Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

Proceedings of the National Academy of Sciences of the United States of America

Volumn 113, Issue 35, 2016, Pages E5163-E5171

  Zhang, Jianwei ^a,b   Chen, Ling Ling ^a   Xing, Feng ^a   Kudrna, David A ^b   Yao, Wen ^b   Copetti, Dario ^a   Mu, Ting ^b,c   Li, Weiming ^a   Song, Jia Ming ^a   Xie, Weibo ^a   Lee, Seunghee ^b   Talag, Jayson ^b   Shao, Lin ^a   An, Yue ^a   Zhang, Chun Liu ^a   Ouyang, Yidan ^a   Sun, Shuai ^a   Jiao, Wen Biao ^a   Lv, Fang ^a   Du, Bogu ^a   Luo, Meizhong ^a   Maldonado, Carlos Ernesto ^b   Goicoechea, Jose Luis ^b   Xiong, Lizhong ^a   Wu, Changyin ^a   Xing, Yongzhong ^a   Zhou, Dao Xiu ^a   Yu, Sibin ^a   Zhao, Yu ^a   Wang, Gongwei ^a   Yu, Yeisoo ^b,d   Luo, Yijie ^a   Zhou, Zhi Wei ^a   Hurtado, Beatriz Elena Padilla ^b   Danowitz, Ann ^b   Wing, Rod A ^b,c   Zhang, Qifa ^a   more..

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF ARIZONA   (United States)

^c INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

^d Phyzen Inc   (South Korea)

Author keywords

Bac by bac strategy; Oryza sativa; Reference genomes; Transcriptome

Indexed keywords

CONTIG; TRANSCRIPTOME;

ARTICLE; CROP IMPROVEMENT; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; HYBRID; JAPONICA RICE; NONHUMAN; ORYZA SATIVA SUBS INDICA; PLANT GENOME; PLANT TISSUE; PRIORITY JOURNAL; RICE; SEGMENTAL DUPLICATION; SUBSPECIES; TRANSCRIPTOMICS; VARIETAS; CHROMOSOMAL MAPPING; CLASSIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC VARIATION; GENETICS; INDEL MUTATION; ORYZA; PLANT CHROMOSOME; PLANT GENE; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENETIC VARIATION; GENOME, PLANT; INDEL MUTATION; ORYZA; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECIES SPECIFICITY;

EID: 84984714310     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1611012113     Document Type: Article

References (63)

1. Ouyang Y, Zhang Q (2013) Understanding reproductive isolation based on the rice model. Annu Rev Plant Biol 64:111-135.
2. IRRI (1991) World Rice Statistics 1990 (International Rice Research Institute, Manila, Philippines).
3. Huang X, et al. (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42(11):961-967.
4. Xie W, et al. (2015) Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection. Proc Natl Acad Sci USA 112(39):E5411-E5419.
5. Yu SB, et al. (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94(17):9226-9231.
6. Hua JP, et al. (2002) Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance. Genetics 162(4):1885-1895.
7. Hua J, et al. (2003) Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 100(5):2574-2579.
8. Huang Y, et al. (2006) Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs. Plant Mol Biol 62(4-5):579-591.
9. Zhou G, et al. (2012) Genetic composition of yield heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 109(39):15847-15852.
10. Huang X, et al. (2015) Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. Nat Commun 6:6258.
11. Goff SA, Zhang Q (2013) Heterosis in elite hybrid rice: Speculation on the genetic and biochemical mechanisms. Curr Opin Plant Biol 16(2):221-227.
12. Wang X, et al. (2014) Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping. Genetics 196(4):937-949.
13. Zhang J, et al. (2016) Building two indica rice reference genomes with PacBio longread and Illumina paired-end sequencing data. Sci Data, 10.1038/sdata.2016.76.
14. van Oeveren J, et al. (2011) Sequence-based physical mapping of complex genomes by whole genome profiling. Genome Res 21(4):618-625.
15. Zhang J, et al. (2016) Genome puzzle master (GPM): An integrated pipeline for building and editing pseudomolecules from fragmented sequences. Bioinformatics, 10.1093/bioinformatics/btw370.
16. Cheng Z, et al. (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14(8):1691-1704.
17. Parra G, Bradnam K, Ning Z, Keane T, Korf I (2009) Assessing the gene space in draft genomes. Nucleic Acids Res 37(1):289-297.
18. Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA (2006) Identifying repeat domains in large genomes. Genome Biol 7(1):R7.
19. Bao W, Kojima KK, Kohany O (2015) Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA 6:11.
20. Chen J, Hu Q, Zhang Y, Lu C, Kuang H (2014) P-MITE: A database for plant miniature inverted-repeat transposable elements. Nucleic Acids Res 42(Database Issue):D1176-D1181.
21. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436(7052):793-800.
22. Kozomara A, Griffiths-Jones S (2014) miRBase: Annotating high confidence micro-RNAs using deep sequencing data. Nucleic Acids Res 42(Database Issue):D68-D73.
23. Xue W, et al. (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40(6):761-767.
24. Fan C, et al. (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112(6):1164-1171.
25. Li Y, et al. (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43(12):1266-1269.
26. Xu C, et al. (2015) Differential expression of GS5 regulates grain size in rice. J Exp Bot 66(9):2611-2623.
27. Sun X, et al. (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37(4):517-527.
28. Liu Q, et al. (2011) A paralog of the MtN3/saliva family recessively confers race-specific resistance to Xanthomonas oryzae in rice. Plant Cell Environ 34(11):1958-1969.
29. Thiel T, et al. (2009) Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. BMC Evol Biol 9:209.
30. Guyot R, Keller B (2004) Ancestral genome duplication in rice. Genome 47(3):610-614.
31. Delcher AL, Phillippy A, Carlton J, Salzberg SL (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 30(11):2478-2483.
32. Finn RD, Clements J, Eddy SR (2011) HMMER web server: Interactive sequence similarity searching. Nucleic Acids Res 39(Web Server Issue):W29-W37.
33. Cingolani P, et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6(2):80-92.
34. Hoff KJ, Stanke M (2013) WebAUGUSTUS-A web service for training AUGUSTUS and predicting genes in eukaryotes. Nucleic Acids Res 41(Web Server Issue):W123-W128.
35. Besemer J, Borodovsky M (2005) GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33(Web Server Issue):W451-W454.
36. Korf I (2004) Gene finding in novel genomes. BMC Bioinformatics 5:59.
37. Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7(Suppl 1):S10-1-S10-12.
38. Dimmer EC, et al. (2012) The UniProt-GO annotation database in 2011. Nucleic Acids Res 40(Database Issue):D565-D570.
39. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2011) GenBank. Nucleic Acids Res 39(Database Issue):D32-D37.
40. Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K (2009) TriFLDB: A database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol 150(3):1135-1146.
41. Lu T, et al. (2008) RICD: A rice indica cDNA database resource for rice functional genomics. BMC Plant Biol 8:118.
42. Exner V, Hirsch-Hoffmann M, Gruissem W, Hennig L (2008) PlantDB - A versatile database for managing plant research. Plant Methods 4:1.
43. Slater GS, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31.
44. She R, et al. (2011) genBlastG: Using BLAST searches to build homologous gene models. Bioinformatics 27(15):2141-2143.
45. Kent WJ (2002) BLAT-The BLAST-like alignment tool. Genome Res 12(4):656-664.
46. Grabherr MG, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644-652.
47. Haas BJ, et al. (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol 9(1):R7.
48. Haas BJ, et al. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31(19):5654-5666.
49. Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28(1):45-48.
50. Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27-30.
51. Dutkowski J, et al. (2013) A gene ontology inferred from molecular networks. Nat Biotechnol 31(1):38-45.
52. Zdobnov EM, Apweiler R (2001) InterProScan-An integration platform for the signaturerecognition methods in InterPro. Bioinformatics 17(9):847-848.
53. Mitchell A, et al. (2015) The InterPro protein families database: The classification resource after 15 years. Nucleic Acids Res 43(Database Issue):D213-D221.
54. Punta M, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40(Database Issue):D290-D301.
55. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955-964.
56. Lagesen K, et al. (2007) RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100-3108.
57. Gardner PP, et al. (2011) Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res 39(Database Issue):D141-D145.
58. Nawrocki EP, Eddy SR (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLOS Comput Biol 3(3):e56.
59. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25.
60. Wang Y, et al. (2012) MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40(7):e49.
61. Wang J, Yao W, Zhu D, Xie W, Zhang Q (2015) Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid. eLife 4:e04250.
62. Munger SC, et al. (2014) RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. Genetics 198(1):59-73.
63. Li B, Dewey CN (2011) RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323.