Patterns in grass genome evolution

Current Opinion in Plant Biology

Volumn 10, Issue 2, 2007, Pages 176-181

  Bennetzen, Jeffrey L ^a  

^a University of Georgia ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENETICS; GENOME; MOLECULAR EVOLUTION; PLANT CHROMOSOME; POACEAE; REVIEW;

CHROMOSOMES, PLANT; EVOLUTION, MOLECULAR; GENOME, PLANT; POACEAE;

MAGNOLIOPHYTA; POACEAE;

EID: 33847298027     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2007.01.010     Document Type: Review

References (57)

1. Bennetzen J.L., and Freeling M. Grasses as a single genetic system: genome composition, collinearity and compatibility. Trends Genet 9 (1993) 259-261
2. Crepet W.L., and Feldman G.D. The earliest remains of grasses in the fossil record. Am J Bot 78 (1991) 1010-1014
3. Paterson A.H., Bowers J.E., and Chapman B.A. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101 (2004) 9903-9908
4. Prasad V., Strömberg C.A.E., Alimohammadian H., and Sahni A. Dinosaur coprolites and the early evolution of grasses and grazers. Science 310 (2005) 1177-1180
5. Kellogg E.A., and Bennetzen J.L. The evolution of nuclear genome structure in seed plants. Am J Bot 91 (2004) 1709-1725
6. Yu J., Hu S., Wang J., Wong G.K., 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 296 (2002) 79-91
7. Goff S.A., Ricke D., Lan T.H., 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 296 (2002) 92-100
8. 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 420 (2002) 316-320
9. Fu H., and Dooner H.K. Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci USA 99 (2002) 9573-9578
10. Ma J., and Bennetzen J.L. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101 (2004) 12404-12410
11. Jabbari K., Cruveiller S., Clay O., Le Saux J., and Bernardi G. The new genes of rice: a closer look. Trends Plant Sci 9 (2004) 281-285
12. Bennetzen J.L., Coleman C., Liu R., Jianxin Ma J., and Ramakrishna W. Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol 7 (2004) 732-736
13. Lai J., Li Y., Messing J., and Dooner H.K. Gene movement by Helitron transposons contributes to the haplotype variability in maize. Proc Natl Acad Sci USA 102 (2005) 9068-9073
14. Morgante M., Brunner S., Pea G., Fengler K., Zuccolo A., and Rafalski A. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37 (2005) 997-1002. This paper describes experiments indicating that a class of mobile DNAs called helitrons are responsible for much of the perceived variation in genic colinearity between maize inbreds and between maize and other grass species. More than 10 000 different gene fragments are predicted to have been acquired and amplified by helitrons in maize, often with fragments from several different genes in the same helitron. Some of these helitrons are expressed, occasionally yielding transcripts that include fused segments from different genes. These processes of fragment acquisition, amplification and exon shuffling are actively occurring in maize, thereby generating much of the perceived genetic diversity in this highly diverse species, and perhaps generating significant levels of functional novelty.
15. Hulbert S.H., Richter T.E., Axtell J.D., and Bennetzen J.L. Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc Natl Acad Sci USA 87 (1990) 4251-4255
16. Moore G., Devos K.M., Wang Z., and Gale M.D. Grasses, line up and form a circle. Curr Biol 5 (1995) 737-739
17. Chen M., SanMiguel P., de Oliveira A.C., Woo S.-S., Zhang H., Wing R.A., and Bennetzen J.L. Microcolinearity in the sh2-homologous regions of the maize, rice and sorghum genomes. Proc Natl Acad Sci USA 94 (1997) 3431-3435
18. Tikhonov A.P., SanMiguel P.J., Nakajima Y., Gorenstein N.M., Bennetzen J.L., and Avramova Z. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 96 (1999) 7409-7414
19. Feuillet C., and Keller B. High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA 96 (1999) 8665-8670
20. Feuillet C., and Keller B. Comparative genomics in the grass family: molecular characterization of grass genome structure and function. Ann Bot 89 (2002) 3-10
21. Bennetzen J.L., and Ma J. The genetic colinearity of rice and other cereals based on genomic sequence analysis. Curr Opin Plant Biol 6 (2003) 128-133
22. Ilic K., SanMiguel P.J., and Bennetzen J.L. A complex history of rearrangement in an orthologous region of the maize, sorghum and rice genomes. Proc Natl Acad Sci USA 100 (2003) 12265-12270
23. Dubcovsky J., Ramakrishna W., SanMiguel P.J., Busso C.S., Yan L., Shiloff B.A., and Bennetzen J.L. Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 125 (2001) 1342-1353
24. Ammiraju J.S.S., Luo M., Goicoechea J.L., Wang W., Kudrna D., Mueller C., Talag J., Kim H.R., Sisneros N.B., Blackmon B., et al. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res 16 (2006) 140-147
25. m). With this array of species, it was possible to determine specific rearrangement events, their timing in the descent of these species, and their apparent mechanisms of origin. Illegitimate recombination was found to be a particularly major contributor to the observed rearrangements.
26. Vandepoele K., Simillion C., and Van de Peer Y. Evidence that rice and other cereals are ancient aneuploids. Plant Cell 9 (2003) 2192-2202
27. Tian C.G., Xiong Y.Q., Liu T.Y., Sun S.H., Chen L.B., and Chen M.S. Evidence for an ancient whole genome duplication event in rice and other cereals. Yi Chuan Xue Bao 32 (2005) 519-527
28. Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol 3 (2005) e38
29. Kashkush K., Feldman M., and Levy A.A. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160 (2002) 1651-1659
30. Bennetzen J.L., Ma J., and Devos K.M. Mechanisms of recent genome size variation in flowering plants. Ann Bot 95 (2005) 127-132
31. Vitte C., and Bennetzen J.L. Analysis of retrotransposon diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci USA 103 (2006) 17638-17643
32. Dong Q., Schlueter S.D., and Brendel B. PlantGDB, plant genome database and analysis tools. Nucleic Acids Res 32 (2004) D354-D359
33. Odland W., Baumgarter A., and Phillips R. Ancestral rice blocks define multiple related regions in the maize genome. Crop Sci 46 (2006) S41-S48
34. Soderlund C., Nelson W., Shoemaker A., and Paterson A. SyMAP: a system for discovering and viewing syntenic regions of FPC maps. Genome Res 16 (2006) 1159-1168
35. Jaiswal P., Ni J., Yap I., Ware D., Spooner W., Youens-Clark K., Ren L., Liang C., Zhao W., Ratnapu K., et al. Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res 34 (2006) D717-D723
36. Ouyang S., Zhu W., Hamilton J., Lin H., Campbell M., Childs K., Thibaud-Nissen F., Malek R.L., Lee Y., Zheng L., et al. The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35 (2007) D883-D887
37. Devos K.M., Pittaway T.S., Reynolds A., and Gale M.D. Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice. Theor Appl Genet 100 (2000) 190-198
38. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436 (2005) 793-800
39. Sorrells M.E., La Rota M., Bermudez-Kandianis C.E., Greene R.A., Kantety R., Munkvold J.D., Miftahudin, Mahmoud A., Ma X., Gustafson P.J., et al. Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13 (2003) 1818-1827
40. The Rice Chromosome 3 Sequencing Consortium. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res 15 (2005) 1284-1291
41. Bowers J.E., Arias M.A., Asher R., Avise J.A., Ball R.T., Brewer G.A., Buss R.W., Chen A.H., Edwards T.M., Estill J.C., et al. Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci USA 102 (2005) 13206-13211. These studies employed DNA sequences that are shared between two sorghum physical maps and the sequenced rice genome to characterize the distribution of genic rearrangements. Greater microcolinearity was observed in euchromatic (i.e. gene-rich and recombination-rich) regions. The authors propose that rearrangements may often be deleterious, and therefore could only accumulate in regions where their removal by recombination is relatively slow.
42. Bruggmann R., Bharti A.K., Gundlach H., Lai J., Young S., Pontaroli A.C., Wei F., Haberer G., Fuks G., Du C., et al. Uneven chromosome contraction and expansion in the maize genome. Genome Res 16 (2006) 1241-1251
43. Devos K.M., Brown J.K., and Bennetzen J.L. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12 (2002) 1075-1079
44. m genomes of wheat. Plant Cell 15 (2003) 1186-1197
45. Kirik A., Salomon S., and Puchta H. Species-specific double-strand break repair and genome evolution in plants. EMBO J 19 (2000) 5562-5566
46. Lai J., Ma J., Swigonova Z., Ramakrishna W., Linton E., Llaca V., Tanyolac B., Park Y.J., Jeong O.Y., Bennetzen J.L., and Messing J. Gene loss and movement in the maize genome. Genome Res 14 (2004) 1924-1931
47. Thomas B.C., Pedersen B., and Freeling M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 16 (2006) 934-946
48. Chapman B.A., Bowers J.E., Feltus F.A., and Paterson A.H. Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc Natl Acad Sci USA 103 (2006) 2730-2735
49. Piegu B., Guyot R., Picault N., Roulin A., Saniyal A., Kim H., Collura K., Brar D.S., Jackson S., Wing R.A., et al. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16 (2006) 1262-1269. This manuscript demonstrates that the recent amplification of three LTR retrotransposons is responsible for the relatively large size of the O. australiensis genome. Members of these LTR retrotransposon families are all present in the O. sativa genome, but with intact element copy numbers of less than 20. The species-specific amplifications of these elements to copy numbers of more than 10 000 each has occurred in the past 2.5 million years, adding ∼600 Mb to the ∼965 Mb genome of O. australiensis.
50. Ma J., SanMiguel P., Lai J., Messing J., and Bennetzen J.L. DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes. Genetics 170 (2005) 1209-1220
51. Akhunov E.D., Goodyear A.W., Geng S., Qi L.-L., Echalier B., Gill B.S., Miftahudin, Gustafson J.P., Lazo G., Chao S., et al. The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res 13 (2003) 753-763
52. Ma J., and Bennetzen J.L. Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. Proc Natl Acad Sci USA 103 (2006) 383-388. This study investigated the divergence and rearrangement of genes, tandem repeats, and LTR retrotransposons in the centromeric region of rice chromosome 8. Unequal homologous recombination was found to be a major contributor to the instability of this region, and this process was particularly active in the core of the centromere that directs spindle attachment. Because meiotic homolog exchange has been observed to be suppressed in this and all other studied eukaryotic centromeric regions, the authors propose that recombination in this area is quite active, but is channeled primarily into non-crossover outcomes and/or sister chromatid exchange.
53. Cheng Z., Dong F., Langdon T., Ouyang S., Buell C.R., Gu M., Blattner F.R., and Jiang J. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14 (2002) 1691-1704
54. Kato A., Lamb J.C., and Birchler J.A. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci USA 101 (2004) 13554-13559
55. Wu J., Yamagata H., Hayashi-Tsugane M., Hijishita S., Fujisawa M., Shibata M., Ito Y., Nakamura M., Sakguchi M., Yoshihara R., et al. Composition and structure of the centromeric region of rice chromosome 8. Plant Cell 16 (2004) 967-976
56. Zhang Y., Huang Y., Zhang L., Li Y., Lu T., Lu Y., Feng Q., Zhao Q., Cheng Z., Xue Y., et al. Structural features of the rice chromosome 4 centromere. Nucleic Acids Res 32 (2004) 2023-2030
57. Nagaki K., Cheng Z., Ouyang S., Talbert P.B., Kim M., Jones K.M., Henikoff S., Buell C.R., and Jiang J. Sequencing of a rice centromere uncovers active genes. Nat Genet 36 (2004) 138-145