng, F.L., and Jiang, J.M. (2022) Identification and functional validation of super-enhancers in Arabidopsis thaliana. PNAS 119: e2215328119 (doi: 10.1073/pnas.2215328119).

Faculty Opinions: https://facultyopinions.com/article/742418289

 

Bethke, P.C, Halterman, D.A., Francis, D.M., Jiang, J.M., Douches, D.S., Charkowski, A.O., and Parsons, J. (2022) Diploid potatoes as a catalyst for change in the potato industry. Am. J. Potato Res. (doi: 10.1007/s12230-022-09888-x).

 

Zhang, A.C., Li, X.X., Zhao, H.N., Jiang, J.M., and Zhang, W.L. (2022) Genome-wide identification of open chromatin in plants using MH-seq. Methods Mol. Biol. 2594: 29-43 (doi: 10.1007/978-1-0716-2815-7_3)

 

Planta, J., Liang, Y.-Y., Xin, H.Y., Chansler, M.T., Prather, L.A., Jiang, N., Jiang, J.M., and Childs, K.L. (2022) Chromosome scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus and Juncus inflexus. G3. (doi: 10.1093/g3journal/jkac211).

 

Shi, P.Y., Sun, H.J., Liu, G.Q., Zhang, X., Zhou, J.W., Song, R.R., Xiao, J., Yuan, C.X., Sun, L., Wang, Z.K., Lou, Q.F., Jiang, J.M., Wang, X.E.and Wang, H.Y. (2022) Chromosome painting reveals inter-chromosomal rearrangements and evolution of the D subgenome of wheat. Plant J. (doi: 10.1111/tpj.15926).

 

Hoopes, G., Meng, X.X., Hamilton, J.P., Achakkagari, S.R., Guesdes, F. de A.F., Bolger, M.E., Coombs, J.J., Esselink, D., Kaiser, N.R., Kodde, L., Kyriakidou, M., Lavrijssen, B., van Lieshout, N., Shereda, R., Tuttle, H.K., Vaillancourt, B., Wood, J.C., de Boer, J.M., Bornowski, N., Bourke, P., Douches, D., van Eck, H.J., Ellis, D., Feldman, M.J., Gardner, K.M., Hopman, J.C.P., Jiang, J.M., De Jong, W.S., Kuhl, J.C., Novy, R.G., Oome, S., Sathuvalli, V., Tan, E.H., Ursum, R.A., Vales, M.I., Vining, K., Visser, R.G.F., Vossen, J., Yencho, G.C., Anglin, N.L., Bachem, C.W.B., Endelman, J.B., Shannon, L.M., Strömvik, M.V., Tai, H.H., Usadel, B., Buell, C.R., and Finkers, R. (2022) Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol. Plant (doi: 10.1016/j.molp.2022.01.003).

 

Yu, F., Zhao, X.W., Chai, J., Ding, X., Li, X.T., Huang, Y.J., Wang, X.H., Wu, J.Y., Zhang, M.Q., Yang, Q.H., Deng, Z.H., and Jiang, J.M. (2022) Chromosome-specific painting unveils chromosomal fusions and distinct allopolyploid species in the Saccharum complex. New Phytol. 233: 1953-1965 (doi: 10.1111/nph.17905).

 

2021

Huang, Y.M., Huang, W., Meng, Z., Braz, G.T., Li, Y.F., Wang, K., Wang, H., Lai, J.S., Jiang, J.M., Dong, Z.B., and Jin, W.W. (2021) Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation. Genome Biol. 22: 237 (doi: 10.1186/s13059-021-02448-2).

 

Bustamante, F.D., do Nascimento, T.H., Montenegro, C., Dias, S., Martins, L.D., Braz, G.T., Benko-Iseppon, A.M., Jiang, J.M., Pedrosa-Harand, A., and Brasileiro-Vidal, A.C. (2021) Oligo-FISH barcode in beans: a new chromosome identification system. Theor. Appl. Genet. (doi: 10.1007/s00122-021-03921-z).

 

Zhang, T., Liu, G.Q., Zhao, H.N., Braz, G.T., and Jiang, J.M. (2021)Chorus2: design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization.Plant Biotech. J. (doi: 10.1111/pbi.13610).

 

Martins, L. do Vale, Bustamante, F. de Oliveira, Oliveira, A.R. da Silva, da Costa, A.F., Feitoza, L. de Lima, Liang, Q.H., Zhao, H.N., Benko-Iseppon, A.M., Muñoz-Amatriaín, M., Pedrosa-Harand, A., Jiang, J.M., and Brasileiro-Vidal, A.C. (2021) BAC- and oligo-FISH mapping reveals chromosome evolution among Vigna angularis, V. unguiculata, and Phaseolus vulgaris.Chromosoma (doi: 10.1007/s00412-021-00758-9).

 

Meng, F.L., Zhao, H.N., Zhu, B., Zhang, T., Yang, M.Y., Li, Y., Han, Y.P., and Jiang, J.M. (2021)Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana.Plant Cell (doi: 10.1093/plcell/koab093).

Highlighted by: Vadde, B.V.L. (2021) Not-so-selfish-DNA? Intronic enhancers fine-tune spatio-temporal gene expression.Plant Cell (doi: 10.1093/plcell/koab095).

 

Brose, J., Lau, K.H., Dang, T.T.T., Hamilton, J.P., Martins, L. do Vale, Hamberger, B., Hamberger, B., Jiang, J.M., O’Connor, S., and Buell, C.R. (2021) The Mitragyna speciosa (Kratom) genome: A resource for data-mining potent pharmaceuticals that impact human health.G3 (doi: 10.1093/g3journal/jkab058).

 

Lin, Y., Zhao, H.N., Kotlarz, M., and Jiang, J.M. (2021) Enhancer-mediated reporter gene expression in Arabidopsis thaliana: a forward genetic screen.Plant J. (doi: 10.1111/tpj.15189).

 

Lovell, J.T., MacQueen, A.H., Mamidi, S., Bonnette, J., Jenkins, J., Napier, J.D., Sreedasyam, A., Healey, A., Session, A., Shu, S.Q., Barry, K., Bonos, S., Boston, L., Daum, C., Deshpande, S., Ewing, A., Grabowski, P.P., Haque, T., Harrison, M., Jiang, J.M., Kudrna, D., Lipzen, A., Pendergast IV T.H., Plott, C., Qi, P., Saski, C.A., Shakirov, E.V., Sims, D., Sharma, M., Sharma, R., Stewart, A., Singan, V.R., Tang, Y.H., Thibivillier, S., Webber, J., Weng, X.Y., Williams, M., Wu, G.A., Yoshinaga, Y., Zane, M., Zhang, L., Zhang, J.Y., Behrman, K.D., Boe, A.R., Fay, P.A., Fritschi, F.B., Jastrow, J.D., Lloyd-Reilley, J., Martínez-Reyna, J.M., Matamala, R., Mitchell, R.B., Rouquette Jr, F.M., Ronald, P., Saha, M., Tobias, C.M., Udvardi, M., Wing, R., Wu, Y.Q., Bartley, L.E., Casler, M., Devos, K.M., Lowry, D.B., Rokhsar, D.S., Grimwood, J., Juenger, T.E., and Schmutz, J. (2021)Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature (doi: 10.1038/s41586-020-03127-1).

 

Salam, B.B., Barbier, F., Danieli, R., Teper-Bamnolker, P., Ziv, C., Spíchal, L., Aruchamy, K., Shnaider, Y., Leibman, D., Shaya, F., Carmeli-Weissberg, M., Gal-On, A., Jiang, J.M., Ori, N., Beveridge, C., and Eshel, D. (2021) Sucrose promotes stem branching through cytokinin. Plant Physiol. (doi: 10.1093/plphys/kiab003).

 

2020

Braz, G.T., Yu, F., Zhao, H.N., Deng, Z.H., Birchler, J.A., and Jiang, J.M. (2020) Preferential meiotic chromosome pairing among homologous chromosomes with cryptic sequence variation in tetraploid maize.New Phytologist (doi: 10.1111/nph.17098).

 

Pham, G.M., Hamilton, J.P., Wood, J.C., Burke, J.T., Zhao, H.Z., Vaillancourt, B., Ou, S.J., Jiang, J.M., and Buell, C.R. (2020) Construction of a chromosome-scale long-read reference genome assembly for potato. GigaScience 9 (doi: 10.1093/gigascience/giaa100).

 

Hamilton, J.P., Godden, G.T., Lanier, E., Bhat, W.W., Kinser, T.J., Vaillancourt, B., Wang, H.Y., Wood, J.C., Jiang, J.M., Soltis, P.S., Soltis, D.E., Hamberger, B., and Buell, C.R. (2020) Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana. GigaScience 9 (doi: 10.1093/gigascience/giaa093).

 

He, L., Zhao, H.N., He, J., Yang, Z.J., Guan, B., Chen, K.L., Hong, Q.B., Wang, J.H., Liu, J.J., and Jiang, J.M. (2020)Extraordinarily conserved chromosomal synteny of Citrus species revealed by chromosome-specific painting. Plant J. (doi: 10.1111/tpj.14894).

 

Braz, G.T., Yu, F., Martins, L. do Vale, and Jiang, J.M. (2020) Fluorescent in situ hybridization using oligonucleotide-based probes. Methods Mol. Biol. 2148: 71-83 (doi: 10.1007/978-1-0716-0623-0_4).

 

Braz, G.T., Martins, L. do Vale, Zhang, T., Albert, P.S., Birchler, J.A., and Jiang, J.M. (2020) A universal chromosome identification system for maize and wild Zea species. Chromosome Res. (doi: 10.1007/s10577-020-09630-5).

 

Butler, N.M., Jansky, S.H., and Jiang, J.M. (2020) First generation genome editing in potato using hairy root transformation. Plant Biotech. J. (doi: 10.1111/pbi.13376).

 

Zhao, H.N., Zhang, W.Z., Zhang, T., Lin, Y., Hu, Y.D., Fang, C., and Jiang, J.M. (2020) Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biol. 21: 24.

 

Sanchez, P.A.G., Babujee, L., Mesa, H.J., Arcibal, E., Gannon, M., Halterman, D., Jahn, M., Jiang, J.M., and Rakotondrafara, A.M. (2020) Overexpression of a modified eIF4E regulates Potato virus Y resistance at the transcriptional level in potato. BMC Genomics 21: 18.

 

2019

Martins, L. do Vale, Yu, F., Zhao, H.N., Dennison, T., Lauter, N., Wang, H.Y., Deng, Z.H., Thompson, A., Semrau, K., Rouillard, J.-M., Birchler, J.A., and Jiang, J.M (2019) Meiotic crossovers characterized by haplotype-specific chromosome painting in maize. Nat. Commu. 10: 4604.

 

Xin, H.Y., Zhang, T., Wu, Y.F., Zhang, W.L., Zhang, P.D., Xi, M.L., and Jiang, J.M. (2019) An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. Plant J. (doi: 10.1111/tpj.14536).

 

Alvarez, J.M., Moyano, T.C., Zhang, T., Gras, D.E., Herrera, F.J., Araus, V., O’Brien, J.A., Carrillo, L., Medina, J., Vicente-Carbajosa, J., Jiang, J.M., and Gutiérrez, R.A. (2019) Local changes in chromatin accessibility and transcriptional networks underlying the nitrate response in Arabidopsis roots. Mol. Plant (doi: 10.1016/j.molp.2019.09.002).

 

Liu, X.Y., Sun, S., Wu, Y., Zhou, Y., Gu, S.W., Yu, H.X., Yi, C.D., Gu, M.H., Jiang, J.M., Liu, B., Zhang, T., and Gong, Z.Y. (2019) Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species. Plant J. (doi: 10.1111/tpj.14522).

 

Zeng, Z.X., Zhang, W.L., Marand, A.P., Zhu, B., Buell, C.R., and Jiang, J.M. (2019) Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato. Genome Biol. 20: 123.

 

Pham, G.M., Braz, G.T., Conway, M., Crisovan, E., Halmilton, J.P., Laimbeer, F.P.E., Manrique-Carpintero, N., Newton, L., Douches, D.S., Jiang, J.M., Veilleux, R.E., and Buell, C.R. (2019) Genome-wide inference of somatic translocation events during potato dihaploid production. Plant Genome 12: 180079.

 

Marand, A.P., Jansky, S.H., Gage, J.L., Hamernik, A.J., de Leon, N., Jiang, J.M. (2019) Residual heterozygosity and epistatic interactions underlie the complex genetic architecture of yield in diploid potato. Genetics 212: 317-332.

 

Jiang, J.M. (2019) Fluorescence in situ hybridization in plants: recent development and future applications. Chromosome Res. 27: 153-165.

 

Lin, Y., Meng, F.L., Fang, C., Zhu, B., and Jiang, J.M. (2019) Rapid validation of transcriptional enhancers using agrobacterium-mediated transient assay. Plant Methods 15: 21.

 

Marand, A.P., Zhao, H.N., Zhang, W.L., Zeng, Z.X., Fang, C., and Jiang, J.M. (2019) Historical meiotic crossover hotspots fueled patterns of evolutionary divergence in rice. Plant Cell 31: 645-662.

Faculty of 1000 Biology: https://f1000.com/prime/734986434.

 

Albert, P.S., Zhang, T., Semrau, K., Rouillard, J.-M., Kao, Y.-H., Wang, C.-J. R., Danilova, T.V., Jiang, J.M., and Birchler, J.A. (2019) Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. Proc. Natl. Acad. Sci. USA 116: 1679-1685.

 

2018

He, L., Braz, G.T., Torres, G.A., and Jiang, J.M. (2018) Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species. Chromosoma 127: 505-513.

 

Wu, S., Lau, K.H., Cao, Q.H., Hamilton, J.P., Sun, H.H., Zhou, C.X., Eserman, L., Gemenet, D.C., Olukolu, B.A., Wang, H.Y., Crisovan, E., Godden, G.T., Jiao, C., Wang, X., Kitavi, M., Manrique-Carpintero, N., Vaillancourt, B., Wiegert-Rininger, K., Yang, X.S., Bao, K., Schaff, J., Kreuze, J., Gruneberg, W., Khan, A., Ghislain, M., Ma, D.F., Jiang, J.M., Mwanga, R.O.M., Leebens-Mack, J., Coin, L.J.M., Yencho, G.C., Buell, C.R., and Fei, Z.J. (2018) Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nat. Commu. 9: 4580.

 

Liao, Y., Zhang, X.M., Li, B., Liu, T.Y., Chen, J.F., Bai, Z.T., Wang, M.J., Shi, J.F., Walling, J.G., Wing, R., Jiang, J.M., and Chen, M.S. (2018) Comparison of Oryza sativa and Oryza brachyantha genomes reveals selection-driven gene escape from the centromeric regions. Plant Cell 30: 1729-1744.

 

Wu, L., Duangpan, S., Bhaskar, P.B., Wielgus, S.M., and Jiang, J.M. (2018) Constitutively expressed RB gene confers a high level but unregulated resistance to potato late blight. Am. J. Potato Res. 95: 575-583.

 

Hou, L.L., Xu, M., Zhang, T., Xu, Z.H., Wang, W.Y., Zhang, J.X., Yu, M.M., Ji, W., Zhu, C.W., Gong, Z.Y., Gu, M.H., Jiang, J.M., Yu, H.X. (2018) Chromosome painting and its applications in cultivated and wild rice. BMC Plant Biol. 18: 110.

 

Yang, X.M., Zhao, H.N., Zhang, T., Zeng, Z.X., Zhang, P.D., Zhu, B., Han, Y.H., Braz, G.T., Casler, M.D., Schmutz, J., and Jiang, J.M. (2018) Amplification and adaptation of centromeric repeats in polyploid switchgrass species. New Phytol. 218: 1645-1657.

 

Dong, Z.B., Yu, J., Li, H., Huang, W., Xu, L., Zhao, Y., Zhang, T., Xu, W.Y., Jiang, J.M., Su, Z., Jin, W.W. (2018) Transcriptional and epigenetic adaptation of maize chromosomes in oat-maize addition lines. Nucleic Acids Res. 46: 5012-5028.

 

Xin, H.Y., Zhang, T., Han, Y.H., Wu, Y.F., Shi, J.S., Xi, M.L., and Jiang, J.M. (2018) Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides. Chromosoma 127: 313-321.

 

Koo, D.-H., Molin, W.T., Saski, C.A., Jiang, J.M., Putta, K., Jugulum, M., Friebe, B., and Gill, B.S. (2018) Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri. Proc. Natl. Acad. Sci. USA 115: 3332-3337.

 

Zhao, H.N., Zhang, W.L., Chen, L.F., Wang, L., Marand, A.P., Wu, Y.F., and Jiang, J.M. (2018) Proliferation of regulatory DNA elements derived from transposable elements in the maize genome. Plant Physiol. 176: 2789-2803.

 

Leisner, C.P., Hamilton, J.P., Crisovan, E., Manrique-Carpintero, N.C., Marand, A.P., Newton, L., Pham, G.M., Jiang, J.M., Douches, D.S., Jansky, S.H., and Buell, C.R. (2018) Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity. Plant J. 94: 562-570.

 

Zhao, D.Y., Hamilton, J.P., Vaillancourt, B., Zhang, W.L., Eizenga, G.C., Cui, Y.H., Jiang, J.M., Buell, C.R., and Jiang, N. (2018) The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum. Nucleic Acids Res. 46: 2380-2397.

 

Braz, G.T., He, L., Zhao, H.N., Zhang, T., Semrau, K., Rouillard, J.-M., Torres, G.A., and Jiang, J.M. (2018) Comparative oligo-FISH mapping: an efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics. 208: 513-523.

 

2017

Marand, A.P., Jansky, S.H., Zhao, H.N., Leisner, C.P., Zhu, X.B., Zeng, Z.X., Crisovan, E., Newton, L., Hamernik, A.J., Veilleux, R.E., Buell, C.R., Jiang, J.M. (2017) Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato. Genome Biol. 18: 203.

 

Butler, N.M., Jiang J.M. and Stupar, R.M. (2017) Crop improvement using genome editing. Plant Breeding Reviews 41: 55-101.

 

Zhao, H.N., Zeng, Z.X., Koo, D.-H., Gill, B.S., Birchler, J.A. and Jiang, J.M. (2017) Recurrent establishment of de novo centromeres in the pericentromeric region of maize chromosome 3. Chromosome Res. 25: 299-311.

 

Salam, B.B., Malka, S.K., Zhu, X.B., Gong, H.L., Ziv, C., Teper-Bamnolker, P., Ori, N., Jiang, J.M., and Eshel, D. (2017) Etiolated stem branching is a result of systemic signaling associated with sucrose level. Plant Physiol. 175: 734-745.

 

Liu, Y., Zhang, W.L., Zhang, K., You, Q., Yan, H.Y., Jiao, Y.N., Jiang, J.M., Xu, W.Y., and Su, Z. (2017) Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness. Scientific Rep. 7: 4093.

 

Bilinski, P., Han, Y.H., Hufford, M.B., Lorant, A., Zhang, P.D., Estep, M.C., Jiang, J.M., and Ross-Ibarra, J. (2017) Genomic abundance is not predictive of tandem repeat localization in grass genomes. PLoS ONE. 12: e0177896.

 

Xuanyuan, G.C., Lu, C.M., Zhang, R.F., and Jiang, J.M. (2017) Overexpression of StNF-YB3.1 reduces photosynthetic capacity and tuber production, and promotes ABA-mediated stomatal closure in potato (Solanum tuberosum L.).. Plant science. 261:50-59.

 

Zhao, D.Y., Hamilton, J.P., Hardigan, M., Yin, D.M., He, T., Vaillancourt, B., Reynoso, M., Pauluzzi, G., Funkhouser, S., Cui, Y.H., Bailey-Serres, J., Jiang, J.M., Buell, C.R., and Jiang, N. (2017) Analysis of ribosome-associated mRNAs in rice reveals the importance of transcript size and GC content in translation. G3. 7:203-219.

 

Marand, A.P., Zhang, T., Zhu, B., and Jiang, J.M. (2017) Towards genome-wide prediction and characterization of enhancers in plants. BBA - Gene Regulatory Mechanisms. 1860:131-139.

 

2016

Koo, D.-H., Zhao, H.N. and Jiang, J.M. (2016) Chromatin-associated transcripts of tandemly repetitive DNA sequences revealed by RNA-FISH. Chromosome Res. 24: 467-480 (doi: 10.1007/s10577-016-9537-5).

 

Jansky, S.H., Charkowski, A.O., Douches, D.S., Gusmini, G., Richael, C., Bethke, P.C., Spooner, D.M., Novy, R.G., De Jong, H., De Jong, W.S., Bamberg, J.B., Thompson, A.L., Bizimungu, B., Holm, D.G., Brown, C.R., Haynes, K.G., Sathuvalli, V.R., Veilleux, R.E., Miller, J.C., Bradeen, J.M., and Jiang, J.M. (2016) Reinventing potato as a diploid inbred line-based crop. Crop Sci. 56: 1412-1422.

 

Zeng, Z.X. and Jiang J.M. (2016) Isolation and proteomics analysis of barley centromeric chromatin using PICh. J. Proteome Res. 15: 1875-1882.

 

Hardigan, M.A., Crisovan, E., Hamilton, J.P., Kim, J., Laimbeer, P., Leisner, C.P., Manrique-Carpintero, N.C., Newton, L., Pham, G.M., Vaillancourt, B., Yang, X.M., Zeng, Z.X., Douches, D.S., Jiang, J.M., Veilleux, R.E., Buell, C.R. (2016) Genomic reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum. Plant Cell 28: 388-405.

 

Khrustaleva, L., Jiang, J.M., and Havey, M.J. (2016)High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion. Theor. Appl. Genet. 129: 535-545.

 

Arcibal, E., Gold, K.M., Flaherty, S., Jiang, J.M., Jahn, M., and Rakotondrafara, A.M. (2016) A mutant eIF4E confers differential resistance to potato virus Y strains and is inherited in a dominant manner in the potato varieties Atlantic and Russet Norkotah. Am. J. Potato Res. 93: 64-71.

 

Zhu, X.B., Gong, H.L., He, Q.Y., Zeng, Z.X., Busse, J.S., Jin, W.W., Bethke, P.C., and Jiang, J.M. (2016) Silencing of vacuolar invertase and asparagine synthetase genes and its impact on acrylamide formation of fried potato products. Plant Biotech. J. 14: 709-718.

 

Zhao, H.N., Zhu, X.B., Wang, K., Gent, J.I., Zhang, W.L., Dawe, R.K., and Jiang, J.M. (2016) Gene expression and chromatin modifications associated with maize centromeres. G3 6: 183-192.

 

Zhang, T., Marand, A.P., and Jiang, J.M. (2016) PlantDHS:a database for DNase I hypersensitive sites in plants. Nucleic Acids Res. 44: D1148-D1153.

 

2015

Zhu, B., Zhang, W.L., Zhang, T., Liu, B., and Jiang, J.M. (2015) Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures. Plant Cell 27:2415-2426

 

Lough, A.N., Faries, K.M., Koo, D.-H., Hussain, A., Roark, L.M., Langewisch, T.L., Backes, T., Kremling, K.A.G., Jiang, J.M., Birchler, J.A., and Newton, K.J. (2015) Cytogenetic and sequence analyses of mitochondrial DNA insertions in nuclear chromosomes of maize. G3 5:2229-2239

 

Zhang, T., Zhang, W.L., and Jiang, J.M. (2015) Genome-wide nucleosome occupancy and positioning and their impact on gene expression and evolution in plants. Plant Physiol. 168: 1406-1416.

 

Gent, J.I., Wang, K., Jiang, J.M., and Dawe, R.K. (2015) Stable patterns of CENH3 occupancy through maize lineages containing genetically similar centromeres. Genetics 200: 1105-1116.

 

Han, Y.H., Zhang, T., Thammapichai, P., Weng, Y.Q., and Jiang, J.M. (2015)Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics 200: 771-779.

 

Gao, D.Y., Jiang, N., Wing, R.A., Jiang, J.M., and Jackson, S.A (2015) Transposons play an important role in the evolution and diversification of centromeres among closely related species. Front. Plant Sci. 6: 216

 

Zhang, W.L. and Jiang, J.M. (2015)Genome-wide mapping of DNase I hypersensitive sites in plants. Methods Mol Biol.1284: 71-89.

 

Jiang, J.M. (2015) The ‘dark matter’ in the plant genomes: non-coding and unannotated DNA sequences associated with open chromatin. Curr. Opin. Plant Biol. 24: 17-23.

 

Iovene, M., Yu, Q.Y., Ming, R., and Jiang, J.M. (2015) Evidence for emergence of sex-determining gene(s) in a centromeric region in Vasconcellea parviflora. Genetics 199: 413-421.

 

2014

Zhang, W.L., Zhang, T., Wu, Y.F., and Jiang, J.M. (2014) Open chromatin in plant genomes. Cytogenet. Genome Res. 143: 18-27.

 

Cook, D.E., Bayless, A.M., Wang, K., Guo, X.L., Song, Q.J., Jiang, J.M., Bent, A.F. (2014) Distinct copy number, coding sequence, and locus methylation patterns underlie Rhg1-mediated soybean resistance to soybean cyst nematode. Plant Physiol. 165: 630-647.

 

Wu, Y.F., Zhang, W.L., and Jiang, J.M. (2014) Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice.PLoS Genet. 10: e1004378.

 

Zhang, H.Q., Koblížková, A., Wang, K., Gong, Z.Y., Oliveira, L., Torres, G.A., Wu, Y.F., Zhang, W.L., Novák, P., Buell, C.R., Macas, J., and Jiang, J.M. (2014) Boom-bust turnovers of megabase-sized centromeric DNA in Solanum species: Rapid evolution of DNA sequences associated with centromeres. Plant Cell 26: 1436-1447.

 

Zhu, X.B., Richael, C., Chamberlain, P., Busse, J.S.,  Bussan, A.J., Jiang, J.M., Bethke, P.C. (2014) Vacuolar invertase gene silencing in potato (Solanum tuberosum L.) improves processing quality by decreasing the frequency of sugar-end defects. PLoS ONE 9: e93381.

 

Wang, L.S., Zeng, Z.X., Zhang, W.L., and Jiang, J.M. (2014) Three potato centromeres are associated with distinct haplotypes with or without megabase-sized satellite repeat arrays. Genetics 196: 397-401.

 

Wang, K., Wu, Y.F., Zhang, W.L., Dawe, R.K., and Jiang, J.M. (2014) Maize centromeres expand and adopt a uniform size in the genetic background of oat. Genome Res. 24: 107-116.

Faculty of 1000 Biology: http://f1000.com/prime/718135806

 

Yang, L.M., Koo, D.-H., Li, D.W., Zhang, T., Jiang, J.M., Luan, F.S., Renner, S.S., Hénnaff, E., Sanseverino, W., Garcia-Mas, J., Casacuberta, J., Senalik, D.A., Simon, P.W., Chen, J.F., Weng, Y.Q. (2014) Next-generation sequencing, FISH mapping, and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis. Plant J. 77: 16-30.

 

2013

Zhang, T., Talbert, P.B., Zhang, W.L., Wu, Y.F., Yang, Z.J., Henikoff, J., Henikoff, S., and Jiang, J.M. (2013) The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres. Proc. Natl. Acad. Sci. USA 110: E4875-E4883.

Commentary:  Heslop-Harrison, J.S. and Schwarzacher, T. (2013) Nucleosomes and centromeric DNA packaging. Proc. Natl. Acad. Sci. USA 110: 19974-19975.

 

Duangpan, S., Zhang, W.L., Wu, Y.F., Jansky, S.H., and Jiang, J.M. (2013) Insertional mutagenesis using Tnt1 retrotransposon in potato. Plant Physiol. 163: 21-29.

 

Iovene, M., Zhang, T., Lou, Q.F., Buell, C.R., Jiang, J.M. (2013) Copy number variation in potato - an asexually propagated autotetraploid species. Plant J. 75: 80-90.

 

Chen, J.F., Huang, Q.F., Gao, D.Y., Wang, J.Y., Lang, Y.S., Liu, T.Y., Li, B., Bai, Z.T., Goicoechea, J.L., Liang, C.Z., Chen, C.B., Zhang, W.L., Sun, S.H., Liao, Y., Zhang, X.M., Yang, L., Song, C.L., Wang, M.J., Shi, J.F., Liu, G., Liu, J.J., Zhou, H.L., Zhou, W.L., Yu, Q.L., An, N., Chen, Y., Cai, Q.L., Wang, B., Liu, B.H., Min, J.M., Huang, Y., Wu, H.L., Li, Z.Y., Zhang,Y., Yin, Y., Song, W.Q., Jiang, J.M., Jackson, S.A., Wing, R.A., Wang, J. and Chen, M.S. (2013) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat. Commun. 4: 1595.

 

He, L., Liu, J., Torres, G.A., Zhang, H.Q., Jiang, J.M., and Xie, C.H. (2013) Interstitial telomeric repeats are enriched in the centromeres of chromosomes in Solanum species. Chromosome Res. 21: 5-13.

 

Zhang, H.K., Bian, Y., Gou, X.W., Zhu, B., Xu, C.M., Qi, B., Li, N., Rustgi, S., Zhou, H., Han, F.P., Jiang, J.M., von Wettstein, D., and Liu, B. (2013) Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat. Proc. Natl. Acad. Sci. USA 110: 3447-3452.