Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.)

Genome Biology and Evolution

Volumn 6, Issue 6, 2014, Pages 1423-1436

  Yin, Hao ^a   Du, Jianchang ^b   Li, Leiting ^a   Jin, Cong ^a   Fan, Lian ^a   Li, Meng ^a   Wu, Jun ^a   Zhang, Shaoling ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Amplification; Cassandra retrotransposon; Pear; Recombination; Rosaceae; TRIM

Indexed keywords

RETROPOSON;

COMPARATIVE STUDY; GENE EXPRESSION REGULATION; GENETIC RECOMBINATION; GENETICS; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENOME; PYRUS; RETROPOSON; ROSACEAE;

BASE SEQUENCE; EVOLUTION, MOLECULAR; GENOME, PLANT; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; PHYLOGENY; PYRUS; RECOMBINATION, GENETIC; RETROELEMENTS; ROSACEAE; TERMINAL REPEAT SEQUENCES;

EID: 84902997341     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu114     Document Type: Article

References (45)

1. Antonius-Klemola K, Kalendar R, Schulman AH. 2006. TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports. Theor Appl Genet. 112: 999-1008.
2. Costas J, Naveira H. 2000. Evolutionary history of the human endogenous retrovirus family ERV9. Mol Biol Evol. 17: 320-330.
3. Devos KM, Brown JK, Bennetzen JL. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12: 1075-1079.
4. Du J, et al. 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean. Plant Cell 24: 21-32.
5. Du J, Grant D, et al. 2010. SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics 11: 113.
6. Du J, Tian Z, Bowen NJ, et al. 2010. Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR Swapping in soybean. Plant Cell 22: 48-61.
7. Du J, Tian Z, Hans CS, et al. 2010. 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.
8. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
9. Gao D, Chen J, Chen M, Meyers BC, Jackson S. 2012. A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS One 7:e32010.
10. Jiang N, Bao Z, et al. 2002. Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161: 1293-1305.
11. Jiang N, Gao D, Xiao H, van der Knaap E. 2009. Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider. Plant J. 60: 181-193.
12. Jiang N, Jordan IK, Wessler SR. 2002. Dasheng and RIRE2. A nonautonomous long terminal repeat element and its putative autonomous partner in the rice genome. Plant Physiol. 130: 1697-1705.
13. Kalendar R, et al. 2008. Cassandra retrotransposons carry independently transcribed 5S RNA. Proc Natl Acad Sci U S A. 105: 5833-5838.
14. Kalendar R, et al. 2004. Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166: 1437-1450.
15. Kalkman C. 2004. Rosaceae. In: Kubitzki K, editor. Flowering plants - Dicotyledons: Celastrales, Oxalidales, Rosales, Cornales, Ericales. Berlin (Germany): Springer. p. 343-386.
16. Kapitonov V, Jurka J. 1996. The age of Alu subfamilies. J Mol Evol. 42: 59-65.
17. Kimura M, Ota T. 1972. On the stochastic model for estimation of mutational distance between homologous proteins. J Mol Evol. 2: 87-90.
18. Krzywinski M, et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19: 1639-1645.
19. Kumar A, Bennetzen JL. 1999. Plant retrotransposons. Annu Rev Genet. 33: 479-532.
20. Ma J, Bennetzen JL. 2004. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A. 101: 12404-12410.
21. Ma J, Bennetzen JL. 2006. Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. Proc Natl Acad Sci U S A. 103: 383-388.
22. Ma J, Devos KM, Bennetzen JL. 2004. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14: 860-869.
23. McCarthy EM, McDonald JF. 2003. LTR-STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362-367.
24. Miyao A, et al. 2003. Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15: 1771-1780.
25. Paterson AH, et al. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492: 423-427.
26. Potter D, et al. 2007. Phylogeny and classification of Rosaceae. Plant Syst Evol. 266: 5-43.
27. Presting GG, Malysheva L, Fuchs J, Schubert I. 1998. A Ty3/gypsy retrotransposon- like sequence localizes to the centromeric regions of cereal chromosomes. Plant J. 16: 721-728.
28. Sabot F, Schulman AH. 2007. Template switching can create complex LTR retrotransposon insertions in Triticeae genomes. BMCGenomics 8: 247.
29. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. 1998. The paleontology of intergene retrotransposons of maize. Nat Genet. 20: 43-45.
30. Schnable PS, et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
31. Shulaev V, et al. 2011. The genome of woodland strawberry (Fragaria vesca). Nat Genet. 43: 109-116.
32. Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28: 2731-2739.
33. Tanskanen JA, Sabot F, Vicient C, Schulman AH. 2007. Life without GAG: the BARE-2 retrotransposon as a parasite's parasite. Gene 390: 166-174.
34. Tian Z, et al. 2009. Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res. 19: 2221-2230.
35. Tian Z, et al. 2012. Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell 24: 4422-4436.
36. Velasco R, et al. 2010. The genome of the domesticated apple (Malus-domestica Borkh.). Nat Genet. 42: 833-839.
37. Verde I, et al. 2013. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 45: 487-494.
38. Vincent C, et al. 2005. Variability, recombination, and mosaic evolution of the barley BARE-1 retrotransposon. J Mol Evol. 61: 275-291.
39. Wicker T, Keller B. 2007. 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.
40. Witte CP, Le QH, Bureau T, Kumar A. 2001. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci U S A. 98: 13778-13783.
41. Wu J, et al. 2012. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 23: 396-408.
42. Yin H, et al. 2013. TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato. PLoS One 8: e68587.
43. Zhang Q, et al. 2012. The genome of Prunus mume. Nat Commun. 3: 1318.
44. Zhao M, et al. 2013. 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.
45. Zhao MX, Ma JX. 2013. Co-evolution of plant LTR-retrotransposons and their host genomes. Protein Cell 4: 493-501.