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For: Duan S, Lu B, Li Z, Tong J, Kong J, Yao W, Li S, Zhu Y. Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences. Biochem Genet 2007;45:113-29. [PMID: 17221300 DOI: 10.1007/s10528-006-9062-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Number Cited by Other Article(s)
1
Kehinde BO, Xie L, Song BK, Zheng X, Fan L. African Cultivated, Wild and Weedy Rice (Oryza spp.): Anticipating Further Genomic Studies. BIOLOGY 2024;13:697. [PMID: 39336124 PMCID: PMC11428565 DOI: 10.3390/biology13090697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 08/31/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024]
2
Labroo MR, Clark LV, Zhang S, Hu F, Tao D, Hamilton RS, Sacks EJ. Solving the mystery of Obake rice in Africa: population structure analyses of Oryza longistaminata reveal three genetic groups and evidence of both recent and ancient introgression with O. sativa. FRONTIERS IN PLANT SCIENCE 2023;14:1278196. [PMID: 38034553 PMCID: PMC10684938 DOI: 10.3389/fpls.2023.1278196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
3
Htet AH, Makabe S, Takahashi H, Samuel PA, Sato YI, Nakamura I. A large deletion within intron 20 sequence of single-copy PolA1 gene as a useful marker for the speciation in Oryza AA-genome species. BREEDING SCIENCE 2022;72:267-273. [PMID: 36408325 PMCID: PMC9653197 DOI: 10.1270/jsbbs.21075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/04/2022] [Indexed: 06/16/2023]
4
Xie C, An W, Liu S, Huang Y, Yang Z, Lin J, Zheng X. Comparative genomic study on the complete plastomes of four officinal Ardisia species in China. Sci Rep 2021;11:22239. [PMID: 34782652 PMCID: PMC8594775 DOI: 10.1038/s41598-021-01561-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 10/21/2021] [Indexed: 11/23/2022]  Open
5
Wambugu PW, Ndjiondjop MN, Henry R. Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. RICE (NEW YORK, N.Y.) 2021;14:6. [PMID: 33415579 PMCID: PMC7790969 DOI: 10.1186/s12284-020-00449-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
6
Ndjiondjop MN, Alachiotis N, Pavlidis P, Goungoulou A, Kpeki SB, Zhao D, Semagn K. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019;132:1145-1158. [PMID: 30578434 PMCID: PMC6449321 DOI: 10.1007/s00122-018-3268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
7
Molecular Diversity of Tidal Swamp Rice (Oryza sativa L.) in South Kalimantan, Indonesia. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
8
Morphological and molecular dissection of wild rices from eastern India suggests distinct speciation between O. rufipogon and O. nivara populations. Sci Rep 2018;8:2773. [PMID: 29426872 PMCID: PMC5807453 DOI: 10.1038/s41598-018-20693-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/22/2018] [Indexed: 11/14/2022]  Open
9
Kim K, Lee SC, Lee J, Yu Y, Yang K, Choi BS, Koh HJ, Waminal NE, Choi HI, Kim NH, Jang W, Park HS, Lee J, Lee HO, Joh HJ, Lee HJ, Park JY, Perumal S, Jayakodi M, Lee YS, Kim B, Copetti D, Kim S, Kim S, Lim KB, Kim YD, Lee J, Cho KS, Park BS, Wing RA, Yang TJ. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Sci Rep 2015;5:15655. [PMID: 26506948 PMCID: PMC4623524 DOI: 10.1038/srep15655] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/30/2015] [Indexed: 12/15/2022]  Open
10
Henry RJ, Nevo E. Exploring natural selection to guide breeding for agriculture. PLANT BIOTECHNOLOGY JOURNAL 2014;12:655-62. [PMID: 24975385 DOI: 10.1111/pbi.12215] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 04/13/2014] [Accepted: 05/15/2014] [Indexed: 05/02/2023]
11
Brozynska M, Omar ES, Furtado A, Crayn D, Simon B, Ishikawa R, Henry RJ. Chloroplast Genome of Novel Rice Germplasm Identified in Northern Australia. TROPICAL PLANT BIOLOGY 2014;7:111-120. [PMID: 25485030 PMCID: PMC4245483 DOI: 10.1007/s12042-014-9142-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/13/2014] [Indexed: 05/04/2023]
12
Wambugu PW, Furtado A, Waters DLE, Nyamongo DO, Henry RJ. Conservation and utilization of African Oryza genetic resources. RICE (NEW YORK, N.Y.) 2013;6:29. [PMID: 24280189 PMCID: PMC4883696 DOI: 10.1186/1939-8433-6-29] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/23/2013] [Indexed: 05/20/2023]
13
Zhu T, Xu PZ, Liu JP, Peng S, Mo XC, Gao LZ. Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions. Mol Phylogenet Evol 2013;70:348-61. [PMID: 24148990 DOI: 10.1016/j.ympev.2013.10.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 08/17/2013] [Accepted: 10/09/2013] [Indexed: 12/17/2022]
14
Banaticla-Hilario MCN, van den Berg RG, Hamilton NRS, McNally KL. Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon. Ecol Evol 2013;3:3047-62. [PMID: 24101993 PMCID: PMC3790550 DOI: 10.1002/ece3.689] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/17/2013] [Accepted: 06/23/2013] [Indexed: 11/11/2022]  Open
15
Scafaro AP, Yamori W, Carmo-Silva AE, Salvucci ME, von Caemmerer S, Atwell BJ. Rubisco activity is associated with photosynthetic thermotolerance in a wild rice (Oryza meridionalis). PHYSIOLOGIA PLANTARUM 2012;146:99-109. [PMID: 22324885 DOI: 10.1111/j.1399-3054.2012.01597.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
16
Scafaro AP, Von Caemmerer S, Evans JR, Atwell BJ. Temperature response of mesophyll conductance in cultivated and wild Oryza species with contrasting mesophyll cell wall thickness. PLANT, CELL & ENVIRONMENT 2011;34:1999-2008. [PMID: 21752031 DOI: 10.1111/j.1365-3040.2011.02398.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
17
Griffin PC, Robin C, Hoffmann AA. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol 2011;9:19. [PMID: 21429199 PMCID: PMC3078099 DOI: 10.1186/1741-7007-9-19] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 03/23/2011] [Indexed: 12/16/2022]  Open
18
Sanyal A, Ammiraju JSS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J, San Miguel P, Mingsheng C, Wing RA, Jackson SA. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum. Mol Biol Evol 2010;27:2487-506. [PMID: 20522726 DOI: 10.1093/molbev/msq133] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
19
Roulin A, Chaparro C, Piégu B, Jackson S, Panaud O. Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rices. Genome Biol Evol 2010;2:132-9. [PMID: 20333229 PMCID: PMC2839358 DOI: 10.1093/gbe/evq005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2010] [Indexed: 11/12/2022]  Open
20
Species Trees from Highly Incongruent Gene Trees in Rice. Syst Biol 2009;58:489-500. [DOI: 10.1093/sysbio/syp054] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
21
Tao J, Luo ZY, Msangi CI, Shu XS, Wen L, Liu SP, Zhou CQ, Liu RX, Hu WX. Relationships among genetic makeup, active ingredient content, and place of origin of the medicinal plant Gastrodia tuber. Biochem Genet 2009;47:8-18. [PMID: 19037723 DOI: 10.1007/s10528-008-9201-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
22
Xu Z, Ramakrishna W. Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history. Gene 2008;412:50-8. [PMID: 18291601 DOI: 10.1016/j.gene.2008.01.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 01/05/2008] [Accepted: 01/08/2008] [Indexed: 01/08/2023]
23
New insights into the history of rice domestication. Trends Genet 2007;23:578-87. [DOI: 10.1016/j.tig.2007.08.012] [Citation(s) in RCA: 357] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 08/16/2007] [Accepted: 08/21/2007] [Indexed: 11/18/2022]
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