Genome-wide Annotation and Comparative Analysis of Long Terminal Repeat Retrotransposons between Pear Species of P. bretschneideri and P. Communis

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Yin, Hao ^a   Du, Jianchang ^b   Wu, Jun ^a   Wei, Shuwei ^a   Xu, Yingxiu ^b   Tao, Shutian ^a   Wu, Juyou ^a   Zhang, Shaoling ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; EPIGENETICS; EVOLUTIONARY RATE; FAMILY; FAMILY STUDY; FRUIT; GENE STRUCTURE; GENOME; LONG TERMINAL REPEAT; PLANT GENOME; RETROPOSON; SPECIES; TRANSPOSON; COMPARATIVE STUDY; GENETICS; GENOME-WIDE ASSOCIATION STUDY; MOLECULAR EVOLUTION; PHYLOGENY; PLANT CHROMOSOME; PYRUS;

PLANT PROTEIN; RETROPOSON;

CHROMOSOMES, PLANT; EVOLUTION, MOLECULAR; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; PHYLOGENY; PLANT PROTEINS; PYRUS; RETROELEMENTS; TERMINAL REPEAT SEQUENCES;

EID: 84949293478     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep17644     Document Type: Article

References (67)

1. Bennetzen, J. L., Ma, J. & Devos, K. M. Mechanisms of recent genome size variation in flowering plants. Ann Bot. 95, 127-132 (2005).
2. Verde, I. et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 45, 487-494 (2013).
3. Tomato Genome, C. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 485, 635-641 (2012).
4. Xu, X. et al. Genome sequence and analysis of the tuber crop potato. Nature. 475, 189-195 (2011).
5. Schnable, P. S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 326, 1112-1115 (2009).
6. Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 8, 973-982 (2007).
7. Xiong, Y. & Eickbush, T. H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9, 3353 (1990).
8. Kalendar, R. et al. Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics. 166, 1437-1450 (2004).
9. Witte, C. P., Le, Q. H., Bureau, T. & Kumar, A. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. P Natl Acad Sci USA. 98, 13778-13783 (2001).
10. Du, J. et al. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J. 63, 584-598 (2010).
11. Wang, H. & Liu, J. S. LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice. BMC Genomics. 9, 382 (2008).
12. Potter, D. et al. Phylogeny and classification of Rosaceae. Plant Syst Evol. 266, 5-43 (2007).
13. Bell, R. L. & Itai, A. Wild Crop Relatives: Genomic and Breeding Resources. Springer (2011).
14. White, A. G., Alspach, P. A., Weskett, R. H. & Brewer, L. R. Heritability of fruit shape in pears. Euphytica. 112, 1-7 (2000).
15. Qin, G. et al. Evaluation of the volatile profile of 33 Pyrus ussuriensis cultivars by HS-SPME with GC-MS. Food Chem. 134, 2367-2382 (2012).
16. Pierantoni, L. et al. Pear scab resistance QTLs via a European pear (Pyrus communis) linkage map. Tree Genet Genomes. 3, 311-317 (2007).
17. Bao, L. et al. Genetic diversity and similarity of pear (Pyrus L.) cultivars native to East Asia revealed by SSR (simple sequence repeat) markers. Genet Resour Crop Ev. 54, 959-971 (2007).
18. Bao, L., Chen, K., Zhang, D., Li, X. & Teng, Y. An assessment of genetic variability and relationships within Asian pears based on AFLP (amplified fragment length polymorphism) markers. Sci Hortic-Amsterdam. 116, 374-380 (2008).
19. Bassil, N. & Postman, J. D. Identification of European and Asian pears using EST-SSRs from Pyrus. Genet Resour Crop Ev. 57, 357-370 (2010).
20. Vavilov, N. I. The origin, variation, immunity and breeding of cultivated plants. Soil Sci. 72, 482 (1951).
21. Bailey, L. H. The standard cyclopedia of horticulture. Macmillan (1919).
22. Wu, J. et al. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 23, 396-408 (2012).
23. Chagne, D. et al. The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PloS one. 9, e92644 (2014).
24. Kim, H. et al. Development of cultivar-specific DNA markers based on retrotransposon-based insertional polymorphism in Japanese pear. Breeding Sci. 62, 53 (2012).
25. Tian, Z. et al. Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res. 19, 2221-2230 (2009).
26. Devos, K. M., Brown, J. K. & Bennetzen, J. L. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12, 1075-1079 (2002).
27. Yin, H. et al. Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.). Genome Bio Evol. 6, 1423-1436 (2014).
28. Paterson, A. H. et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 457, 551-556 (2009).
29. Consortium IRGS. The map-based sequence of the rice genome. Nature. 436, 793-800 (2005).
30. Kalendar, R. et al. Cassandra retrotransposons carry independently transcribed 5S RNA. P Natl Acad Sci USA. 105, 5833-5838 (2008).
31. Sabot, F. & Schulman, A. H. Template switching can create complex LTR retrotransposon insertions in Triticeae genomes. BMC Genomics. 8, 247 (2007).
32. Gao, D., Chen, J., Chen, M., Meyers, B. C. & Jackson, S. A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PloS one. 7, e32010 (2012).
33. Jiang, N. et al. Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics. 161, 1293-1305 (2002).
34. Presting, G. G., Malysheva, L., Fuchs, J. & Schubert, I. A. Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J. 16, 721-728 (1998).
35. Tian, Z. et al. Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean. Plant Cell. 24, 1-15 (2012).
36. Xu, Y. & Du, J. Young but not relatively old retrotransposons are preferentially located in gene-rich euchromatic regions in tomato (Solanum lycopersicum) plants. Plant J. 80, 582-591 (2014).
37. Ma, J. & Bennetzen, J. L. Rapid recent growth and divergence of rice nuclear genomes. P Natl Acad Sci USA. 101, 12404-12410 (2004).
38. SanMiguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y. & Bennetzen, J. L. The paleontology of intergene retrotransposons of maize. Nat Genet. 20, 43-45 (1998).
39. Domingues, D. S. et al. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics. 13, 137 (2012).
40. Wicker, T. & Keller, B. Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res. 17, 1072-1081 (2007).
41. Kumar, A. The evolution of plant retroviruses: moving to green pastures. Trends Plant Sci. 3, 371-374 (1998).
42. Miguel, C., Simoes, M., Oliveira, M. M. & Rocheta, M. Envelope-like retrotransposons in the plant kingdom: evidence of their presence in gymnosperms (Pinus pinaster). J Mol Evol. 67, 517-525 (2008).
43. Peterson-Burch, B. D., Wright, D. A., Laten, H. M. & Voytas, D. F. Retroviruses in plants? Trends Genet. 16, 151-152 (2000).
44. Huang, S. et al. The genome of the cucumber, Cucumis sativus L. Nature Genet. 41, 1275-1281 (2009).
45. He, N. et al. Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun. 4, doi: 10.1038/ncomms3445 (2013).
46. van Bakel, H. et al. The draft genome and transcriptome of Cannabis sativa. Genome Boil. 12, R102 (2011).
47. Shulaev, V. et al. The genome of woodland strawberry (Fragaria vesca). Nat Genet. 43, 109-116 (2011).
48. Zhang, Q. et al. The genome of Prunus mume. Nat Commun. 3, 1318 (2012).
49. Velasco, R. et al. The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet. 42, 833-839 (2010).
50. Fawcett, J. A., Maere, S. & Van de Peer, Y. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. P Natl Acad Sci USA. 106, 5737-5742 (2009).
51. Gaut, B., Yang, L., Takuno, S. & Eguiarte, L. E. The patterns and causes of variation in plant nucleotide substitution rates. Annu Rev Ecol Evol S. 42, 245-266 (2011).
52. Kumar, A. & Bennetzen, J. L. Plant retrotransposons. Annu Rev Genet. 33, 479-532 (1999).
53. Ma, J., Devos, K. M. & Bennetzen, J. L. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14, 860-869 (2004).
54. Wang, H., Xu, Z. & Yu, H. LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice. BMC Genomics. 9, 565 (2008).
55. Gaut, B. S. Molecular clocks and nucleotide substitution rates in higher plants. Evol Biol. 30, 93-120 (1998).
56. Ma, J. & Bennetzen, J. L. Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. P Natl Acad Sci USA. 103, 383-388 (2006).
57. Pereira, V. Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol. 5, R79 (2004).
58. Zhao, M. et al. Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication. Plant J. 76, 211-222 (2013).
59. Gaut, B. S., Wright, S. I., Rizzon, C., Dvorak, J. & Anderson, L. K. Recombination: an underappreciated factor in the evolution of plant genomes. Nat Rev Genet. 8, 77-84 (2007).
60. McCarthy, E. M. & McDonald, J. F. LTR-STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics. 19, 362-367 (2003).
61. Rezvoy, C., Charif, D., Gueguen, L. & Marais, G. A. MareyMap: an R-based tool with graphical interface for estimating recombination rates. Bioinformatics. 23, 2188-2189 (2007).
62. Wu, J. et al. High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. J Exp Bot, doi: 10.1093/jxb/eru311 (2014).
63. Yin, H. et al. TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato. PloS one. 8, e68587 (2013).
64. Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 5, 113 (2004).
65. Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28, 2731-2739 (2011).
66. Li, L., Stoeckert, C. J. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003).
67. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24, 1586-1591 (2007).