Rapid divergence and expansion of the X chromosome in papaya

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

Volumn 109, Issue 34, 2012, Pages 13716-13721

  Gschwend, Andrea R ^a   Yu, Qingyi ^b,c   Tong, Eric J ^c   Zeng, Fanchang ^a   Han, Jennifer ^a   VanBuren, Robert ^a   Aryal, Rishi ^a   Charlesworth, Deborah ^d   Moore, Paul H ^c   Paterson, Andrew H ^e   Ming, Ray ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c HAWAII AGRICULTURE RESEARCH CENTER   (United States)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

^e UNIVERSITY OF GEORGIA   (United States)

Author keywords

Carica papaya; Centromere of X chromosome; Gene gains and losses; Sex chromosome evolution; Suppression of recombination

Indexed keywords

ALLELE; ARTICLE; AUTOSOME; MONOECY; PAPAYA; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; VASCONCELLEA MONOICA; X CHROMOSOME; Y CHROMOSOME;

ALLELES; CARICA; CENTROMERE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; DNA TRANSPOSABLE ELEMENTS; GENES, PLANT; MODELS, GENETIC; RECOMBINATION, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; SEX CHROMOSOMES; TRANSCRIPTION, GENETIC;

EID: 84865298231     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1121096109     Document Type: Article

References (42)

1. Liu Z, et al. (2004) A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427:348-352.
2. Yu Q, et al. (2008) Low X/Y divergence in four pairs of papaya sex-linked genes. Plant J 53:124-132.
3. Na J-K, et al. (2012) Construction of physical maps for the sex-specific regions of papaya sex chromosomes. BMC Genomics, 10.1186/1471-2164-13-176.
4. Yu Q, et al. (2008) Recent origin of dioecious and gynodiouecious Y chromosomes in papaya. Trop Plant Biol 1:49-57.
5. Ming R, Wang J, Moore PH, Paterson AH (2007) Sex chromosomes in flowering plants. Am J Bot 94:141-150.
6. Wu X, et al. (2010) The origin of the non-recombining region of sex chromosomes in Carica and Vasconcellea. Plant J 63:801-810.
7. Peichel CL, et al. (2004) The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome. Curr Biol 14:1416-1424.
8. Filatov DA (2005) Evolutionary history of Silene latifolia sex chromosomes revealed by genetic mapping of four genes. Genetics 170:975-979.
9. Yin T, et al. (2008) Genome structure and emerging evidence of an incipient sex chromosome in Populus. Genome Res 18:422-430.
10. Spigler RB, Lewers KS, Main DS, Ashman TL (2008) Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome. Heredity (Edinb) 101:507-517.
11. Damasceno Junior PC, Da Costa FR, Pereira TNS, Neto MF, Pereira MG (2009) Karyotype determination in three Caricaceae species emphasizing the cultivated form (C. papaya L.). Caryologia 62:10-15.
12. Charchar FJ, et al. (2003) Complex events in the evolution of the human pseudoautosomal region 2 (PAR2). Genome Res 13:281-286.
13. Ross MT, et al. (2005) The DNA sequence of the human X chromosome. Nature 434:325-337.
14. Bellott DW, et al. (2010) Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature 466:612-616.
15. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208-218.
16. Ming R, et al. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991-996.
17. Wang J, et al. (2012) Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proc Natl Acad Sci USA 109:13710-13715.
18. Carvalho FA, Renner SS (2012) The phylogeny of the Caricaceae. Genetics and Genomics of Papaya, eds Ming R, Moore PH (Springer, Hyderberg).
19. Bull JJ (1983) Evolution of Sex Determining Mechanisms (Benjamin/Cummings, Menlo Park, CA).
20. Ohno S (1967) Sex chromosomes and sex linked genes. Monographs on Endocrinology, eds Labhart A, Mann T, Samuels LT (Springer, Heidelberg).
21. Bergero R, Forrest A, Kamau E, Charlesworth D (2007) Evolutionary strata on the X chromosomes of the dioecious plant Silene latifolia: Evidence from new sex-linked genes. Genetics 175:1945-1954.
22. Murphy WJ, et al. (2007) A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes. Genomics 89:189-196.
23. Raudsepp T, et al. (2004) Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping. Proc Natl Acad Sci USA 101:2386-2391.
24. Ihara N, et al. (2004) A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Res 14(10A):1987-1998.
25. Leticia C, et al. (2009) Physical mapping of the elephant X chromosome: Conservation of gene order over 105 million years. Chromosome Res 17:917-926.
26. Sandstedt SA, Tucker PK (2004) Evolutionary strata on the mouse X chromosome correspond to strata on the human X chromosome. Genome Res 14:267-272.
27. Zhang W, Wang X, Yu Q, Ming R, Jiang J (2008) DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya. Genome Res 18:1938-1943.
28. Bergero R, Charlesworth D (2011) Preservation of the Y transcriptome in a 10-millionyear- old plant sex chromosome system. Curr Biol 21:1470-1474.
29. Chibalina MV, Filatov DA (2011) Plant Y chromosome degeneration is retarded by haploid purifying selection. Curr Biol 21:1475-1479.
30. Soderlund C, Nelson W, Shoemaker A, Paterson A (2006) SyMAP: A system for discovering and viewing syntenic regions of FPC maps. Genome Res 16:1159-1168.
31. Darling AE, Mau B, Perna NT (2010) progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5:e11147.
32. Flutre T, Duprat E, Feuillet C, Quesneville H (2011) Considering transposable element diversification in de novo annotation approaches. PLoS ONE 6:e16526.
33. Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21:i351-i358.
34. Bao Z, Eddy SR (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 12:1269-1276.
35. Li W, Godzik A (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659.
36. Jurka J, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462-467.
37. Nagarajan N, et al. (2008) Genome-wide analysis of repetitive elements in papaya. Trop Plant Biol 1:191-201.
38. Blas AL, et al. (2010) Cloning of the papaya chromoplast-specific lycopene β-cyclase, CpCYC-b, controlling fruit flesh color reveals conserved microsynteny and a recombination hot spot. Plant Physiol 152:2013-2022.
39. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221-224.
40. Librado P, Rozas J (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
41. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-426.
42. Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S (2010) Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci USA 107:18724-18728.