Comparison of genes among cereals

Current Opinion in Plant Biology

Volumn 6, Issue 2, 2003, Pages 121-127

  Ware, Doreen ^a   Stein, Lincoln ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EMBRYOPHYTA;

EID: 0037393134     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(03)00012-8     Document Type: Review

References (65)

1. Chen M, SanMiguel P, de Oliveira AC, Woo SS, Zhang H, Wing RA, Bennetzen JL: Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci USA 1997, 94:3431-3435.
2. Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, Bennetzen JL, Avramova Z: Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 1999, 96:7409-7414.
3. Bennetzen JL: Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 2000, 12:1021-1029.
4. Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A: The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 2000, 12:381-391.
5. Fu H, Park W, Yan X, Zheng Z, Shen B, Dooner HK: The highly recombinogenic bz locus lies in an unusually gene-rich region of the maize genome. Proc Natl Acad Sci USA 2001, 98:8903-8908. The authors investigated the high rate of recombination that had been identified previously at the bz locus of maize. This is one of the first gene-dense regions to be identified in maize. It contains a 32-kb region of the genome that includes ten genes, eight of which are transcribed, with an average distance of 1 kb of intergenic space between the genes. The gene-rich island is bordered on both ends by retrotransposons blocks.
6. Dubcovsky J, Ramakrishna W, SanMiguel PJ, Busso CS, Yan L, Shiloff BA, Bennetzen JL: Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 2001, 125:1342-1353. This is one of the first detailed examinations of the level of microcollinearity between barley and rice. The authors selected bacterial artificial chromosomes for genomic sequencing from a previously identified collinear region from barley chromosome 5 and rice chromosome 3. They found four conserved regions containing four predicted genes with similar exon number, size, and location. However, the orientation and number of the genes differed between rice and barley in some cases. The authors did not observe extensive similarity beyond the exon structures, untranslated regions, and promoter sequences. The differences in distances between genes in barley and rice were explained by the insertion of different transposable retroelements into each species.
7. Song R, Llaca V, Messing J: Mosaic organization of orthologous sequences in grass genomes. Genome Res 2002, 12:1549-1555. This is the most comprehensive comparison of sequence among the cereals to date. The authors expand on their previous work in maize [11•] to look at collinear regions in sorghum and two cultivars of rice. Their results support a mosaic organization of the orthologous regions in which conserved sequences are interspersed with non-conserved sequences. Gene amplification, gene movement, and retrotransposition account for the majority of the non-conserved sequences. The analysis also suggests that gene amplification is frequently linked with gene movement.
8. Sandhu D, Gill KS: Gene-containing regions of wheat and the other grass genomes. Plant Physiol 2002, 128:803-811. Deletion lines were used to localize gene-containing regions of the wheat genome. The work suggests that gene-containing regions are found in about 10% of the wheat genome. The locations of the gene-containing regions on genetic and physical maps show that recombination is confined to these regions. The density and number of genes in each region vary along with the recombination frequency. Comparison with orthologous regions in rice suggests that the gene density in wheat is about half that in rice, and that the difference between the rice and wheat genomes is due to the amplification of gene-poor regions in wheat.
9. Yao H, Zhou Q, Li J, Smith H, Yandeau M, Nikolau BJ, Schnable PS: Molecular characterization of meiotic recombination across the 140-kb multigenic a 1-sh2 interval of maize. Proc Natl Acad Sci USA 2002, 99:6157-6162. The authors looked at recombinant-rich regions of the maize genome and mapped the recombination hot spots. Three of the hotspots are genic, and one is not. The non-genic spot was present at low copy number in the maize genome. This finding indicates that recombination-active portions of the genome are low copy, and that the retrotransposon portion of the maize genome is relatively inactive.
10. SanMiguel PJ, Ramakrishna W, Bennetzen JL, Busso CS, Dubcovsky J: Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A(m). Funct Integr Genomics 2002, 2:70-80. The work described in this paper follows up on work done in rice and barley [1] to include a sequenced bacterial artificial chromosome from wheat. In a region that is conserved between rice and barley [11•], one gene was found to be present in the same orientation in wheat and rice but inverted in barley. The results showed that the wheat genome is a complex mixture of different sequence elements but has a general pattern of content that is similar to those of rice and barley.
11. Song R, Llaca V, Linton E, Messing J: Sequence, regulation, and evolution of the maize 22-kD alpha zein gene family. Genome Res 2001, 11:1817-1825. The authors sequenced all 23 members of the 22-kD α-zein gene family of maize, forming the largest contiguous maize region sequenced to date. On the basis of cDNA database analysis, seven of the α-zein genes were expressed, and these expressed genes were interspersed with non-expressed genes. The authors suggest that the amplification of blocks of genes explains the rapid and compact expansion of the α-zein cluster during the evolution of maize.
12. Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
13. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al.: A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296:92-100. The shotgun sequences of two rice cultivars were published concurrently. This paper reports on Syngenta's analysis of the Nipponbare sequence, which covers 93% of the genome. Gene predictions from the assembly are compared to cereal ESTs and the Arabidopsis predictions. The paper reports on synteny with other cereals and with Arabidopsis, and on the genes classes found in rice. The authors find that 98% of known maize, wheat, and barley proteins are also found in rice.
14. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al.: A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296:79-92. The shotgun sequences of two rice cultivars were published concurrently. The authors of this paper report on the shotgun sequence of the cultivar Indica by the Beijing Genomics Institute. The authors compare the gene predictions for rice with those for Arabidopsis, and summarize information on the structure of the genes and the functions assigned to them by homology.
15. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y et al.: The genome sequence and structure of rice chromosome 1. Nature 2002, 420:312-316. The completed sequencing of chromosomes 1 and 4 by the IRGSP was reported concurrently. In this paper, the authors describe the structure of longest rice chromosome, chromosome 1. They describe biological insights provided by the completely sequenced chromosome, including the presence of gene families and the location of the gene families on the whole chromosome. The authors also discuss the significance of finishing the sequence.
16. Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X et al.: Sequence and analysis of rice chromosome 4. Nature 2002, 420:316-320. The completed sequencing of chromosomes 1 and 4 by the IRGSP was reported concurrently. In this paper, the authors describe the finished sequence of chromosome 4. They compare this sequence to that of chromosome 4 of the rice subspecies Indica, and find that there is an overall conserved synteny that diverges with single nucleotide polymorphisms, insertions, and deletions.
17. Gale MD, Devos KM: Comparative genetics in the grasses. Proc Natl Acad Sci USA 1998, 95:1971-1974.
18. Devos KM, Gale MD: Genome relationships: the grass model in current research. Plant Cell 2000, 12:637-646.
19. Arumuganathan K, Earle ED: Nuclear DNA content of some important plant species. Plant Mol Biol Reporter 1991, 25:208-218.
20. Keller B, Feuillet C: Colinearity and gene density in grass genomes. Trends Plant Sci 2000, 5:246-251.
21. Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F et al.: 'Green revolution' genes encode mutant gibberellin response modulators. Nature 1999, 400:256-261.
22. Tikhonov AP, Bennetzen JL, Avramova ZV: Structural domains and matrix attachment regions along colinear chromosomal segments of maize and sorghum. Plant Cell 2000, 12:249-264.
23. Bancroft I: Insights into the structural and functional evolution of plant genomes afforded by the nucleotide sequences of chromosomes 2 and 4 of Arabidopsis thaliana. Yeast 2000, 17:1-5.
24. Gaut BS, Doebley JF: DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 1997, 94:6809-6814.
25. Xu F, Lagudah ES, Moose SP, Riechers DE: Tandemly duplicated safener-induced glutathione S-transferase genes from Triticum tauschii contribute to genome- and organ-specific expression in hexaploid wheat. Plant Physiol 2002, 130:362-373. The authors describe the isolation of two glutathione S-transferase genes from wheat chromosome 6. The two genes have different expression levels and patterns in the different genomes of hexaploid wheat. An analysis of the available rice genome found the regions that were most homologous to the wheat glutathione S-transferase genes were found on rice chromosome 10 rather than chromosome 2. Rice chromosome 2 had previously been identified as the syntenic region for wheat chromosome 6.
26. Yuan Q, Hill J, Hsiao J, Moffat K, Ouyang S, Cheng Z, Jiang J, Buell CR: Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol Genet Genomics 2002, 267:713-720. The authors discuss the high density of duplicated genes found in a 239-kb region of rice chromosome 10L, and the insertion of a large piece of the chloroplast genome into this region. This segment of the rice genome is the same as that described by Xu et al. [25••] who reported that it contains the closest homologues of the glutathione S-transferase genes found on wheat chromosome 6.
27. dbEST: database of expressed sequence tags. http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html
28. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J: The TIGR gene indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 2001, 29:159-164.
29. Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J et al.: Cross-referencing eukaryotic genomes: TIGR orthologous gene alignments (TOGA). Genome Res 2002, 12:493-502.
30. Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J et al.: A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 2002, 14:525-535.
31. Brendel V, Kurtz S, Walbot V: Comparative genomics of Arabidopsis and maize: prospects and limitations. Genome Biol 2002, 3:REVIEWS1005.
32. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al.: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
33. The C. elegans Sequencing Consortium: Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998, 282:2012-2018.
34. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF et al.: The genome sequence of Drosophila melanogaster. Science 2000, 287:2185-2195.
35. Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science 2000, 290:1151-1155.
36. Ku HM, Vision T, Liu J, Tanksley SD: Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA 2000, 97:9121-9126.
37. Vision TJ, Brown DG, Tanksley SD: The origins of genomic duplications in Arabidopsis. Science 2000, 290:2114-2117.
38. Hulbert SH, Webb CA, Smith SM, Sun Q: Resistance gene complexes: evolution and utilization. Annu Rev Phytopathol 2001, 39:285-312.
39. Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P: A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 2000, 10:908-915.
40. Panstruga R, Buschges R, Piffanelli P, Schulze-Lefert P: A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res 1998, 26:1056-1062.
41. Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, Keller B: Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J 2001, 26:307-316. The authors sequenced the largest contiguous block of the wheat genome to date. They found gene clusters, isolated genes and several new retrotransposon elements within this genomic sequence. One of the new retrotransposon elements was found to be closely associated with gene sequences.
42. Feuillet C, Keller B: High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA 1999, 96:8265-8270.
43. Wei F, Wing RA, Wise RP: Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell 2002, 14:1903-1917.
44. Meyers BC, Chin DB, Shen KA, Sivaramakrishnan S, Lavelle DO, Zhang Z, Michelmore RW: The major resistance gene cluster in lettuce is highly duplicated and spans several megabases. Plant Cell 1998, 10:1817-1832.
45. Messing J: Do plants have more genes than humans? Trends Plant Sci 2001, 6:195-196.
46. Gaut BS, Morton BR, McCaig BC, Clegg MT: Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 1996, 93:10274-10279.
47. Clay O, Bernardi G: The isochores in human chromosomes 21 and 22. Biochem Biophys Res Commun 2001, 285:855-856.
48. Sumner AT, de la Torre J, Stuppia L: The distribution of genes on chromosomes: a cytological approach. J Mol Evol 1993, 37:117-122.
49. Werner JE, Endo TR, Gill BS: Toward a cytogenetically based physical map of the wheat genome. Proc Natl Acad Sci USA 1992, 89:11307-11311.
50. Gill KS, Gill BS, Endo TR, Taylor T: Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics 1996, 144:1883-1891.
51. Faris JD, Haen KM, Gill BS: Saturation mapping of a gene-rich recombination hot spot region in wheat. Genetics 2000, 154:823-835.
52. Sandhu D, Champoux JA, Bondareva SN, Gill KS: Identification and physical localization of useful genes and markers to a major gene-rich region on wheat group 1S chromosomes. Genetics 2001, 157:1735-1747.
53. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z et al.: Nested retrotransposons in the intergenic regions of the maize genome. Science 1996, 274:765-768.
54. Brooks SA, Huang L, Gill BS, Fellers JP: Analysis of 106 kb of contiguous DNA sequence from the D genome of wheat reveals high gene density and a complex arrangement of genes related to disease resistance. Genome 2002, 45:963-972.
55. Rahman S, Abrahams S, Abbott D, Mukai Y, Samuel M, Morell M, Appels R: A complex arrangement of genes at a starch branching enzyme I locus in the D-genome donor of wheat. Genome 1997, 40:465-474.
56. Rostoks N, Park YJ, Ramakrishna W, Ma J, Druka A, Shiloff BA, SanMiguel PJ, Jiang Z, Brueggeman R, Sandhu D et al.: Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley. Funct Integr Genomics 2002, 2:51-59.
57. Bennetzen JL, Schrick K, Springer PS, Brown WE, SanMiguel P: Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 1994, 37:565-576.
58. Gruenbaum Y, Naveh-Many T, Cedar H, Razin A: Sequence specificity of methylation in higher plant DNA. Nature 1981, 292:860-862.
59. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL: The paleontology of intergene retrotransposons of maize. Nat Genet 1998, 20:43-45.
60. Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y, Kay SA, Schultz PG, Cooke MP: A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell 2001, 106:413-415.
61. Hofmann K, Bucher P, Falquet L, Bairoch A: The PROSITE database, its status in 1999. Nucleic Acids Res 1999, 27:215-219.
62. Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res 2000, 28:263-266.
63. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD et al.: InterPro - an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 2000, 16:1145-1150.
64. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD et al.: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001, 29:37-40.
65. Lewis S, Ashburner M, Reese MG: Annotating eukaryote genomes. Curr Opin Struct Biol 2000, 10:349-354.