8 Kobayashi N, Ikeda R, Vaughan D A, et al. Resistance to Tungro in some wild relatives of rice. Int Rice Res Newslett, 1991, 16: 13-17
[2]
9 黄运平, 覃瑞. 野生稻资源的研究与利用. 湖北农业科学, 2002, 40: 16-19
[3]
12 Yang Z. Computational Molecular Evolution. Oxford: Oxford University Press, 2006
[4]
17 Wyman S K, Jansen R K, Boore J L. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 2004, 20: 3252-3255
[5]
18 Altschul S F, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol, 1990, 215: 403-410
[6]
19 Tamura K, Dudley J, Nei M, et al. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Bio Evol, 2007, 24: 1596-1599
[7]
20 Ge S, Sang T, Lu B-R, et al. Phylogeny of the genus Oryza as revealed by molecular approaches. In: Rice Genetics IV Proceedings of the Fourth International Rice Genetics Symposium: 25 October, 2000. Los Ba？os, Laguna, Philippines. 2001, 89-105
[8]
21 Zhu T, Xu P Z, Liu J P, et al. 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, 2014, 70: 348-361
[9]
22 Swofford D L. PAUP*: phylogenetic analysis using parsimony, version 4.0 b10. Sinauer Associates, 1998
[10]
23 Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol, 2003, 52: 696-704
[11]
25 Huelsenbeck J P, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 2001, 17: 754-755
[12]
26 Yang Z. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci, 1997, 13: 555-556
[13]
34 Bricker T M, Frankel L K. The structure and function of CP47 and CP43 in Photosystem II. Photosynth Res, 2002, 72: 131-146
[14]
35 Arnold K, Bordoli L, Kopp J, et al. The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 2006, 22: 195-201
[15]
36 Wu Z Q, Ge S. The phylogeny of the BEP clade in grasses revisited: Evidence from the whole-genome sequences of chloroplasts. Mol Phylogenet Evol, 2012, 62: 573-578
[16]
37 Mohr G, Perlman P S, Lambowitz A M. Evolutionary relationships among group-II intron-encoded proteins and identification of a conserved domain that may be related to Maturase function. Nucleic Acids Res, 1993, 21: 4991-4997
[17]
38 Wim F. J. Vermaas J G K W, Arntzen C J. Sequencing and modification of psbB, the gene encoding the CP-47 protein of Photosystem II, in the cyanobacterium Synechocystis 6803. Plant Mol Biol, 1987, 4: 317-326
[18]
43 Molina J, Sikora M, Garud N, et al. Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci USA, 2011, 108: 8351-8356
[19]
44 Khush G S. Origin, dispersal, cultivation and variation of rice. Plant Mol Biol, 1997, 35: 25-34
[20]
45 Li C, Zhou A, Sang T. Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol, 2006, 170: 185-193
[21]
46 Chanfreau G, Jacquier A. Catalytic site components common to both splicing steps of a group-II intron. Science, 1994, 266: 1383-1387
[22]
47 Kelchner S A. Group II introns as phylogenetic tools: Structure function, and evolutionary constraints. Am J Bot, 2002, 89: 1651-1669
[23]
51 Clarke S M, Eaton-Rye J J. Amino acid deletions in loop C of the chlorophyll a-binding protein CP47 alter the chloride requirement and/or prevent the assembly of photosystem II. Plant Mol Biol, 2000, 44: 591-601
[24]
1 Zou X H, Zhang F M, Zhang J G, et al. Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol, 2008, 9: R49
[25]
2 刘铁燕, 陈明生. 稻属植物的基因组进化. 生物多样性, 2014, 22: 51-65
[26]
3 Lu F, Ammiraju J S, Sanyal A, et al. Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA, 2009, 106: 2071-2076
[27]
4 Sang T, Ge S. The puzzle of rice domestication. J Integr Plant Biol, 2007, 49: 760-768
[28]
5 Sun C Q, Wang X K, Li Z C, et al. Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.) using RFLP markers. Theor Appl Genet, 2001, 102: 157-162
7 Khush G S, Ling K C, Aquino R C, et al. Breeding for resistance to grassy stunt in rice. Plant Breeding Papers; Int Congr of the Society for the Advancement of Breeding Researches in Asia & Oceania, 1977. 3-9
[31]
10 Brar D S, Khush G S. Alien introgression in rice. In: Sasaki T, Moore G, eds. Oryza: From Molecule to Plant. Dordrecht: Kluwer Academic Publishers, 1997. 35-47
[32]
11 Shimada H, Sugiura M. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucleic Acids Res, 1991, 19: 983-995
[33]
13 Yang Z, Swanson W J, Vacquier V D. Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. Mol Biol Evol, 2000, 17: 1446-1455
[34]
14 Wong W S, Yang Z, Goldman N, et al. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics, 2004, 168: 1041-1051
[35]
15 Waters D L E, Nock C J, Ishikawa R, et al. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. Ecol Evol, 2012, 2: 211-217
[36]
16 Darling A C E, Mau B, Blattner F R, et al. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res, 2004, 14: 1394-1403
[37]
24 Posada D, Crandall K A. MODELTEST: testing the model of DNA substitution. Bioinformatics, 1998, 14: 817-818
[38]
27 Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol, 1998, 15: 568-573
[39]
28 Nielsen R, Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 1998, 148: 929-936
[40]
29 Zhang J, Nielsen R, Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol, 2005, 22: 2472-2479
[41]
30 Doron-Faigenboim A, Stern A, Mayrose I, et al. Selecton: A server for detecting evolutionary forces at a single amino-acid site. Bioinformatics, 2005, 21: 2101-2103
[42]
31 Doron-Faigenboim A, Pupko T. A combined empirical and mechanistic codon model. Mol Biol Evol, 2007, 24: 388-397
[43]
32 Hao D C, Chen S L, Xiao P G. Molecular evolution and positive Darwinian selection of the chloroplast maturase matK. J Plant Res, 2010, 123: 241-247
[44]
33 Hamel P P, Dreyfuss B W, Xie Z, et al. Essential histidine and tryptophan residues in CcsA, a system II polytopic cytochrome c biogenesis protein. J Biol Chem, 2003, 278: 2593-2603
[45]
39 Igloi G, Meinke A, Dory I, et al. Nucleotide sequence of the maize chloroplast rpo B/C1/C2 operon: Comparison between the derived protein primary structures from various organisms with respect to functional domains. Mol Gen Genet, 1990, 221: 379-394
[46]
40 Chen Z, Schertz K F, Mullet J E, et al. Characterization and expression of rpoC2 in CMS and fertile lines of sorghum. Plant Mol Biol, 1995, 28: 799-809
[47]
41 Williamson M P. The structure and function of proline-rich regions in proteins. Biochem J, 1994, 297(Pt 2): 249-260
[48]
42 Zhou W, Wang Z, Xing W, et al. Plasticity in latitudinal patterns of leaf N and P of Oryza rufipogon in China. Plant Biol (Stuttg), 2014, 10.1111/plb.12147
[49]
48 Xie Z, Merchant S. The plastid-encoded ccsA gene is required for heme attachment to chloroplast c-type cytochromes. J Biol Chem, 1996, 271: 4632-4639
[50]
49 Simon J, Hederstedt L. Composition and function of cytochrome c biogenesis System II. FEBS J, 2011, 278: 4179-4188
[51]
50 Cummings M P, King L M, Kellogg E A. Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae). Mol Biol Evol, 1994, 11: 1-8
