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Genome-wide association mapping of date palm fruit traits.
Hazzouri KM, Gros-Balthazard M, Flowers JM, Copetti D, Lemansour A, Lebrun M, Masmoudi K, Ferrand S, Dhar MI, Fresquez ZA, Rosas U, Zhang J, Talag J, Lee S, Kudrna D, Powell RF, Leitch IJ, Krueger RR, Wing RA, Amiri KMA, Purugganan MD. Hazzouri KM, et al. Among authors: lee s. Nat Commun. 2019 Oct 15;10(1):4680. doi: 10.1038/s41467-019-12604-9. Nat Commun. 2019. PMID: 31615981 Free PMC article.
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA. Stein JC, et al. Among authors: lee s. Nat Genet. 2018 Feb;50(2):285-296. doi: 10.1038/s41588-018-0040-0. Epub 2018 Jan 22. Nat Genet. 2018. PMID: 29358651
Genomic variation in 3,010 diverse accessions of Asian cultivated rice.
Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo MEB, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann JC, Zhang J, Li J, Hamilton RS, Wing RA, Ruan J, Zhang G, Wei C, Alexandrov N, McNally KL, Li Z, Leung H. Wang W, et al. Among authors: lee s. Nature. 2018 May;557(7703):43-49. doi: 10.1038/s41586-018-0063-9. Epub 2018 Apr 25. Nature. 2018. PMID: 29695866 Free PMC article.
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.
Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KF, Rounsley S, Wing RA. Wang M, et al. Among authors: lee s. Nat Genet. 2014 Sep;46(9):982-8. doi: 10.1038/ng.3044. Epub 2014 Jul 27. Nat Genet. 2014. PMID: 25064006 Free PMC article.
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.
Zhang J, Chen LL, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, Ouyang Y, Sun S, Jiao WB, Lv F, Du B, Luo M, Maldonado CE, Goicoechea JL, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou ZW, Hurtado BE, Danowitz A, Wing RA, Zhang Q. Zhang J, et al. Among authors: lee s. Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):E5163-71. doi: 10.1073/pnas.1611012113. Epub 2016 Aug 17. Proc Natl Acad Sci U S A. 2016. PMID: 27535938 Free PMC article.
Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data.
Zhang J, Chen LL, Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao WB, Xing F, Lee S, Talag J, Song JM, Du B, Xie W, Luo M, Maldonado CE, Goicoechea JL, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Hurtado BE, Danowitz A, Wing RA, Zhang Q. Zhang J, et al. Among authors: lee s. Sci Data. 2016 Sep 13;3:160076. doi: 10.1038/sdata.2016.76. Sci Data. 2016. PMID: 27622467 Free PMC article.
Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti.
Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Childs KL, Eguiarte LE, Lee S, Liu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF, Sanderson MJ. Copetti D, et al. Among authors: lee s. Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):12003-12008. doi: 10.1073/pnas.1706367114. Epub 2017 Oct 23. Proc Natl Acad Sci U S A. 2017. PMID: 29078296 Free PMC article.
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