Genome sequence comparison reveals a candidate gene involved in male–hermaphrodite differentiation in papaya (Carica papaya) trees
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The sex type of papaya (Carica papaya) is determined by the pair of sex chromosomes (XX, female; XY, male; and XYh, hermaphrodite), in which there is a non-recombining genomic region in the Y and Yh chromosomes. This region is presumed to be involved in determination of males and hermaphrodites; it is designated as the male-specific region in the Y chromosome (MSY) and the hermaphrodite-specific region in the Yh chromosome (HSY). Here, we identified the genes determining male and hermaphrodite sex types by comparing MSY and HSY genomic sequences. In the MSY and HSY genomic regions, we identified 14,528 nucleotide substitutions and 965 short indels with a large gap and two highly diverged regions. In the predicted genes expressed in flower buds, we found no nucleotide differences leading to amino acid changes between the MSY and HSY. However, we found an HSY-specific transposon insertion in a gene (SVP like) showing a similarity to the Short Vegetative Phase (SVP) gene. Study of SVP-like transcripts revealed that the MSY allele encoded an intact protein, while the HSY allele encoded a truncated protein. Our findings demonstrated that the SVP-like gene is a candidate gene for male-hermaphrodite determination in papaya.
KeywordsCarica papaya Sex chromosome Yh chromosome Y chromosome Short Vegetative Phase like
This work is supported by JSPS (Japan Society for the Promotion of Science) Grant no. 25450004, and the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry (PROBRAIN). This work was also supported in part by Grants for Excellent Graduate Schools, MEXT (Ministry of Education, Culture, Sports, Science and Technology), Japan.
- Carvalho FA, Renner SS (2013) The phylogeny of the Caricaceae. In: Ming R, Moore PH (eds) Genetics and genomics of Papaya. Springer, New York, pp 81–92Google Scholar
- Matsumura H, Yoshida K, Luo S, Kimura E, Fujibe T, Albertyn Z, Barrero RA, Krueger DH, Kahl G, Schroth GP, Terauchi R (2010) High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing. PLoS One 5:e12010CrossRefPubMedCentralPubMedGoogle Scholar
- Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang M-L, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na J-K, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Perez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo M-C, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–997CrossRefPubMedCentralPubMedGoogle Scholar
- Wang JP, Na JK, Yu QY, Gschwend AR, Han J, Zeng FC, Aryal R, VanBuren R, Murray JE, Zhang WL, Navajas-Perez R, Feltus FA, Lemke C, Tong EJ, Chen CX, Wai CM, Singh R, Wang ML, Min XJ, Alam M, Charlesworth D, Moore PH, Jiang JM, Paterson AH, Ming R (2012) Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proc Natl Acad Sci USA 109:13710–13715CrossRefPubMedCentralPubMedGoogle Scholar